diff --git a/bin/macos/3.1.2/LICENSE b/bin/macos/3.1.2/LICENSE new file mode 100644 index 0000000..b359b0b --- /dev/null +++ b/bin/macos/3.1.2/LICENSE @@ -0,0 +1,10 @@ +Unless otherwise specified by LICENSE(.txt) files in individual +directories, or within individual files or functions, all code is distributed under the MIT License: + +Copyright (c) 2020, CATO developers, All rights reserved. + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file diff --git a/bin/macos/3.1.2/VERSION b/bin/macos/3.1.2/VERSION new file mode 100644 index 0000000..7d77428 --- /dev/null +++ b/bin/macos/3.1.2/VERSION @@ -0,0 +1,4 @@ +CATO 3.1.2 +Operating system: macos (MACI64) +Compiled on: 17-May-2021 16:43:35 +Compiled using: MATLAB Compiler 6.5 (R2017b) \ No newline at end of file diff --git a/bin/macos/3.1.2/functional_pipeline b/bin/macos/3.1.2/functional_pipeline new file mode 100755 index 0000000..9763d66 Binary files /dev/null and b/bin/macos/3.1.2/functional_pipeline differ diff --git a/bin/macos/3.1.2/functional_preprocessing/preprocess_default.sh b/bin/macos/3.1.2/functional_preprocessing/preprocess_default.sh new file mode 100755 index 0000000..ff323b1 --- /dev/null +++ b/bin/macos/3.1.2/functional_preprocessing/preprocess_default.sh @@ -0,0 +1,159 @@ +#!/bin/bash +# +# (Example) preprocessing script for functional MRI data: +# 1. Performs slice timing correction using FSL tool slicetimer if variable +# sliceTimingCorrection is TRUE. +# 2. Performs motion correction using FSL tool MCFLIRT. +# 3. Computes a rs-fMRI reference image by averaging all (motion corrected) +# rs-fMRI frames (using FSL). +# 4. Computes the registration matrix between the rs-fMRI reference image and +# the T1 image (using Freesurfer). +# 5. Registers the T1 parcellation to the reference rs-fMRI image (using +# Freesurfer). + +# https://google.github.io/styleguide/shellguide.html + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Usage +####################################### +usage() +{ + cat << EOF +(Example) preprocessing script for functional MRI data: + 1. Performs slice timing correction using FSL tool slicetimer if + variable sliceTimingCorrection is TRUE. + 2. Performs motion correction using FSL tool MCFLIRT. + 3. Computes a rs-fMRI reference image by averaging all (motion + corrected) rs-fMRI frames (using FSL). + 4. Computes the registration matrix between the rs-fMRI reference + image and the T1 image (using Freesurfer). + 5. Registers the T1 parcellation to the reference rs-fMRI image + (using Freesurfer). +EOF +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --fmriFile=*) + fmriFile=${1#*=} + shift + ;; + --fmriProcessedFile=*) + fmriProcessedFile=${1#*=} + shift + ;; + --slicetimerOptions=*) + slicetimerOptions=${1#*=} + shift + ;; + --sliceTimingCorrection=*) + sliceTimingCorrection=${1#*=} + shift + ;; + --fmriReferenceFile=*) + fmriReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --motionParametersFile=*) + motionParametersFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '$1'" + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR + +parse_input "$@" + +# TODO: convert MNC to NIFTI +cp "$fmriFile" "$fmriProcessedFile" + +# perform slice timing correction +if [ "$sliceTimingCorrection" = true ] ; then + slicetimer -i "$fmriProcessedFile" -o "${fmriProcessedFile/.nii.gz/_stc.nii.gz}" \ + $slicetimerOptions + mv "${fmriProcessedFile/.nii.gz/_stc.nii.gz}" "$fmriProcessedFile" +fi + +# perform motion correction +mcflirt -in "$fmriProcessedFile" -plots +mv "${fmriProcessedFile/.nii.gz/_mcf.nii.gz}" "$fmriProcessedFile" +mv "${fmriProcessedFile/.nii.gz/_mcf.par}" "$motionParametersFile" + +# create reference volume +fslmaths "$fmriProcessedFile" -Tmean "$fmriReferenceFile" + +# compute registration matrix +if [[ "$freesurferDir" =~ \ |\' ]] || [[ "$fmriReferenceFile" =~ \ |\' ]] || [[ "$registrationMatrixFile" =~ \ |\' ]]; then + echo "bbregister cannot handle filenames with spaces. Variable freesurferDir, fmriReferenceFile or registrationMatrixFile contains spaces." >&2 + exit 1 +fi + +bbregister --s "$freesurferDir" --mov "$fmriReferenceFile" --reg "$registrationMatrixFile" \ + --bold --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$fmriReferenceFile" \ + --reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO add registration of MTR weighted image + +exit 0 diff --git a/bin/macos/3.1.2/structural_pipeline b/bin/macos/3.1.2/structural_pipeline new file mode 100755 index 0000000..c5e3001 Binary files /dev/null and b/bin/macos/3.1.2/structural_pipeline differ diff --git a/bin/macos/3.1.2/structural_preprocessing/preprocess_eddy.sh b/bin/macos/3.1.2/structural_preprocessing/preprocess_eddy.sh new file mode 100755 index 0000000..4b7c375 --- /dev/null +++ b/bin/macos/3.1.2/structural_preprocessing/preprocess_eddy.sh @@ -0,0 +1,197 @@ +#!/bin/bash +# +# (Example) preprocessing script that: +# 1. Runs FSL eddy to correct for eddy current distortions and motion artifacts in the DWI data. +# 2. Updates the b-vectors to adjust for the DWI corrections. +# 3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes. +# 4. Computes the registration matrix between DWI reference image and the T1 image using bbregister. +# 5. Registers the Freesurfer segmentation to the DWI reference image. + +# https://google.github.io/styleguide/shellguide.html + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Usage +####################################### +usage() +{ + echo "(Example) preprocessing script that:" + echo "1. Runs FSL eddy to correct for eddy current distortions and motion artifacts in the DWI data." + echo "2. Updates the b-vectors to adjust for the DWI corrections." + echo "3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes." + echo "4. Computes the registration matrix between DWI reference image and the T1 image using bbregister." + echo "5. Registers the Freesurfer segmentation to the DWI reference image." +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --b0Scans=*) + b0Scans=${1#*=} + shift + ;; + --dwiProcessedFile=*) + dwiProcessedFile=${1#*=} + shift + ;; + --dwiFile=*) + dwiFile=${1#*=} + shift + ;; + --dwiReferenceFile=*) + dwiReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + --processedBvecsFile=*) + processedBvecsFile=${1#*=} + shift + ;; + --processedBvalsFile=*) + processedBvalsFile=${1#*=} + shift + ;; + --acqpFile=*) + acqpFile=${1#*=} + shift + ;; + --indexFile=*) + indexFile=${1#*=} + shift + ;; + --eddyVersion=*) + eddyVersion=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '$1'" + shift + ;; + esac + done + +} + +computeReferenceB0(){ + + # use b0 scan(s) to create reference volume + for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiReferenceFile/.nii.gz/_indv_$i.nii.gz}" $((i- 1)) 1 + done + + fslmerge -t "$dwiReferenceFile" "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + fslmaths "$dwiReferenceFile" -Tmean "$dwiReferenceFile" + rm "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + + +} + +####################################### +# Run Eddy +####################################### +runEddy() { + + # Create index file for eddy + nScans=$(mri_info --nframes "$dwiProcessedFile" | tail -n1) + for i in $(eval echo {1..$nScans}); do + echo -n "1 "; + done > "$indexFile" + + $eddyVersion -v --imain="$dwiProcessedFile" \ + --mask="$brainMaskFile" \ + --acqp="$acqpFile" \ + --index="$indexFile" \ + --bvecs="$processedBvecsFile" --bvals="$processedBvalsFile" \ + --out="$dwiProcessedFile" + + # replace bvecs by their rotated counterparts + [ ! -f "${dwiProcessedFile}.eddy_rotated_bvecs" ] && + error "could not find rotated bvecs (use FSL 5.0.9 or higher)" + mv "${dwiProcessedFile}.eddy_rotated_bvecs" "$processedBvecsFile" + + # Clean eddy output + rm "$brainMaskFile" + +} + +####################################### +# Main function. +####################################### +trap error ERR + +parse_input "$@" + +# TODO: check FSL version + +# TODO: convert MNC to NIFTI +cp "$dwiFile" "$dwiProcessedFile" + +# Load b0-scans list and parse them into an array +b0Scans=(${b0Scans//,/ }) + +# Create a mask of the brain based on the b0-reference +computeReferenceB0 + +bet "$dwiReferenceFile" "$dwiProcessedFile" -m -n # creates ${dwiProcessedFile/.nii.gz/_mask.nii.gz} +brainMaskFile=${dwiProcessedFile/.nii.gz/_mask.nii.gz} +rm "$dwiReferenceFile" # we will create a new reference b0 after eddy correction + +runEddy + +# Create new eddy current and movement corrected reference b0-scan +computeReferenceB0 + +# Compute registration matrix from FS to subject space +bbregister --s "$freesurferDir" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \ + --dti --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# Register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$dwiReferenceFile" \ + --reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO: add registration of MTR weighted image + +exit 0 diff --git a/bin/macos/3.1.2/structural_preprocessing/preprocess_minimal.sh b/bin/macos/3.1.2/structural_preprocessing/preprocess_minimal.sh new file mode 100755 index 0000000..52e8ec8 --- /dev/null +++ b/bin/macos/3.1.2/structural_preprocessing/preprocess_minimal.sh @@ -0,0 +1,125 @@ +#!/bin/bash +# +# (Example) preprocessing script that: +# 1. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes. +# 2. Computes the registration matrix between DWI reference image and the T1 image using bbregister. +# 3. Registers the Freesurfer segmentation to the DWI reference image. + +# https://google.github.io/styleguide/shellguide.html + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Usage +####################################### +usage() +{ + echo "(Example) preprocessing script that:" + echo "1. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes." + echo "2. Computes the registration matrix between DWI reference image and the T1 image using bbregister." + echo "3. Registers the Freesurfer segmentation to the DWI reference image." +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --b0Scans=*) + b0Scans=${1#*=} + shift + ;; + --dwiProcessedFile=*) + dwiProcessedFile=${1#*=} + shift + ;; + --dwiFile=*) + dwiFile=${1#*=} + shift + ;; + --dwiReferenceFile=*) + dwiReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '$1'" + shift + ;; + esac +done +} + +####################################### +# Main function. +####################################### +trap error ERR + +parse_input "$@" + + +# TODO: include conversion MNC to NIFTI +cp "$dwiFile" "$dwiProcessedFile" + +# Load b0-scans list and parse them into an array +b0Scans=(${b0Scans//,/ }) + +# use b0 scan(s) to create reference volume +for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiReferenceFile/.nii.gz/_indv_$i.nii.gz}" $((i - 1)) 1 +done +fslmerge -t "$dwiReferenceFile" "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz +fslmaths "$dwiReferenceFile" -Tmean "$dwiReferenceFile" +rm "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + +# compute registration matrix +bbregister --s "$freesurferDir" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \ + --dti --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$dwiReferenceFile" \ + --reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO add registration of MTR weighted image + +exit 0 diff --git a/bin/macos/3.1.2/structural_preprocessing/preprocess_topup_eddy.sh b/bin/macos/3.1.2/structural_preprocessing/preprocess_topup_eddy.sh new file mode 100755 index 0000000..bf8e33f --- /dev/null +++ b/bin/macos/3.1.2/structural_preprocessing/preprocess_topup_eddy.sh @@ -0,0 +1,208 @@ +#!/bin/bash +# +# (Example) preprocessing script that: +# 1. Runs FSL eddy and FSL topup to correct for susceptibility induced distortions, eddy current distortions and motion artifacts in the DWI data. +# 2. Updates the b-vectors to adjust for the DWI corrections. +# 3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes. +# 4. Computes the registration matrix between DWI reference image and the T1 image using bbregister. +# 5. Registers the Freesurfer segmentation to the DWI reference image. + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 +} + +####################################### +# Usage +####################################### +usage() +{ + echo "(Example) preprocessing script that:" + echo "1. Runs FSL eddy and FSL topup to correct for susceptibility induced distortions, eddy current distortions and motion artifacts in the DWI data." + echo "2. Updates the b-vectors to adjust for the DWI corrections." + echo "3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes." + echo "4. Computes the registration matrix between DWI reference image and the T1 image using bbregister." + echo "5. Registers the Freesurfer segmentation to the DWI reference image." +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --b0Scans=*) + b0Scans=${1#*=} + shift + ;; + --dwiProcessedFile=*) + dwiProcessedFile=${1#*=} + shift + ;; + --dwiFiles=*) + dwiFiles=${1#*=} + shift + ;; + --dwiReferenceFile=*) + dwiReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + --processedBvecsFile=*) + processedBvecsFile=${1#*=} + shift + ;; + --processedBvalsFile=*) + processedBvalsFile=${1#*=} + shift + ;; + --acqpFile=*) + acqpFile=${1#*=} + shift + ;; + --indexFile=*) + indexFile=${1#*=} + shift + ;; + --eddyVersion=*) + eddyVersion=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '${1}'" + shift + ;; + esac + done +} + +####################################### +# Parse input +####################################### +computeReferenceB0(){ + + # use b0 scan(s) to create reference volume + for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiReferenceFile/.nii.gz/_indv_$i.nii.gz}" $((i- 1)) 1 + done + + fslmerge -t "$dwiReferenceFile" "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + fslmaths "$dwiReferenceFile" -Tmean "$dwiReferenceFile" + rm "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + +} + +####################################### +# Main function +####################################### + +trap error ERR + +parse_input "$@" + +dwiFiles=(${dwiFiles//,/ }) +fslmerge -t "$dwiProcessedFile" "${dwiFiles[@]}" + +# TODO: check FSL version > 5.0.9 + +# Load b0-scans list and parse them into an array +b0Scans=(${b0Scans//,/ }) + +dwiB0ScansFile=${dwiProcessedFile/.nii.gz/_b0.nii.gz} +dwiB0UnwarpedScansFile=${dwiProcessedFile/.nii.gz/_b0_unwarped.nii.gz} +brainMaskFile=${dwiProcessedFile/.nii.gz/_mask.nii.gz} # DO NOT CHANGE: HARDCODED IN FSL + +# ------------------------------------- +# Topup +# ------------------------------------- + +# Extract b0-scan(s) and put them (temporary) in dwiReferenceFile +for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiB0ScansFile/.nii.gz/_indv_$i.nii.gz}" $((i - 1)) 1 +done +fslmerge -t "$dwiB0ScansFile" "${dwiB0ScansFile/.nii.gz/_indv_}"*.nii.gz +rm "${dwiB0ScansFile/.nii.gz/_indv_}"*.nii.gz + +# Run topup +topup -v --imain="$dwiB0ScansFile" --config=b02b0.cnf \ +--datain="$acqpFile" --out="${dwiProcessedFile/.nii.gz/}" \ +--iout="$dwiB0UnwarpedScansFile" --subsamp=1 +rm "${dwiB0ScansFile/.nii.gz/}".{nii.gz,topup_log} + +# ------------------------------------- +# Eddy +# ------------------------------------- + +# Create reference b0-image from unwarped b0-scans +fslmaths "$dwiB0UnwarpedScansFile" -Tmean "$dwiReferenceFile" +bet "$dwiReferenceFile" "$dwiProcessedFile" -m -n # creates $brainMaskFile +rm "$dwiReferenceFile" "$dwiB0UnwarpedScansFile" + +# Run eddy current correction +$eddyVersion -v --imain="$dwiProcessedFile" \ + --mask="$brainMaskFile" \ + --acqp="$acqpFile" \ + --index="$indexFile" \ + --bvecs="$processedBvecsFile" --bvals="$processedBvalsFile" \ + --topup="${dwiProcessedFile/.nii.gz/}" \ + --out="$dwiProcessedFile" + +# clean up +# rm ${dwiProcessedFile/.nii.gz/_fieldcoef.nii.gz} ${dwiProcessedFile/.nii.gz/_movpar.txt} +rm "$brainMaskFile" + +mv "${dwiProcessedFile}".eddy_rotated_bvecs "$processedBvecsFile" + +# ------------------------------------- +# DWI and Freesurfer registration +# ------------------------------------- + +# Create new eddy current and movement corrected reference b0-scan +computeReferenceB0 + +# Compute registration matrix from FS to subject space +bbregister --s "$freesurferDir" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \ +--dti --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# Register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$dwiReferenceFile" \ +--reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO: add registration of MTR weighted image + +exit 0 diff --git a/bin/macos/3.1.2/templates/BB50human/BB50human.annot.ctab b/bin/macos/3.1.2/templates/BB50human/BB50human.annot.ctab new file mode 100644 index 0000000..d9cea91 --- /dev/null +++ b/bin/macos/3.1.2/templates/BB50human/BB50human.annot.ctab @@ -0,0 +1,78 @@ +1000 ctx-lh-FA 206 226 156 0 +1001 ctx-lh-FB 200 219 138 0 +1002 ctx-lh-FBA 200 200 120 0 +1003 ctx-lh-FC 187 204 115 0 +1004 ctx-lh-FCBm 85 193 170 0 +1005 ctx-lh-FDdelta 19 132 80 0 +1006 ctx-lh-FDL 27 240 160 0 +1007 ctx-lh-FDm 13 201 111 0 +1008 ctx-lh-FDp 69 168 123 0 +1009 ctx-lh-FE 27 178 138 0 +1010 ctx-lh-FF 49 172 192 0 +1011 ctx-lh-FG 61 127 118 0 +1012 ctx-lh-FH 77 135 106 0 +1013 ctx-lh-FL 80 145 146 0 +1014 ctx-lh-H 41 55 101 0 +1015 ctx-lh-IA 204 61 211 0 +1016 ctx-lh-IB 137 67 135 0 +1017 ctx-lh-LA 124 215 246 0 +1018 ctx-lh-LC1 0 133 185 0 +1019 ctx-lh-LC2 68 165 227 0 +1020 ctx-lh-LE 169 219 224 0 +1021 ctx-lh-unknown 50 50 50 0 +1022 ctx-lh-OA 253 252 187 0 +1023 ctx-lh-OB 251 250 146 0 +1024 ctx-lh-OC 247 222 71 0 +1025 ctx-lh-PB 247 67 148 0 +1026 ctx-lh-PC 239 87 150 0 +1027 ctx-lh-PEm 248 167 210 0 +1028 ctx-lh-PEp 250 150 200 0 +1029 ctx-lh-PF 250 180 224 0 +1030 ctx-lh-PFD 255 190 200 0 +1031 ctx-lh-PG 248 193 224 0 +1032 ctx-lh-PH 232 73 130 0 +1033 ctx-lh-TA 240 85 102 0 +1034 ctx-lh-TB 233 65 98 0 +1035 ctx-lh-TE1 235 181 136 0 +1036 ctx-lh-TE2 204 140 82 0 +1037 ctx-lh-TF 184 47 79 0 +1038 ctx-lh-TG 247 198 127 0 +2000 ctx-rh-FA 206 226 156 0 +2001 ctx-rh-FB 200 219 138 0 +2002 ctx-rh-FBA 200 200 120 0 +2003 ctx-rh-FC 187 204 115 0 +2004 ctx-rh-FCBm 85 193 170 0 +2005 ctx-rh-FDdelta 19 132 80 0 +2006 ctx-rh-FDL 27 240 160 0 +2007 ctx-rh-FDm 13 201 111 0 +2008 ctx-rh-FDp 69 168 123 0 +2009 ctx-rh-FE 27 178 138 0 +2010 ctx-rh-FF 49 172 192 0 +2011 ctx-rh-FG 61 127 118 0 +2012 ctx-rh-FH 77 135 106 0 +2013 ctx-rh-FL 80 145 146 0 +2014 ctx-rh-H 41 55 101 0 +2015 ctx-rh-IA 204 61 211 0 +2016 ctx-rh-IB 137 67 135 0 +2017 ctx-rh-LA 124 215 246 0 +2018 ctx-rh-LC1 0 133 185 0 +2019 ctx-rh-LC2 68 165 227 0 +2020 ctx-rh-LE 169 219 224 0 +2021 ctx-rh-unknown 50 50 50 0 +2022 ctx-rh-OA 253 252 187 0 +2023 ctx-rh-OB 251 250 146 0 +2024 ctx-rh-OC 247 222 71 0 +2025 ctx-rh-PB 247 67 148 0 +2026 ctx-rh-PC 239 87 150 0 +2027 ctx-rh-PEm 248 167 210 0 +2028 ctx-rh-PEp 250 150 200 0 +2029 ctx-rh-PF 250 180 224 0 +2030 ctx-rh-PFD 255 190 200 0 +2031 ctx-rh-PG 248 193 224 0 +2032 ctx-rh-PH 232 73 130 0 +2033 ctx-rh-TA 240 85 102 0 +2034 ctx-rh-TB 233 65 98 0 +2035 ctx-rh-TE1 235 181 136 0 +2036 ctx-rh-TE2 204 140 82 0 +2037 ctx-rh-TF 184 47 79 0 +2038 ctx-rh-TG 247 198 127 0 diff --git a/bin/macos/3.1.2/templates/BB50human/ROIs_BB50human.txt b/bin/macos/3.1.2/templates/BB50human/ROIs_BB50human.txt new file mode 100644 index 0000000..b0b12ea --- /dev/null +++ b/bin/macos/3.1.2/templates/BB50human/ROIs_BB50human.txt @@ -0,0 +1,78 @@ +1000 +1001 +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +2000 +2001 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 diff --git a/bin/macos/3.1.2/templates/BB50human/lh.BB50human.gcs b/bin/macos/3.1.2/templates/BB50human/lh.BB50human.gcs new file mode 100644 index 0000000..bbd6c51 Binary files /dev/null and b/bin/macos/3.1.2/templates/BB50human/lh.BB50human.gcs differ diff --git a/bin/macos/3.1.2/templates/BB50human/parcellate_BB50human.sh b/bin/macos/3.1.2/templates/BB50human/parcellate_BB50human.sh new file mode 100755 index 0000000..027e488 --- /dev/null +++ b/bin/macos/3.1.2/templates/BB50human/parcellate_BB50human.sh @@ -0,0 +1,105 @@ +#!/bin/bash +# +# Parcellate BB50human atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=BB50human + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/macos/3.1.2/templates/BB50human/rh.BB50human.gcs b/bin/macos/3.1.2/templates/BB50human/rh.BB50human.gcs new file mode 100644 index 0000000..98ba293 Binary files /dev/null and b/bin/macos/3.1.2/templates/BB50human/rh.BB50human.gcs differ diff --git a/bin/macos/3.1.2/templates/aparc/ROIs_aparc.txt b/bin/macos/3.1.2/templates/aparc/ROIs_aparc.txt new file mode 100644 index 0000000..7e3d0d7 --- /dev/null +++ b/bin/macos/3.1.2/templates/aparc/ROIs_aparc.txt @@ -0,0 +1,82 @@ +10 +11 +12 +13 +17 +18 +26 +49 +50 +51 +52 +53 +54 +58 +1001 +1002 +1003 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +2001 +2002 +2003 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 diff --git a/bin/macos/3.1.2/templates/aparc/aparc.annot.ctab b/bin/macos/3.1.2/templates/aparc/aparc.annot.ctab new file mode 100644 index 0000000..cc1ad96 --- /dev/null +++ b/bin/macos/3.1.2/templates/aparc/aparc.annot.ctab @@ -0,0 +1,1159 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-bankssts 25 100 40 0 +1002 ctx-lh-caudalanteriorcingulate 125 100 160 0 +1003 ctx-lh-caudalmiddlefrontal 100 25 0 0 +1004 ctx-lh-corpuscallosum 120 70 50 0 +1005 ctx-lh-cuneus 220 20 100 0 +1006 ctx-lh-entorhinal 220 20 10 0 +1007 ctx-lh-fusiform 180 220 140 0 +1008 ctx-lh-inferiorparietal 220 60 220 0 +1009 ctx-lh-inferiortemporal 180 40 120 0 +1010 ctx-lh-isthmuscingulate 140 20 140 0 +1011 ctx-lh-lateraloccipital 20 30 140 0 +1012 ctx-lh-lateralorbitofrontal 35 75 50 0 +1013 ctx-lh-lingual 225 140 140 0 +1014 ctx-lh-medialorbitofrontal 200 35 75 0 +1015 ctx-lh-middletemporal 160 100 50 0 +1016 ctx-lh-parahippocampal 20 220 60 0 +1017 ctx-lh-paracentral 60 220 60 0 +1018 ctx-lh-parsopercularis 220 180 140 0 +1019 ctx-lh-parsorbitalis 20 100 50 0 +1020 ctx-lh-parstriangularis 220 60 20 0 +1021 ctx-lh-pericalcarine 120 100 60 0 +1022 ctx-lh-postcentral 220 20 20 0 +1023 ctx-lh-posteriorcingulate 220 180 220 0 +1024 ctx-lh-precentral 60 20 220 0 +1025 ctx-lh-precuneus 160 140 180 0 +1026 ctx-lh-rostralanteriorcingulate 80 20 140 0 +1027 ctx-lh-rostralmiddlefrontal 75 50 125 0 +1028 ctx-lh-superiorfrontal 20 220 160 0 +1029 ctx-lh-superiorparietal 20 180 140 0 +1030 ctx-lh-superiortemporal 140 220 220 0 +1031 ctx-lh-supramarginal 80 160 20 0 +1032 ctx-lh-frontalpole 100 0 100 0 +1033 ctx-lh-temporalpole 70 70 70 0 +1034 ctx-lh-transversetemporal 150 150 200 0 +1035 ctx-lh-insula 255 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-bankssts 25 100 40 0 +2002 ctx-rh-caudalanteriorcingulate 125 100 160 0 +2003 ctx-rh-caudalmiddlefrontal 100 25 0 0 +2004 ctx-rh-corpuscallosum 120 70 50 0 +2005 ctx-rh-cuneus 220 20 100 0 +2006 ctx-rh-entorhinal 220 20 10 0 +2007 ctx-rh-fusiform 180 220 140 0 +2008 ctx-rh-inferiorparietal 220 60 220 0 +2009 ctx-rh-inferiortemporal 180 40 120 0 +2010 ctx-rh-isthmuscingulate 140 20 140 0 +2011 ctx-rh-lateraloccipital 20 30 140 0 +2012 ctx-rh-lateralorbitofrontal 35 75 50 0 +2013 ctx-rh-lingual 225 140 140 0 +2014 ctx-rh-medialorbitofrontal 200 35 75 0 +2015 ctx-rh-middletemporal 160 100 50 0 +2016 ctx-rh-parahippocampal 20 220 60 0 +2017 ctx-rh-paracentral 60 220 60 0 +2018 ctx-rh-parsopercularis 220 180 140 0 +2019 ctx-rh-parsorbitalis 20 100 50 0 +2020 ctx-rh-parstriangularis 220 60 20 0 +2021 ctx-rh-pericalcarine 120 100 60 0 +2022 ctx-rh-postcentral 220 20 20 0 +2023 ctx-rh-posteriorcingulate 220 180 220 0 +2024 ctx-rh-precentral 60 20 220 0 +2025 ctx-rh-precuneus 160 140 180 0 +2026 ctx-rh-rostralanteriorcingulate 80 20 140 0 +2027 ctx-rh-rostralmiddlefrontal 75 50 125 0 +2028 ctx-rh-superiorfrontal 20 220 160 0 +2029 ctx-rh-superiorparietal 20 180 140 0 +2030 ctx-rh-superiortemporal 140 220 220 0 +2031 ctx-rh-supramarginal 80 160 20 0 +2032 ctx-rh-frontalpole 100 0 100 0 +2033 ctx-rh-temporalpole 70 70 70 0 +2034 ctx-rh-transversetemporal 150 150 200 0 +2035 ctx-rh-insula 255 192 32 0 +3000 wm-lh-unknown 230 250 230 0 +3001 wm-lh-bankssts 230 155 215 0 +3002 wm-lh-caudalanteriorcingulate 130 155 95 0 +3003 wm-lh-caudalmiddlefrontal 155 230 255 0 +3004 wm-lh-corpuscallosum 135 185 205 0 +3005 wm-lh-cuneus 35 235 155 0 +3006 wm-lh-entorhinal 35 235 245 0 +3007 wm-lh-fusiform 75 35 115 0 +3008 wm-lh-inferiorparietal 35 195 35 0 +3009 wm-lh-inferiortemporal 75 215 135 0 +3010 wm-lh-isthmuscingulate 115 235 115 0 +3011 wm-lh-lateraloccipital 235 225 115 0 +3012 wm-lh-lateralorbitofrontal 220 180 205 0 +3013 wm-lh-lingual 30 115 115 0 +3014 wm-lh-medialorbitofrontal 55 220 180 0 +3015 wm-lh-middletemporal 95 155 205 0 +3016 wm-lh-parahippocampal 235 35 195 0 +3017 wm-lh-paracentral 195 35 195 0 +3018 wm-lh-parsopercularis 35 75 115 0 +3019 wm-lh-parsorbitalis 235 155 205 0 +3020 wm-lh-parstriangularis 35 195 235 0 +3021 wm-lh-pericalcarine 135 155 195 0 +3022 wm-lh-postcentral 35 235 235 0 +3023 wm-lh-posteriorcingulate 35 75 35 0 +3024 wm-lh-precentral 195 235 35 0 +3025 wm-lh-precuneus 95 115 75 0 +3026 wm-lh-rostralanteriorcingulate 175 235 115 0 +3027 wm-lh-rostralmiddlefrontal 180 205 130 0 +3028 wm-lh-superiorfrontal 235 35 95 0 +3029 wm-lh-superiorparietal 235 75 115 0 +3030 wm-lh-superiortemporal 115 35 35 0 +3031 wm-lh-supramarginal 175 95 235 0 +3032 wm-lh-frontalpole 155 255 155 0 +3033 wm-lh-temporalpole 185 185 185 0 +3034 wm-lh-transversetemporal 105 105 55 0 +3035 wm-lh-insula 254 191 31 0 +4000 wm-rh-unknown 230 250 230 0 +4001 wm-rh-bankssts 230 155 215 0 +4002 wm-rh-caudalanteriorcingulate 130 155 95 0 +4003 wm-rh-caudalmiddlefrontal 155 230 255 0 +4004 wm-rh-corpuscallosum 135 185 205 0 +4005 wm-rh-cuneus 35 235 155 0 +4006 wm-rh-entorhinal 35 235 245 0 +4007 wm-rh-fusiform 75 35 115 0 +4008 wm-rh-inferiorparietal 35 195 35 0 +4009 wm-rh-inferiortemporal 75 215 135 0 +4010 wm-rh-isthmuscingulate 115 235 115 0 +4011 wm-rh-lateraloccipital 235 225 115 0 +4012 wm-rh-lateralorbitofrontal 220 180 205 0 +4013 wm-rh-lingual 30 115 115 0 +4014 wm-rh-medialorbitofrontal 55 220 180 0 +4015 wm-rh-middletemporal 95 155 205 0 +4016 wm-rh-parahippocampal 235 35 195 0 +4017 wm-rh-paracentral 195 35 195 0 +4018 wm-rh-parsopercularis 35 75 115 0 +4019 wm-rh-parsorbitalis 235 155 205 0 +4020 wm-rh-parstriangularis 35 195 235 0 +4021 wm-rh-pericalcarine 135 155 195 0 +4022 wm-rh-postcentral 35 235 235 0 +4023 wm-rh-posteriorcingulate 35 75 35 0 +4024 wm-rh-precentral 195 235 35 0 +4025 wm-rh-precuneus 95 115 75 0 +4026 wm-rh-rostralanteriorcingulate 175 235 115 0 +4027 wm-rh-rostralmiddlefrontal 180 205 130 0 +4028 wm-rh-superiorfrontal 235 35 95 0 +4029 wm-rh-superiorparietal 235 75 115 0 +4030 wm-rh-superiortemporal 115 35 35 0 +4031 wm-rh-supramarginal 175 95 235 0 +4032 wm-rh-frontalpole 155 255 155 0 +4033 wm-rh-temporalpole 185 185 185 0 +4034 wm-rh-transversetemporal 105 105 55 0 +4035 wm-rh-insula 254 191 31 0 +1100 ctx-lh-Unknown 0 0 0 0 +1101 ctx-lh-Corpus_callosum 50 50 50 0 +1102 ctx-lh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +1103 ctx-lh-G_cingulate-Isthmus 60 25 25 0 +1104 ctx-lh-G_cingulate-Main_part 25 60 60 0 +1200 ctx-lh-G_cingulate-caudal_ACC 25 60 61 0 +1201 ctx-lh-G_cingulate-rostral_ACC 25 90 60 0 +1202 ctx-lh-G_cingulate-posterior 25 120 60 0 +1205 ctx-lh-S_cingulate-caudal_ACC 25 150 60 0 +1206 ctx-lh-S_cingulate-rostral_ACC 25 180 60 0 +1207 ctx-lh-S_cingulate-posterior 25 210 60 0 +1210 ctx-lh-S_pericallosal-caudal 25 150 90 0 +1211 ctx-lh-S_pericallosal-rostral 25 180 90 0 +1212 ctx-lh-S_pericallosal-posterior 25 210 90 0 +1105 ctx-lh-G_cuneus 180 20 20 0 +1106 ctx-lh-G_frontal_inf-Opercular_part 220 20 100 0 +1107 ctx-lh-G_frontal_inf-Orbital_part 140 60 60 0 +1108 ctx-lh-G_frontal_inf-Triangular_part 180 220 140 0 +1109 ctx-lh-G_frontal_middle 140 100 180 0 +1110 ctx-lh-G_frontal_superior 180 20 140 0 +1111 ctx-lh-G_frontomarginal 140 20 140 0 +1112 ctx-lh-G_insular_long 21 10 10 0 +1113 ctx-lh-G_insular_short 225 140 140 0 +1114 ctx-lh-G_and_S_occipital_inferior 23 60 180 0 +1115 ctx-lh-G_occipital_middle 180 60 180 0 +1116 ctx-lh-G_occipital_superior 20 220 60 0 +1117 ctx-lh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +1118 ctx-lh-G_occipit-temp_med-Lingual_part 220 180 140 0 +1119 ctx-lh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +1120 ctx-lh-G_orbital 220 60 20 0 +1121 ctx-lh-G_paracentral 60 100 60 0 +1122 ctx-lh-G_parietal_inferior-Angular_part 20 60 220 0 +1123 ctx-lh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +1124 ctx-lh-G_parietal_superior 220 180 220 0 +1125 ctx-lh-G_postcentral 20 180 140 0 +1126 ctx-lh-G_precentral 60 140 180 0 +1127 ctx-lh-G_precuneus 25 20 140 0 +1128 ctx-lh-G_rectus 20 60 100 0 +1129 ctx-lh-G_subcallosal 60 220 20 0 +1130 ctx-lh-G_subcentral 60 20 220 0 +1131 ctx-lh-G_temporal_inferior 220 220 100 0 +1132 ctx-lh-G_temporal_middle 180 60 60 0 +1133 ctx-lh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +1134 ctx-lh-G_temp_sup-Lateral_aspect 220 60 220 0 +1135 ctx-lh-G_temp_sup-Planum_polare 65 220 60 0 +1136 ctx-lh-G_temp_sup-Planum_tempolare 25 140 20 0 +1137 ctx-lh-G_and_S_transverse_frontopolar 13 0 250 0 +1138 ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +1139 ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +1140 ctx-lh-Lat_Fissure-post_sgt 61 60 100 0 +1141 ctx-lh-Medial_wall 25 25 25 0 +1142 ctx-lh-Pole_occipital 140 20 60 0 +1143 ctx-lh-Pole_temporal 220 180 20 0 +1144 ctx-lh-S_calcarine 63 180 180 0 +1145 ctx-lh-S_central 221 20 10 0 +1146 ctx-lh-S_central_insula 21 220 20 0 +1147 ctx-lh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +1148 ctx-lh-S_cingulate-Marginalis_part 221 20 100 0 +1149 ctx-lh-S_circular_insula_anterior 221 60 140 0 +1150 ctx-lh-S_circular_insula_inferior 221 20 220 0 +1151 ctx-lh-S_circular_insula_superior 61 220 220 0 +1152 ctx-lh-S_collateral_transverse_ant 100 200 200 0 +1153 ctx-lh-S_collateral_transverse_post 10 200 200 0 +1154 ctx-lh-S_frontal_inferior 221 220 20 0 +1155 ctx-lh-S_frontal_middle 141 20 100 0 +1156 ctx-lh-S_frontal_superior 61 220 100 0 +1157 ctx-lh-S_frontomarginal 21 220 60 0 +1158 ctx-lh-S_intermedius_primus-Jensen 141 60 20 0 +1159 ctx-lh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +1160 ctx-lh-S_occipital_anterior 61 20 180 0 +1161 ctx-lh-S_occipital_middle_and_Lunatus 101 60 220 0 +1162 ctx-lh-S_occipital_superior_and_transversalis 21 20 140 0 +1163 ctx-lh-S_occipito-temporal_lateral 221 140 20 0 +1164 ctx-lh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +1165 ctx-lh-S_orbital-H_shapped 101 20 20 0 +1166 ctx-lh-S_orbital_lateral 221 100 20 0 +1167 ctx-lh-S_orbital_medial-Or_olfactory 181 200 20 0 +1168 ctx-lh-S_paracentral 21 180 140 0 +1169 ctx-lh-S_parieto_occipital 101 100 180 0 +1170 ctx-lh-S_pericallosal 181 220 20 0 +1171 ctx-lh-S_postcentral 21 140 200 0 +1172 ctx-lh-S_precentral-Inferior-part 21 20 240 0 +1173 ctx-lh-S_precentral-Superior-part 21 20 200 0 +1174 ctx-lh-S_subcentral_ant 61 180 60 0 +1175 ctx-lh-S_subcentral_post 61 180 250 0 +1176 ctx-lh-S_suborbital 21 20 60 0 +1177 ctx-lh-S_subparietal 101 60 60 0 +1178 ctx-lh-S_supracingulate 21 220 220 0 +1179 ctx-lh-S_temporal_inferior 21 180 180 0 +1180 ctx-lh-S_temporal_superior 223 220 60 0 +1181 ctx-lh-S_temporal_transverse 221 60 60 0 +2100 ctx-rh-Unknown 0 0 0 0 +2101 ctx-rh-Corpus_callosum 50 50 50 0 +2102 ctx-rh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +2103 ctx-rh-G_cingulate-Isthmus 60 25 25 0 +2104 ctx-rh-G_cingulate-Main_part 25 60 60 0 +2105 ctx-rh-G_cuneus 180 20 20 0 +2106 ctx-rh-G_frontal_inf-Opercular_part 220 20 100 0 +2107 ctx-rh-G_frontal_inf-Orbital_part 140 60 60 0 +2108 ctx-rh-G_frontal_inf-Triangular_part 180 220 140 0 +2109 ctx-rh-G_frontal_middle 140 100 180 0 +2110 ctx-rh-G_frontal_superior 180 20 140 0 +2111 ctx-rh-G_frontomarginal 140 20 140 0 +2112 ctx-rh-G_insular_long 21 10 10 0 +2113 ctx-rh-G_insular_short 225 140 140 0 +2114 ctx-rh-G_and_S_occipital_inferior 23 60 180 0 +2115 ctx-rh-G_occipital_middle 180 60 180 0 +2116 ctx-rh-G_occipital_superior 20 220 60 0 +2117 ctx-rh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +2118 ctx-rh-G_occipit-temp_med-Lingual_part 220 180 140 0 +2119 ctx-rh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +2120 ctx-rh-G_orbital 220 60 20 0 +2121 ctx-rh-G_paracentral 60 100 60 0 +2122 ctx-rh-G_parietal_inferior-Angular_part 20 60 220 0 +2123 ctx-rh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +2124 ctx-rh-G_parietal_superior 220 180 220 0 +2125 ctx-rh-G_postcentral 20 180 140 0 +2126 ctx-rh-G_precentral 60 140 180 0 +2127 ctx-rh-G_precuneus 25 20 140 0 +2128 ctx-rh-G_rectus 20 60 100 0 +2129 ctx-rh-G_subcallosal 60 220 20 0 +2130 ctx-rh-G_subcentral 60 20 220 0 +2131 ctx-rh-G_temporal_inferior 220 220 100 0 +2132 ctx-rh-G_temporal_middle 180 60 60 0 +2133 ctx-rh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +2134 ctx-rh-G_temp_sup-Lateral_aspect 220 60 220 0 +2135 ctx-rh-G_temp_sup-Planum_polare 65 220 60 0 +2136 ctx-rh-G_temp_sup-Planum_tempolare 25 140 20 0 +2137 ctx-rh-G_and_S_transverse_frontopolar 13 0 250 0 +2138 ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +2139 ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +2140 ctx-rh-Lat_Fissure-post_sgt 61 60 100 0 +2141 ctx-rh-Medial_wall 25 25 25 0 +2142 ctx-rh-Pole_occipital 140 20 60 0 +2143 ctx-rh-Pole_temporal 220 180 20 0 +2144 ctx-rh-S_calcarine 63 180 180 0 +2145 ctx-rh-S_central 221 20 10 0 +2146 ctx-rh-S_central_insula 21 220 20 0 +2147 ctx-rh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +2148 ctx-rh-S_cingulate-Marginalis_part 221 20 100 0 +2149 ctx-rh-S_circular_insula_anterior 221 60 140 0 +2150 ctx-rh-S_circular_insula_inferior 221 20 220 0 +2151 ctx-rh-S_circular_insula_superior 61 220 220 0 +2152 ctx-rh-S_collateral_transverse_ant 100 200 200 0 +2153 ctx-rh-S_collateral_transverse_post 10 200 200 0 +2154 ctx-rh-S_frontal_inferior 221 220 20 0 +2155 ctx-rh-S_frontal_middle 141 20 100 0 +2156 ctx-rh-S_frontal_superior 61 220 100 0 +2157 ctx-rh-S_frontomarginal 21 220 60 0 +2158 ctx-rh-S_intermedius_primus-Jensen 141 60 20 0 +2159 ctx-rh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +2160 ctx-rh-S_occipital_anterior 61 20 180 0 +2161 ctx-rh-S_occipital_middle_and_Lunatus 101 60 220 0 +2162 ctx-rh-S_occipital_superior_and_transversalis 21 20 140 0 +2163 ctx-rh-S_occipito-temporal_lateral 221 140 20 0 +2164 ctx-rh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +2165 ctx-rh-S_orbital-H_shapped 101 20 20 0 +2166 ctx-rh-S_orbital_lateral 221 100 20 0 +2167 ctx-rh-S_orbital_medial-Or_olfactory 181 200 20 0 +2168 ctx-rh-S_paracentral 21 180 140 0 +2169 ctx-rh-S_parieto_occipital 101 100 180 0 +2170 ctx-rh-S_pericallosal 181 220 20 0 +2171 ctx-rh-S_postcentral 21 140 200 0 +2172 ctx-rh-S_precentral-Inferior-part 21 20 240 0 +2173 ctx-rh-S_precentral-Superior-part 21 20 200 0 +2174 ctx-rh-S_subcentral_ant 61 180 60 0 +2175 ctx-rh-S_subcentral_post 61 180 250 0 +2176 ctx-rh-S_suborbital 21 20 60 0 +2177 ctx-rh-S_subparietal 101 60 60 0 +2178 ctx-rh-S_supracingulate 21 220 220 0 +2179 ctx-rh-S_temporal_inferior 21 180 180 0 +2180 ctx-rh-S_temporal_superior 223 220 60 0 +2181 ctx-rh-S_temporal_transverse 221 60 60 0 +2200 ctx-rh-G_cingulate-caudal_ACC 25 60 61 0 +2201 ctx-rh-G_cingulate-rostral_ACC 25 90 60 0 +2202 ctx-rh-G_cingulate-posterior 25 120 60 0 +2205 ctx-rh-S_cingulate-caudal_ACC 25 150 60 0 +2206 ctx-rh-S_cingulate-rostral_ACC 25 180 60 0 +2207 ctx-rh-S_cingulate-posterior 25 210 60 0 +2210 ctx-rh-S_pericallosal-caudal 25 150 90 0 +2211 ctx-rh-S_pericallosal-rostral 25 180 90 0 +2212 ctx-rh-S_pericallosal-posterior 25 210 90 0 +3100 wm-lh-Unknown 0 0 0 0 +3101 wm-lh-Corpus_callosum 50 50 50 0 +3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +3103 wm-lh-G_cingulate-Isthmus 60 25 25 0 +3104 wm-lh-G_cingulate-Main_part 25 60 60 0 +3105 wm-lh-G_cuneus 180 20 20 0 +3106 wm-lh-G_frontal_inf-Opercular_part 220 20 100 0 +3107 wm-lh-G_frontal_inf-Orbital_part 140 60 60 0 +3108 wm-lh-G_frontal_inf-Triangular_part 180 220 140 0 +3109 wm-lh-G_frontal_middle 140 100 180 0 +3110 wm-lh-G_frontal_superior 180 20 140 0 +3111 wm-lh-G_frontomarginal 140 20 140 0 +3112 wm-lh-G_insular_long 21 10 10 0 +3113 wm-lh-G_insular_short 225 140 140 0 +3114 wm-lh-G_and_S_occipital_inferior 23 60 180 0 +3115 wm-lh-G_occipital_middle 180 60 180 0 +3116 wm-lh-G_occipital_superior 20 220 60 0 +3117 wm-lh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +3118 wm-lh-G_occipit-temp_med-Lingual_part 220 180 140 0 +3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +3120 wm-lh-G_orbital 220 60 20 0 +3121 wm-lh-G_paracentral 60 100 60 0 +3122 wm-lh-G_parietal_inferior-Angular_part 20 60 220 0 +3123 wm-lh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +3124 wm-lh-G_parietal_superior 220 180 220 0 +3125 wm-lh-G_postcentral 20 180 140 0 +3126 wm-lh-G_precentral 60 140 180 0 +3127 wm-lh-G_precuneus 25 20 140 0 +3128 wm-lh-G_rectus 20 60 100 0 +3129 wm-lh-G_subcallosal 60 220 20 0 +3130 wm-lh-G_subcentral 60 20 220 0 +3131 wm-lh-G_temporal_inferior 220 220 100 0 +3132 wm-lh-G_temporal_middle 180 60 60 0 +3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +3134 wm-lh-G_temp_sup-Lateral_aspect 220 60 220 0 +3135 wm-lh-G_temp_sup-Planum_polare 65 220 60 0 +3136 wm-lh-G_temp_sup-Planum_tempolare 25 140 20 0 +3137 wm-lh-G_and_S_transverse_frontopolar 13 0 250 0 +3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +3140 wm-lh-Lat_Fissure-post_sgt 61 60 100 0 +3141 wm-lh-Medial_wall 25 25 25 0 +3142 wm-lh-Pole_occipital 140 20 60 0 +3143 wm-lh-Pole_temporal 220 180 20 0 +3144 wm-lh-S_calcarine 63 180 180 0 +3145 wm-lh-S_central 221 20 10 0 +3146 wm-lh-S_central_insula 21 220 20 0 +3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +3148 wm-lh-S_cingulate-Marginalis_part 221 20 100 0 +3149 wm-lh-S_circular_insula_anterior 221 60 140 0 +3150 wm-lh-S_circular_insula_inferior 221 20 220 0 +3151 wm-lh-S_circular_insula_superior 61 220 220 0 +3152 wm-lh-S_collateral_transverse_ant 100 200 200 0 +3153 wm-lh-S_collateral_transverse_post 10 200 200 0 +3154 wm-lh-S_frontal_inferior 221 220 20 0 +3155 wm-lh-S_frontal_middle 141 20 100 0 +3156 wm-lh-S_frontal_superior 61 220 100 0 +3157 wm-lh-S_frontomarginal 21 220 60 0 +3158 wm-lh-S_intermedius_primus-Jensen 141 60 20 0 +3159 wm-lh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +3160 wm-lh-S_occipital_anterior 61 20 180 0 +3161 wm-lh-S_occipital_middle_and_Lunatus 101 60 220 0 +3162 wm-lh-S_occipital_superior_and_transversalis 21 20 140 0 +3163 wm-lh-S_occipito-temporal_lateral 221 140 20 0 +3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +3165 wm-lh-S_orbital-H_shapped 101 20 20 0 +3166 wm-lh-S_orbital_lateral 221 100 20 0 +3167 wm-lh-S_orbital_medial-Or_olfactory 181 200 20 0 +3168 wm-lh-S_paracentral 21 180 140 0 +3169 wm-lh-S_parieto_occipital 101 100 180 0 +3170 wm-lh-S_pericallosal 181 220 20 0 +3171 wm-lh-S_postcentral 21 140 200 0 +3172 wm-lh-S_precentral-Inferior-part 21 20 240 0 +3173 wm-lh-S_precentral-Superior-part 21 20 200 0 +3174 wm-lh-S_subcentral_ant 61 180 60 0 +3175 wm-lh-S_subcentral_post 61 180 250 0 +3176 wm-lh-S_suborbital 21 20 60 0 +3177 wm-lh-S_subparietal 101 60 60 0 +3178 wm-lh-S_supracingulate 21 220 220 0 +3179 wm-lh-S_temporal_inferior 21 180 180 0 +3180 wm-lh-S_temporal_superior 223 220 60 0 +3181 wm-lh-S_temporal_transverse 221 60 60 0 +4100 wm-rh-Unknown 0 0 0 0 +4101 wm-rh-Corpus_callosum 50 50 50 0 +4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +4103 wm-rh-G_cingulate-Isthmus 60 25 25 0 +4104 wm-rh-G_cingulate-Main_part 25 60 60 0 +4105 wm-rh-G_cuneus 180 20 20 0 +4106 wm-rh-G_frontal_inf-Opercular_part 220 20 100 0 +4107 wm-rh-G_frontal_inf-Orbital_part 140 60 60 0 +4108 wm-rh-G_frontal_inf-Triangular_part 180 220 140 0 +4109 wm-rh-G_frontal_middle 140 100 180 0 +4110 wm-rh-G_frontal_superior 180 20 140 0 +4111 wm-rh-G_frontomarginal 140 20 140 0 +4112 wm-rh-G_insular_long 21 10 10 0 +4113 wm-rh-G_insular_short 225 140 140 0 +4114 wm-rh-G_and_S_occipital_inferior 23 60 180 0 +4115 wm-rh-G_occipital_middle 180 60 180 0 +4116 wm-rh-G_occipital_superior 20 220 60 0 +4117 wm-rh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +4118 wm-rh-G_occipit-temp_med-Lingual_part 220 180 140 0 +4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +4120 wm-rh-G_orbital 220 60 20 0 +4121 wm-rh-G_paracentral 60 100 60 0 +4122 wm-rh-G_parietal_inferior-Angular_part 20 60 220 0 +4123 wm-rh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +4124 wm-rh-G_parietal_superior 220 180 220 0 +4125 wm-rh-G_postcentral 20 180 140 0 +4126 wm-rh-G_precentral 60 140 180 0 +4127 wm-rh-G_precuneus 25 20 140 0 +4128 wm-rh-G_rectus 20 60 100 0 +4129 wm-rh-G_subcallosal 60 220 20 0 +4130 wm-rh-G_subcentral 60 20 220 0 +4131 wm-rh-G_temporal_inferior 220 220 100 0 +4132 wm-rh-G_temporal_middle 180 60 60 0 +4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +4134 wm-rh-G_temp_sup-Lateral_aspect 220 60 220 0 +4135 wm-rh-G_temp_sup-Planum_polare 65 220 60 0 +4136 wm-rh-G_temp_sup-Planum_tempolare 25 140 20 0 +4137 wm-rh-G_and_S_transverse_frontopolar 13 0 250 0 +4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +4140 wm-rh-Lat_Fissure-post_sgt 61 60 100 0 +4141 wm-rh-Medial_wall 25 25 25 0 +4142 wm-rh-Pole_occipital 140 20 60 0 +4143 wm-rh-Pole_temporal 220 180 20 0 +4144 wm-rh-S_calcarine 63 180 180 0 +4145 wm-rh-S_central 221 20 10 0 +4146 wm-rh-S_central_insula 21 220 20 0 +4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +4148 wm-rh-S_cingulate-Marginalis_part 221 20 100 0 +4149 wm-rh-S_circular_insula_anterior 221 60 140 0 +4150 wm-rh-S_circular_insula_inferior 221 20 220 0 +4151 wm-rh-S_circular_insula_superior 61 220 220 0 +4152 wm-rh-S_collateral_transverse_ant 100 200 200 0 +4153 wm-rh-S_collateral_transverse_post 10 200 200 0 +4154 wm-rh-S_frontal_inferior 221 220 20 0 +4155 wm-rh-S_frontal_middle 141 20 100 0 +4156 wm-rh-S_frontal_superior 61 220 100 0 +4157 wm-rh-S_frontomarginal 21 220 60 0 +4158 wm-rh-S_intermedius_primus-Jensen 141 60 20 0 +4159 wm-rh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +4160 wm-rh-S_occipital_anterior 61 20 180 0 +4161 wm-rh-S_occipital_middle_and_Lunatus 101 60 220 0 +4162 wm-rh-S_occipital_superior_and_transversalis 21 20 140 0 +4163 wm-rh-S_occipito-temporal_lateral 221 140 20 0 +4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +4165 wm-rh-S_orbital-H_shapped 101 20 20 0 +4166 wm-rh-S_orbital_lateral 221 100 20 0 +4167 wm-rh-S_orbital_medial-Or_olfactory 181 200 20 0 +4168 wm-rh-S_paracentral 21 180 140 0 +4169 wm-rh-S_parieto_occipital 101 100 180 0 +4170 wm-rh-S_pericallosal 181 220 20 0 +4171 wm-rh-S_postcentral 21 140 200 0 +4172 wm-rh-S_precentral-Inferior-part 21 20 240 0 +4173 wm-rh-S_precentral-Superior-part 21 20 200 0 +4174 wm-rh-S_subcentral_ant 61 180 60 0 +4175 wm-rh-S_subcentral_post 61 180 250 0 +4176 wm-rh-S_suborbital 21 20 60 0 +4177 wm-rh-S_subparietal 101 60 60 0 +4178 wm-rh-S_supracingulate 21 220 220 0 +4179 wm-rh-S_temporal_inferior 21 180 180 0 +4180 wm-rh-S_temporal_superior 223 220 60 0 +4181 wm-rh-S_temporal_transverse 221 60 60 0 +5001 Left-UnsegmentedWhiteMatter 20 30 40 0 +5002 Right-UnsegmentedWhiteMatter 20 30 40 0 +5100 fmajor 204 102 102 0 +5101 fminor 204 102 102 0 +5102 lh.atr 255 255 102 0 +5103 lh.cab 153 204 0 0 +5104 lh.ccg 0 153 153 0 +5105 lh.cst 204 153 255 0 +5106 lh.ilf 255 153 51 0 +5107 lh.slfp 204 204 204 0 +5108 lh.slft 153 255 255 0 +5109 lh.unc 102 153 255 0 +5110 rh.atr 255 255 102 0 +5111 rh.cab 153 204 0 0 +5112 rh.ccg 0 153 153 0 +5113 rh.cst 204 153 255 0 +5114 rh.ilf 255 153 51 0 +5115 rh.slfp 204 204 204 0 +5116 rh.slft 153 255 255 0 +5117 rh.unc 102 153 255 0 +6000 CST-orig 0 255 0 0 +6001 CST-hammer 255 255 0 0 +6002 CST-CVS 0 255 255 0 +6003 CST-flirt 0 0 255 0 +6010 Left-SLF1 236 16 231 0 +6020 Right-SLF1 237 18 232 0 +6030 Left-SLF3 236 13 227 0 +6040 Right-SLF3 236 17 228 0 +6050 Left-CST 1 255 1 0 +6060 Right-CST 2 255 1 0 +6070 Left-SLF2 236 14 230 0 +6080 Right-SLF2 237 14 230 0 +7001 Lateral-nucleus 72 132 181 0 +7002 Basolateral-nucleus 243 243 243 0 +7003 Basal-nucleus 207 63 79 0 +7004 Centromedial-nucleus 121 20 135 0 +7005 Central-nucleus 197 60 248 0 +7006 Medial-nucleus 2 149 2 0 +7007 Cortical-nucleus 221 249 166 0 +7008 Accessory-Basal-nucleus 232 146 35 0 +7009 Corticoamygdaloid-transitio 20 60 120 0 +7010 Anterior-amygdaloid-area-AAA 250 250 0 0 +7011 Fusion-amygdala-HP-FAH 122 187 222 0 +7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 +7013 Endopiriform-nucleus 10 49 255 0 +7014 Lateral-nucleus-olfactory-tract 205 184 144 0 +7015 Paralaminar-nucleus 45 205 165 0 +7016 Intercalated-nucleus 117 160 175 0 +7017 Prepiriform-cortex 221 217 21 0 +7018 Periamygdaloid-cortex 20 60 120 0 +7019 Envelope-Amygdala 141 21 100 0 +7020 Extranuclear-Amydala 225 140 141 0 +7100 Brainstem-inferior-colliculus 42 201 168 0 +7101 Brainstem-cochlear-nucleus 168 104 162 0 +8001 Thalamus-Anterior 74 130 181 0 +8002 Thalamus-Ventral-anterior 242 241 240 0 +8003 Thalamus-Lateral-dorsal 206 65 78 0 +8004 Thalamus-Lateral-posterior 120 21 133 0 +8005 Thalamus-Ventral-lateral 195 61 246 0 +8006 Thalamus-Ventral-posterior-medial 3 147 6 0 +8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 +8008 Thalamus-intralaminar 232 146 33 0 +8009 Thalamus-centromedian 4 114 14 0 +8010 Thalamus-mediodorsal 121 184 220 0 +8011 Thalamus-medial 235 11 175 0 +8012 Thalamus-pulvinar 12 46 250 0 +8013 Thalamus-lateral-geniculate 203 182 143 0 +8014 Thalamus-medial-geniculate 42 204 167 0 +11100 ctx_lh_Unknown 0 0 0 0 +11101 ctx_lh_G_and_S_frontomargin 23 220 60 0 +11102 ctx_lh_G_and_S_occipital_inf 23 60 180 0 +11103 ctx_lh_G_and_S_paracentral 63 100 60 0 +11104 ctx_lh_G_and_S_subcentral 63 20 220 0 +11105 ctx_lh_G_and_S_transv_frontopol 13 0 250 0 +11106 ctx_lh_G_and_S_cingul-Ant 26 60 0 0 +11107 ctx_lh_G_and_S_cingul-Mid-Ant 26 60 75 0 +11108 ctx_lh_G_and_S_cingul-Mid-Post 26 60 150 0 +11109 ctx_lh_G_cingul-Post-dorsal 25 60 250 0 +11110 ctx_lh_G_cingul-Post-ventral 60 25 25 0 +11111 ctx_lh_G_cuneus 180 20 20 0 +11112 ctx_lh_G_front_inf-Opercular 220 20 100 0 +11113 ctx_lh_G_front_inf-Orbital 140 60 60 0 +11114 ctx_lh_G_front_inf-Triangul 180 220 140 0 +11115 ctx_lh_G_front_middle 140 100 180 0 +11116 ctx_lh_G_front_sup 180 20 140 0 +11117 ctx_lh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +11118 ctx_lh_G_insular_short 225 140 140 0 +11119 ctx_lh_G_occipital_middle 180 60 180 0 +11120 ctx_lh_G_occipital_sup 20 220 60 0 +11121 ctx_lh_G_oc-temp_lat-fusifor 60 20 140 0 +11122 ctx_lh_G_oc-temp_med-Lingual 220 180 140 0 +11123 ctx_lh_G_oc-temp_med-Parahip 65 100 20 0 +11124 ctx_lh_G_orbital 220 60 20 0 +11125 ctx_lh_G_pariet_inf-Angular 20 60 220 0 +11126 ctx_lh_G_pariet_inf-Supramar 100 100 60 0 +11127 ctx_lh_G_parietal_sup 220 180 220 0 +11128 ctx_lh_G_postcentral 20 180 140 0 +11129 ctx_lh_G_precentral 60 140 180 0 +11130 ctx_lh_G_precuneus 25 20 140 0 +11131 ctx_lh_G_rectus 20 60 100 0 +11132 ctx_lh_G_subcallosal 60 220 20 0 +11133 ctx_lh_G_temp_sup-G_T_transv 60 60 220 0 +11134 ctx_lh_G_temp_sup-Lateral 220 60 220 0 +11135 ctx_lh_G_temp_sup-Plan_polar 65 220 60 0 +11136 ctx_lh_G_temp_sup-Plan_tempo 25 140 20 0 +11137 ctx_lh_G_temporal_inf 220 220 100 0 +11138 ctx_lh_G_temporal_middle 180 60 60 0 +11139 ctx_lh_Lat_Fis-ant-Horizont 61 20 220 0 +11140 ctx_lh_Lat_Fis-ant-Vertical 61 20 60 0 +11141 ctx_lh_Lat_Fis-post 61 60 100 0 +11142 ctx_lh_Medial_wall 25 25 25 0 +11143 ctx_lh_Pole_occipital 140 20 60 0 +11144 ctx_lh_Pole_temporal 220 180 20 0 +11145 ctx_lh_S_calcarine 63 180 180 0 +11146 ctx_lh_S_central 221 20 10 0 +11147 ctx_lh_S_cingul-Marginalis 221 20 100 0 +11148 ctx_lh_S_circular_insula_ant 221 60 140 0 +11149 ctx_lh_S_circular_insula_inf 221 20 220 0 +11150 ctx_lh_S_circular_insula_sup 61 220 220 0 +11151 ctx_lh_S_collat_transv_ant 100 200 200 0 +11152 ctx_lh_S_collat_transv_post 10 200 200 0 +11153 ctx_lh_S_front_inf 221 220 20 0 +11154 ctx_lh_S_front_middle 141 20 100 0 +11155 ctx_lh_S_front_sup 61 220 100 0 +11156 ctx_lh_S_interm_prim-Jensen 141 60 20 0 +11157 ctx_lh_S_intrapariet_and_P_trans 143 20 220 0 +11158 ctx_lh_S_oc_middle_and_Lunatus 101 60 220 0 +11159 ctx_lh_S_oc_sup_and_transversal 21 20 140 0 +11160 ctx_lh_S_occipital_ant 61 20 180 0 +11161 ctx_lh_S_oc-temp_lat 221 140 20 0 +11162 ctx_lh_S_oc-temp_med_and_Lingual 141 100 220 0 +11163 ctx_lh_S_orbital_lateral 221 100 20 0 +11164 ctx_lh_S_orbital_med-olfact 181 200 20 0 +11165 ctx_lh_S_orbital-H_Shaped 101 20 20 0 +11166 ctx_lh_S_parieto_occipital 101 100 180 0 +11167 ctx_lh_S_pericallosal 181 220 20 0 +11168 ctx_lh_S_postcentral 21 140 200 0 +11169 ctx_lh_S_precentral-inf-part 21 20 240 0 +11170 ctx_lh_S_precentral-sup-part 21 20 200 0 +11171 ctx_lh_S_suborbital 21 20 60 0 +11172 ctx_lh_S_subparietal 101 60 60 0 +11173 ctx_lh_S_temporal_inf 21 180 180 0 +11174 ctx_lh_S_temporal_sup 223 220 60 0 +11175 ctx_lh_S_temporal_transverse 221 60 60 0 +12100 ctx_rh_Unknown 0 0 0 0 +12101 ctx_rh_G_and_S_frontomargin 23 220 60 0 +12102 ctx_rh_G_and_S_occipital_inf 23 60 180 0 +12103 ctx_rh_G_and_S_paracentral 63 100 60 0 +12104 ctx_rh_G_and_S_subcentral 63 20 220 0 +12105 ctx_rh_G_and_S_transv_frontopol 13 0 250 0 +12106 ctx_rh_G_and_S_cingul-Ant 26 60 0 0 +12107 ctx_rh_G_and_S_cingul-Mid-Ant 26 60 75 0 +12108 ctx_rh_G_and_S_cingul-Mid-Post 26 60 150 0 +12109 ctx_rh_G_cingul-Post-dorsal 25 60 250 0 +12110 ctx_rh_G_cingul-Post-ventral 60 25 25 0 +12111 ctx_rh_G_cuneus 180 20 20 0 +12112 ctx_rh_G_front_inf-Opercular 220 20 100 0 +12113 ctx_rh_G_front_inf-Orbital 140 60 60 0 +12114 ctx_rh_G_front_inf-Triangul 180 220 140 0 +12115 ctx_rh_G_front_middle 140 100 180 0 +12116 ctx_rh_G_front_sup 180 20 140 0 +12117 ctx_rh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +12118 ctx_rh_G_insular_short 225 140 140 0 +12119 ctx_rh_G_occipital_middle 180 60 180 0 +12120 ctx_rh_G_occipital_sup 20 220 60 0 +12121 ctx_rh_G_oc-temp_lat-fusifor 60 20 140 0 +12122 ctx_rh_G_oc-temp_med-Lingual 220 180 140 0 +12123 ctx_rh_G_oc-temp_med-Parahip 65 100 20 0 +12124 ctx_rh_G_orbital 220 60 20 0 +12125 ctx_rh_G_pariet_inf-Angular 20 60 220 0 +12126 ctx_rh_G_pariet_inf-Supramar 100 100 60 0 +12127 ctx_rh_G_parietal_sup 220 180 220 0 +12128 ctx_rh_G_postcentral 20 180 140 0 +12129 ctx_rh_G_precentral 60 140 180 0 +12130 ctx_rh_G_precuneus 25 20 140 0 +12131 ctx_rh_G_rectus 20 60 100 0 +12132 ctx_rh_G_subcallosal 60 220 20 0 +12133 ctx_rh_G_temp_sup-G_T_transv 60 60 220 0 +12134 ctx_rh_G_temp_sup-Lateral 220 60 220 0 +12135 ctx_rh_G_temp_sup-Plan_polar 65 220 60 0 +12136 ctx_rh_G_temp_sup-Plan_tempo 25 140 20 0 +12137 ctx_rh_G_temporal_inf 220 220 100 0 +12138 ctx_rh_G_temporal_middle 180 60 60 0 +12139 ctx_rh_Lat_Fis-ant-Horizont 61 20 220 0 +12140 ctx_rh_Lat_Fis-ant-Vertical 61 20 60 0 +12141 ctx_rh_Lat_Fis-post 61 60 100 0 +12142 ctx_rh_Medial_wall 25 25 25 0 +12143 ctx_rh_Pole_occipital 140 20 60 0 +12144 ctx_rh_Pole_temporal 220 180 20 0 +12145 ctx_rh_S_calcarine 63 180 180 0 +12146 ctx_rh_S_central 221 20 10 0 +12147 ctx_rh_S_cingul-Marginalis 221 20 100 0 +12148 ctx_rh_S_circular_insula_ant 221 60 140 0 +12149 ctx_rh_S_circular_insula_inf 221 20 220 0 +12150 ctx_rh_S_circular_insula_sup 61 220 220 0 +12151 ctx_rh_S_collat_transv_ant 100 200 200 0 +12152 ctx_rh_S_collat_transv_post 10 200 200 0 +12153 ctx_rh_S_front_inf 221 220 20 0 +12154 ctx_rh_S_front_middle 141 20 100 0 +12155 ctx_rh_S_front_sup 61 220 100 0 +12156 ctx_rh_S_interm_prim-Jensen 141 60 20 0 +12157 ctx_rh_S_intrapariet_and_P_trans 143 20 220 0 +12158 ctx_rh_S_oc_middle_and_Lunatus 101 60 220 0 +12159 ctx_rh_S_oc_sup_and_transversal 21 20 140 0 +12160 ctx_rh_S_occipital_ant 61 20 180 0 +12161 ctx_rh_S_oc-temp_lat 221 140 20 0 +12162 ctx_rh_S_oc-temp_med_and_Lingual 141 100 220 0 +12163 ctx_rh_S_orbital_lateral 221 100 20 0 +12164 ctx_rh_S_orbital_med-olfact 181 200 20 0 +12165 ctx_rh_S_orbital-H_Shaped 101 20 20 0 +12166 ctx_rh_S_parieto_occipital 101 100 180 0 +12167 ctx_rh_S_pericallosal 181 220 20 0 +12168 ctx_rh_S_postcentral 21 140 200 0 +12169 ctx_rh_S_precentral-inf-part 21 20 240 0 +12170 ctx_rh_S_precentral-sup-part 21 20 200 0 +12171 ctx_rh_S_suborbital 21 20 60 0 +12172 ctx_rh_S_subparietal 101 60 60 0 +12173 ctx_rh_S_temporal_inf 21 180 180 0 +12174 ctx_rh_S_temporal_sup 223 220 60 0 +12175 ctx_rh_S_temporal_transverse 221 60 60 0 +13100 wm_lh_Unknown 0 0 0 0 +13101 wm_lh_G_and_S_frontomargin 23 220 60 0 +13102 wm_lh_G_and_S_occipital_inf 23 60 180 0 +13103 wm_lh_G_and_S_paracentral 63 100 60 0 +13104 wm_lh_G_and_S_subcentral 63 20 220 0 +13105 wm_lh_G_and_S_transv_frontopol 13 0 250 0 +13106 wm_lh_G_and_S_cingul-Ant 26 60 0 0 +13107 wm_lh_G_and_S_cingul-Mid-Ant 26 60 75 0 +13108 wm_lh_G_and_S_cingul-Mid-Post 26 60 150 0 +13109 wm_lh_G_cingul-Post-dorsal 25 60 250 0 +13110 wm_lh_G_cingul-Post-ventral 60 25 25 0 +13111 wm_lh_G_cuneus 180 20 20 0 +13112 wm_lh_G_front_inf-Opercular 220 20 100 0 +13113 wm_lh_G_front_inf-Orbital 140 60 60 0 +13114 wm_lh_G_front_inf-Triangul 180 220 140 0 +13115 wm_lh_G_front_middle 140 100 180 0 +13116 wm_lh_G_front_sup 180 20 140 0 +13117 wm_lh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +13118 wm_lh_G_insular_short 225 140 140 0 +13119 wm_lh_G_occipital_middle 180 60 180 0 +13120 wm_lh_G_occipital_sup 20 220 60 0 +13121 wm_lh_G_oc-temp_lat-fusifor 60 20 140 0 +13122 wm_lh_G_oc-temp_med-Lingual 220 180 140 0 +13123 wm_lh_G_oc-temp_med-Parahip 65 100 20 0 +13124 wm_lh_G_orbital 220 60 20 0 +13125 wm_lh_G_pariet_inf-Angular 20 60 220 0 +13126 wm_lh_G_pariet_inf-Supramar 100 100 60 0 +13127 wm_lh_G_parietal_sup 220 180 220 0 +13128 wm_lh_G_postcentral 20 180 140 0 +13129 wm_lh_G_precentral 60 140 180 0 +13130 wm_lh_G_precuneus 25 20 140 0 +13131 wm_lh_G_rectus 20 60 100 0 +13132 wm_lh_G_subcallosal 60 220 20 0 +13133 wm_lh_G_temp_sup-G_T_transv 60 60 220 0 +13134 wm_lh_G_temp_sup-Lateral 220 60 220 0 +13135 wm_lh_G_temp_sup-Plan_polar 65 220 60 0 +13136 wm_lh_G_temp_sup-Plan_tempo 25 140 20 0 +13137 wm_lh_G_temporal_inf 220 220 100 0 +13138 wm_lh_G_temporal_middle 180 60 60 0 +13139 wm_lh_Lat_Fis-ant-Horizont 61 20 220 0 +13140 wm_lh_Lat_Fis-ant-Vertical 61 20 60 0 +13141 wm_lh_Lat_Fis-post 61 60 100 0 +13142 wm_lh_Medial_wall 25 25 25 0 +13143 wm_lh_Pole_occipital 140 20 60 0 +13144 wm_lh_Pole_temporal 220 180 20 0 +13145 wm_lh_S_calcarine 63 180 180 0 +13146 wm_lh_S_central 221 20 10 0 +13147 wm_lh_S_cingul-Marginalis 221 20 100 0 +13148 wm_lh_S_circular_insula_ant 221 60 140 0 +13149 wm_lh_S_circular_insula_inf 221 20 220 0 +13150 wm_lh_S_circular_insula_sup 61 220 220 0 +13151 wm_lh_S_collat_transv_ant 100 200 200 0 +13152 wm_lh_S_collat_transv_post 10 200 200 0 +13153 wm_lh_S_front_inf 221 220 20 0 +13154 wm_lh_S_front_middle 141 20 100 0 +13155 wm_lh_S_front_sup 61 220 100 0 +13156 wm_lh_S_interm_prim-Jensen 141 60 20 0 +13157 wm_lh_S_intrapariet_and_P_trans 143 20 220 0 +13158 wm_lh_S_oc_middle_and_Lunatus 101 60 220 0 +13159 wm_lh_S_oc_sup_and_transversal 21 20 140 0 +13160 wm_lh_S_occipital_ant 61 20 180 0 +13161 wm_lh_S_oc-temp_lat 221 140 20 0 +13162 wm_lh_S_oc-temp_med_and_Lingual 141 100 220 0 +13163 wm_lh_S_orbital_lateral 221 100 20 0 +13164 wm_lh_S_orbital_med-olfact 181 200 20 0 +13165 wm_lh_S_orbital-H_Shaped 101 20 20 0 +13166 wm_lh_S_parieto_occipital 101 100 180 0 +13167 wm_lh_S_pericallosal 181 220 20 0 +13168 wm_lh_S_postcentral 21 140 200 0 +13169 wm_lh_S_precentral-inf-part 21 20 240 0 +13170 wm_lh_S_precentral-sup-part 21 20 200 0 +13171 wm_lh_S_suborbital 21 20 60 0 +13172 wm_lh_S_subparietal 101 60 60 0 +13173 wm_lh_S_temporal_inf 21 180 180 0 +13174 wm_lh_S_temporal_sup 223 220 60 0 +13175 wm_lh_S_temporal_transverse 221 60 60 0 +14100 wm_rh_Unknown 0 0 0 0 +14101 wm_rh_G_and_S_frontomargin 23 220 60 0 +14102 wm_rh_G_and_S_occipital_inf 23 60 180 0 +14103 wm_rh_G_and_S_paracentral 63 100 60 0 +14104 wm_rh_G_and_S_subcentral 63 20 220 0 +14105 wm_rh_G_and_S_transv_frontopol 13 0 250 0 +14106 wm_rh_G_and_S_cingul-Ant 26 60 0 0 +14107 wm_rh_G_and_S_cingul-Mid-Ant 26 60 75 0 +14108 wm_rh_G_and_S_cingul-Mid-Post 26 60 150 0 +14109 wm_rh_G_cingul-Post-dorsal 25 60 250 0 +14110 wm_rh_G_cingul-Post-ventral 60 25 25 0 +14111 wm_rh_G_cuneus 180 20 20 0 +14112 wm_rh_G_front_inf-Opercular 220 20 100 0 +14113 wm_rh_G_front_inf-Orbital 140 60 60 0 +14114 wm_rh_G_front_inf-Triangul 180 220 140 0 +14115 wm_rh_G_front_middle 140 100 180 0 +14116 wm_rh_G_front_sup 180 20 140 0 +14117 wm_rh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +14118 wm_rh_G_insular_short 225 140 140 0 +14119 wm_rh_G_occipital_middle 180 60 180 0 +14120 wm_rh_G_occipital_sup 20 220 60 0 +14121 wm_rh_G_oc-temp_lat-fusifor 60 20 140 0 +14122 wm_rh_G_oc-temp_med-Lingual 220 180 140 0 +14123 wm_rh_G_oc-temp_med-Parahip 65 100 20 0 +14124 wm_rh_G_orbital 220 60 20 0 +14125 wm_rh_G_pariet_inf-Angular 20 60 220 0 +14126 wm_rh_G_pariet_inf-Supramar 100 100 60 0 +14127 wm_rh_G_parietal_sup 220 180 220 0 +14128 wm_rh_G_postcentral 20 180 140 0 +14129 wm_rh_G_precentral 60 140 180 0 +14130 wm_rh_G_precuneus 25 20 140 0 +14131 wm_rh_G_rectus 20 60 100 0 +14132 wm_rh_G_subcallosal 60 220 20 0 +14133 wm_rh_G_temp_sup-G_T_transv 60 60 220 0 +14134 wm_rh_G_temp_sup-Lateral 220 60 220 0 +14135 wm_rh_G_temp_sup-Plan_polar 65 220 60 0 +14136 wm_rh_G_temp_sup-Plan_tempo 25 140 20 0 +14137 wm_rh_G_temporal_inf 220 220 100 0 +14138 wm_rh_G_temporal_middle 180 60 60 0 +14139 wm_rh_Lat_Fis-ant-Horizont 61 20 220 0 +14140 wm_rh_Lat_Fis-ant-Vertical 61 20 60 0 +14141 wm_rh_Lat_Fis-post 61 60 100 0 +14142 wm_rh_Medial_wall 25 25 25 0 +14143 wm_rh_Pole_occipital 140 20 60 0 +14144 wm_rh_Pole_temporal 220 180 20 0 +14145 wm_rh_S_calcarine 63 180 180 0 +14146 wm_rh_S_central 221 20 10 0 +14147 wm_rh_S_cingul-Marginalis 221 20 100 0 +14148 wm_rh_S_circular_insula_ant 221 60 140 0 +14149 wm_rh_S_circular_insula_inf 221 20 220 0 +14150 wm_rh_S_circular_insula_sup 61 220 220 0 +14151 wm_rh_S_collat_transv_ant 100 200 200 0 +14152 wm_rh_S_collat_transv_post 10 200 200 0 +14153 wm_rh_S_front_inf 221 220 20 0 +14154 wm_rh_S_front_middle 141 20 100 0 +14155 wm_rh_S_front_sup 61 220 100 0 +14156 wm_rh_S_interm_prim-Jensen 141 60 20 0 +14157 wm_rh_S_intrapariet_and_P_trans 143 20 220 0 +14158 wm_rh_S_oc_middle_and_Lunatus 101 60 220 0 +14159 wm_rh_S_oc_sup_and_transversal 21 20 140 0 +14160 wm_rh_S_occipital_ant 61 20 180 0 +14161 wm_rh_S_oc-temp_lat 221 140 20 0 +14162 wm_rh_S_oc-temp_med_and_Lingual 141 100 220 0 +14163 wm_rh_S_orbital_lateral 221 100 20 0 +14164 wm_rh_S_orbital_med-olfact 181 200 20 0 +14165 wm_rh_S_orbital-H_Shaped 101 20 20 0 +14166 wm_rh_S_parieto_occipital 101 100 180 0 +14167 wm_rh_S_pericallosal 181 220 20 0 +14168 wm_rh_S_postcentral 21 140 200 0 +14169 wm_rh_S_precentral-inf-part 21 20 240 0 +14170 wm_rh_S_precentral-sup-part 21 20 200 0 +14171 wm_rh_S_suborbital 21 20 60 0 +14172 wm_rh_S_subparietal 101 60 60 0 +14173 wm_rh_S_temporal_inf 21 180 180 0 +14174 wm_rh_S_temporal_sup 223 220 60 0 +14175 wm_rh_S_temporal_transverse 221 60 60 0 diff --git a/bin/macos/3.1.2/templates/aparc/parcellate_aparc.sh b/bin/macos/3.1.2/templates/aparc/parcellate_aparc.sh new file mode 100755 index 0000000..4715be4 --- /dev/null +++ b/bin/macos/3.1.2/templates/aparc/parcellate_aparc.sh @@ -0,0 +1,77 @@ +#!/bin/bash +# +# Parcellate aparc atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + + + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +subjectDir=$(pwd) +freesurferDir=${subjectDir}/${freesurferDir} + +# Create parcellation +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/aparc+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + + +exit 0 diff --git a/bin/macos/3.1.2/templates/economo/ROIs_economo.txt b/bin/macos/3.1.2/templates/economo/ROIs_economo.txt new file mode 100644 index 0000000..f0aa163 --- /dev/null +++ b/bin/macos/3.1.2/templates/economo/ROIs_economo.txt @@ -0,0 +1,87 @@ +4 +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 +2039 +2040 +2041 +2042 +2043 +2044 diff --git a/bin/macos/3.1.2/templates/economo/economo.annot.ctab b/bin/macos/3.1.2/templates/economo/economo.annot.ctab new file mode 100644 index 0000000..3f0209a --- /dev/null +++ b/bin/macos/3.1.2/templates/economo/economo.annot.ctab @@ -0,0 +1,388 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-FA 206 226 156 0 +1003 ctx-lh-FB 200 219 138 0 +1004 ctx-lh-FC 187 204 115 0 +1005 ctx-lh-FCBm 85 193 170 0 +1006 ctx-lh-FD 13 201 111 0 +1007 ctx-lh-FDdelta 19 132 80 0 +1008 ctx-lh-FDT 69 168 123 0 +1009 ctx-lh-FE 27 178 138 0 +1010 ctx-lh-FF 49 172 192 0 +1011 ctx-lh-FG 61 127 118 0 +1012 ctx-lh-FH 77 135 106 0 +1013 ctx-lh-FJK 29 154 135 0 +1014 ctx-lh-FLMN 80 145 146 0 +1015 ctx-lh-HA 41 55 101 0 +1016 ctx-lh-HB 50 72 127 0 +1017 ctx-lh-HC 60 87 146 0 +1018 ctx-lh-IA 204 61 211 0 +1019 ctx-lh-IB 137 67 135 0 +1020 ctx-lh-LA1 124 215 246 0 +1021 ctx-lh-LA2 162 221 249 0 +1022 ctx-lh-LC1 0 133 185 0 +1023 ctx-lh-LC2 68 165 227 0 +1024 ctx-lh-LC3 118 179 215 0 +1025 ctx-lh-LD 122 212 215 0 +1026 ctx-lh-LE 169 219 224 0 +1027 ctx-lh-OA 253 252 187 0 +1028 ctx-lh-OB 251 250 146 0 +1029 ctx-lh-OC 247 222 71 0 +1030 ctx-lh-PA 230 42 133 0 +1031 ctx-lh-PB 247 67 148 0 +1032 ctx-lh-PC 239 87 150 0 +1033 ctx-lh-PD 188 53 121 0 +1034 ctx-lh-PE 248 167 210 0 +1035 ctx-lh-PF 250 180 224 0 +1036 ctx-lh-PG 248 193 224 0 +1037 ctx-lh-PH 232 73 130 0 +1038 ctx-lh-TA 240 85 102 0 +1039 ctx-lh-TB 233 65 98 0 +1040 ctx-lh-TC 239 64 107 0 +1041 ctx-lh-TD 245 79 113 0 +1042 ctx-lh-TE 235 181 136 0 +1043 ctx-lh-TF 184 47 79 0 +1044 ctx-lh-TG 247 198 127 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-FA 206 226 156 0 +2003 ctx-rh-FB 200 219 138 0 +2004 ctx-rh-FC 187 204 115 0 +2005 ctx-rh-FCBm 85 193 170 0 +2006 ctx-rh-FD 13 201 111 0 +2007 ctx-rh-FDdelta 19 132 80 0 +2008 ctx-rh-FDT 69 168 123 0 +2009 ctx-rh-FE 27 178 138 0 +2010 ctx-rh-FF 49 172 192 0 +2011 ctx-rh-FG 61 127 118 0 +2012 ctx-rh-FH 77 135 106 0 +2013 ctx-rh-FJK 29 154 135 0 +2014 ctx-rh-FLMN 80 145 146 0 +2015 ctx-rh-HA 41 55 101 0 +2016 ctx-rh-HB 50 72 127 0 +2017 ctx-rh-HC 60 87 146 0 +2018 ctx-rh-IA 204 61 211 0 +2019 ctx-rh-IB 137 67 135 0 +2020 ctx-rh-LA1 124 215 246 0 +2021 ctx-rh-LA2 162 221 249 0 +2022 ctx-rh-LC1 0 133 185 0 +2023 ctx-rh-LC2 68 165 227 0 +2024 ctx-rh-LC3 118 179 215 0 +2025 ctx-rh-LD 122 212 215 0 +2026 ctx-rh-LE 169 219 224 0 +2027 ctx-rh-OA 253 252 187 0 +2028 ctx-rh-OB 251 250 146 0 +2029 ctx-rh-OC 247 222 71 0 +2030 ctx-rh-PA 230 42 133 0 +2031 ctx-rh-PB 247 67 148 0 +2032 ctx-rh-PC 239 87 150 0 +2033 ctx-rh-PD 188 53 121 0 +2034 ctx-rh-PE 248 167 210 0 +2035 ctx-rh-PF 250 180 224 0 +2036 ctx-rh-PG 248 193 224 0 +2037 ctx-rh-PH 232 73 130 0 +2038 ctx-rh-TA 240 85 102 0 +2039 ctx-rh-TB 233 65 98 0 +2040 ctx-rh-TC 239 64 107 0 +2041 ctx-rh-TD 245 79 113 0 +2042 ctx-rh-TE 235 181 136 0 +2043 ctx-rh-TF 184 47 79 0 +2044 ctx-rh-TG 247 198 127 0 diff --git a/bin/macos/3.1.2/templates/economo/lh.economo.gcs b/bin/macos/3.1.2/templates/economo/lh.economo.gcs new file mode 100644 index 0000000..b22869e Binary files /dev/null and b/bin/macos/3.1.2/templates/economo/lh.economo.gcs differ diff --git a/bin/macos/3.1.2/templates/economo/parcellate_economo.sh b/bin/macos/3.1.2/templates/economo/parcellate_economo.sh new file mode 100755 index 0000000..f89b886 --- /dev/null +++ b/bin/macos/3.1.2/templates/economo/parcellate_economo.sh @@ -0,0 +1,105 @@ +#!/bin/bash +# +# Parcellate economo atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=economo + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/macos/3.1.2/templates/economo/rh.economo.gcs b/bin/macos/3.1.2/templates/economo/rh.economo.gcs new file mode 100644 index 0000000..d69797f Binary files /dev/null and b/bin/macos/3.1.2/templates/economo/rh.economo.gcs differ diff --git a/bin/macos/3.1.2/templates/lausanne120/ROIs_lausanne120.txt b/bin/macos/3.1.2/templates/lausanne120/ROIs_lausanne120.txt new file mode 100644 index 0000000..e75cf39 --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne120/ROIs_lausanne120.txt @@ -0,0 +1,114 @@ +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +1045 +1046 +1047 +1048 +1049 +1050 +1051 +1052 +1053 +1054 +1055 +1056 +1057 +1058 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 +2039 +2040 +2041 +2042 +2043 +2044 +2045 +2046 +2047 +2048 +2049 +2050 +2051 +2052 +2053 +2054 +2055 +2056 +2057 +2058 diff --git a/bin/macos/3.1.2/templates/lausanne120/lausanne120.annot.ctab b/bin/macos/3.1.2/templates/lausanne120/lausanne120.annot.ctab new file mode 100644 index 0000000..d29710f --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne120/lausanne120.annot.ctab @@ -0,0 +1,416 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-bankssts_1 25 100 40 0 +1003 ctx-lh-caudalanteriorcingulate_1 125 100 160 0 +1004 ctx-lh-caudalmiddlefrontal_1 100 25 0 0 +1005 ctx-lh-cuneus_1 220 20 100 0 +1006 ctx-lh-entorhinal_1 220 20 10 0 +1007 ctx-lh-fusiform_1 180 220 140 0 +1008 ctx-lh-fusiform_2 180 194 140 0 +1009 ctx-lh-inferiorparietal_1 220 60 220 0 +1010 ctx-lh-inferiorparietal_2 212 60 220 0 +1011 ctx-lh-inferiortemporal_1 180 40 120 0 +1012 ctx-lh-inferiortemporal_2 162 40 120 0 +1013 ctx-lh-isthmuscingulate_1 140 20 140 0 +1014 ctx-lh-lateraloccipital_1 20 30 140 0 +1015 ctx-lh-lateraloccipital_2 20 30 127 0 +1016 ctx-lh-lateralorbitofrontal_1 35 75 50 0 +1017 ctx-lh-lateralorbitofrontal_2 35 72 50 0 +1018 ctx-lh-lingual_1 225 140 140 0 +1019 ctx-lh-lingual_2 227 140 140 0 +1020 ctx-lh-medialorbitofrontal_1 200 35 75 0 +1021 ctx-lh-middletemporal_1 160 100 50 0 +1022 ctx-lh-middletemporal_2 152 100 50 0 +1023 ctx-lh-parahippocampal_1 20 220 60 0 +1024 ctx-lh-paracentral_1 60 220 60 0 +1025 ctx-lh-parsopercularis_1 220 180 140 0 +1026 ctx-lh-parsorbitalis_1 20 100 50 0 +1027 ctx-lh-parstriangularis_1 220 60 20 0 +1028 ctx-lh-pericalcarine_1 120 100 60 0 +1029 ctx-lh-postcentral_1 220 20 20 0 +1030 ctx-lh-postcentral_2 219 20 20 0 +1031 ctx-lh-postcentral_3 221 20 20 0 +1032 ctx-lh-posteriorcingulate_1 220 180 220 0 +1033 ctx-lh-precentral_1 60 20 220 0 +1034 ctx-lh-precentral_2 60 20 211 0 +1035 ctx-lh-precentral_3 60 20 212 0 +1036 ctx-lh-precentral_4 60 20 213 0 +1037 ctx-lh-precuneus_1 160 140 180 0 +1038 ctx-lh-precuneus_2 160 140 162 0 +1039 ctx-lh-rostralanteriorcingulate_1 80 20 140 0 +1040 ctx-lh-rostralmiddlefrontal_1 75 50 125 0 +1041 ctx-lh-rostralmiddlefrontal_2 75 50 122 0 +1042 ctx-lh-rostralmiddlefrontal_3 75 50 123 0 +1043 ctx-lh-superiorfrontal_1 20 220 160 0 +1044 ctx-lh-superiorfrontal_2 20 194 160 0 +1045 ctx-lh-superiorfrontal_3 20 195 160 0 +1046 ctx-lh-superiorfrontal_4 20 196 160 0 +1047 ctx-lh-superiorparietal_1 20 180 140 0 +1048 ctx-lh-superiorparietal_2 20 162 140 0 +1049 ctx-lh-superiorparietal_3 20 163 140 0 +1050 ctx-lh-superiortemporal_1 140 220 220 0 +1051 ctx-lh-superiortemporal_2 140 220 202 0 +1052 ctx-lh-supramarginal_1 80 160 20 0 +1053 ctx-lh-supramarginal_2 80 152 20 0 +1054 ctx-lh-frontalpole_1 100 0 100 0 +1055 ctx-lh-temporalpole_1 70 70 70 0 +1056 ctx-lh-transversetemporal_1 150 150 200 0 +1057 ctx-lh-insula_1 255 192 32 0 +1058 ctx-lh-insula_2 227 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-bankssts_1 25 100 40 0 +2003 ctx-rh-caudalanteriorcingulate_1 125 100 160 0 +2004 ctx-rh-caudalmiddlefrontal_1 100 25 0 0 +2005 ctx-rh-cuneus_1 220 20 100 0 +2006 ctx-rh-entorhinal_1 220 20 10 0 +2007 ctx-rh-fusiform_1 180 220 140 0 +2008 ctx-rh-fusiform_2 180 194 140 0 +2009 ctx-rh-inferiorparietal_1 220 60 220 0 +2010 ctx-rh-inferiorparietal_2 212 60 220 0 +2011 ctx-rh-inferiorparietal_3 213 60 220 0 +2012 ctx-rh-inferiortemporal_1 180 40 120 0 +2013 ctx-rh-inferiortemporal_2 162 40 120 0 +2014 ctx-rh-isthmuscingulate_1 140 20 140 0 +2015 ctx-rh-lateraloccipital_1 20 30 140 0 +2016 ctx-rh-lateraloccipital_2 20 30 127 0 +2017 ctx-rh-lateraloccipital_3 20 30 128 0 +2018 ctx-rh-lateralorbitofrontal_1 35 75 50 0 +2019 ctx-rh-lateralorbitofrontal_2 35 72 50 0 +2020 ctx-rh-lingual_1 225 140 140 0 +2021 ctx-rh-lingual_2 227 140 140 0 +2022 ctx-rh-medialorbitofrontal_1 200 35 75 0 +2023 ctx-rh-medialorbitofrontal_2 182 35 75 0 +2024 ctx-rh-middletemporal_1 160 100 50 0 +2025 ctx-rh-middletemporal_2 152 100 50 0 +2026 ctx-rh-parahippocampal_1 20 220 60 0 +2027 ctx-rh-paracentral_1 60 220 60 0 +2028 ctx-rh-parsopercularis_1 220 180 140 0 +2029 ctx-rh-parsorbitalis_1 20 100 50 0 +2030 ctx-rh-parstriangularis_1 220 60 20 0 +2031 ctx-rh-pericalcarine_1 120 100 60 0 +2032 ctx-rh-postcentral_1 220 20 20 0 +2033 ctx-rh-postcentral_2 219 20 20 0 +2034 ctx-rh-posteriorcingulate_1 220 180 220 0 +2035 ctx-rh-precentral_1 60 20 220 0 +2036 ctx-rh-precentral_2 60 20 211 0 +2037 ctx-rh-precentral_3 60 20 212 0 +2038 ctx-rh-precuneus_1 160 140 180 0 +2039 ctx-rh-precuneus_2 160 140 162 0 +2040 ctx-rh-rostralanteriorcingulate_1 80 20 140 0 +2041 ctx-rh-rostralmiddlefrontal_1 75 50 125 0 +2042 ctx-rh-rostralmiddlefrontal_2 75 50 122 0 +2043 ctx-rh-superiorfrontal_1 20 220 160 0 +2044 ctx-rh-superiorfrontal_2 20 194 160 0 +2045 ctx-rh-superiorfrontal_3 20 195 160 0 +2046 ctx-rh-superiorfrontal_4 20 196 160 0 +2047 ctx-rh-superiorparietal_1 20 180 140 0 +2048 ctx-rh-superiorparietal_2 20 162 140 0 +2049 ctx-rh-superiorparietal_3 20 163 140 0 +2050 ctx-rh-superiortemporal_1 140 220 220 0 +2051 ctx-rh-superiortemporal_2 140 220 202 0 +2052 ctx-rh-supramarginal_1 80 160 20 0 +2053 ctx-rh-supramarginal_2 80 152 20 0 +2054 ctx-rh-frontalpole_1 100 0 100 0 +2055 ctx-rh-temporalpole_1 70 70 70 0 +2056 ctx-rh-transversetemporal_1 150 150 200 0 +2057 ctx-rh-insula_1 255 192 32 0 +2058 ctx-rh-insula_2 227 192 32 0 \ No newline at end of file diff --git a/bin/macos/3.1.2/templates/lausanne120/lh.lausanne120.gcs b/bin/macos/3.1.2/templates/lausanne120/lh.lausanne120.gcs new file mode 100644 index 0000000..fa9a3a8 Binary files /dev/null and b/bin/macos/3.1.2/templates/lausanne120/lh.lausanne120.gcs differ diff --git a/bin/macos/3.1.2/templates/lausanne120/parcellate_lausanne120.sh b/bin/macos/3.1.2/templates/lausanne120/parcellate_lausanne120.sh new file mode 100755 index 0000000..4acd611 --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne120/parcellate_lausanne120.sh @@ -0,0 +1,106 @@ +#!/bin/bash +# +# Parcellate lausanne120 atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=lausanne120 + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/macos/3.1.2/templates/lausanne120/rh.lausanne120.gcs b/bin/macos/3.1.2/templates/lausanne120/rh.lausanne120.gcs new file mode 100644 index 0000000..fa23595 Binary files /dev/null and b/bin/macos/3.1.2/templates/lausanne120/rh.lausanne120.gcs differ diff --git a/bin/macos/3.1.2/templates/lausanne250/ROIs_lausanne250.txt b/bin/macos/3.1.2/templates/lausanne250/ROIs_lausanne250.txt new file mode 100644 index 0000000..ccdd7f1 --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne250/ROIs_lausanne250.txt @@ -0,0 +1,219 @@ +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +1045 +1046 +1047 +1048 +1049 +1050 +1051 +1052 +1053 +1054 +1055 +1056 +1057 +1058 +1059 +1060 +1061 +1062 +1063 +1064 +1065 +1066 +1067 +1068 +1069 +1070 +1071 +1072 +1073 +1074 +1075 +1076 +1077 +1078 +1079 +1080 +1081 +1082 +1083 +1084 +1085 +1086 +1087 +1088 +1089 +1090 +1091 +1092 +1093 +1094 +1095 +1096 +1097 +1098 +1099 +1100 +1101 +1102 +1103 +1104 +1105 +1106 +1107 +1108 +1109 +1110 +1111 +1112 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 +2039 +2040 +2041 +2042 +2043 +2044 +2045 +2046 +2047 +2048 +2049 +2050 +2051 +2052 +2053 +2054 +2055 +2056 +2057 +2058 +2059 +2060 +2061 +2062 +2063 +2064 +2065 +2066 +2067 +2068 +2069 +2070 +2071 +2072 +2073 +2074 +2075 +2076 +2077 +2078 +2079 +2080 +2081 +2082 +2083 +2084 +2085 +2086 +2087 +2088 +2089 +2090 +2091 +2092 +2093 +2094 +2095 +2096 +2097 +2098 +2099 +2100 +2101 +2102 +2103 +2104 +2105 +2106 +2107 +2108 +2109 diff --git a/bin/macos/3.1.2/templates/lausanne250/lausanne250.annot.ctab b/bin/macos/3.1.2/templates/lausanne250/lausanne250.annot.ctab new file mode 100644 index 0000000..b487c97 --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne250/lausanne250.annot.ctab @@ -0,0 +1,521 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-bankssts_1 25 100 40 0 +1003 ctx-lh-bankssts_2 25 77 40 0 +1004 ctx-lh-caudalanteriorcingulate_1 125 100 160 0 +1005 ctx-lh-caudalmiddlefrontal_1 100 25 0 0 +1006 ctx-lh-caudalmiddlefrontal_2 82 25 0 0 +1007 ctx-lh-caudalmiddlefrontal_3 83 25 0 0 +1008 ctx-lh-cuneus_1 220 20 100 0 +1009 ctx-lh-entorhinal_1 220 20 10 0 +1010 ctx-lh-fusiform_1 180 220 140 0 +1011 ctx-lh-fusiform_2 180 194 140 0 +1012 ctx-lh-fusiform_3 180 195 140 0 +1013 ctx-lh-fusiform_4 180 196 140 0 +1014 ctx-lh-inferiorparietal_1 220 60 220 0 +1015 ctx-lh-inferiorparietal_2 212 60 220 0 +1016 ctx-lh-inferiorparietal_3 213 60 220 0 +1017 ctx-lh-inferiorparietal_4 214 60 220 0 +1018 ctx-lh-inferiorparietal_5 215 60 220 0 +1019 ctx-lh-inferiortemporal_1 180 40 120 0 +1020 ctx-lh-inferiortemporal_2 162 40 120 0 +1021 ctx-lh-inferiortemporal_3 163 40 120 0 +1022 ctx-lh-inferiortemporal_4 164 40 120 0 +1023 ctx-lh-isthmuscingulate_1 140 20 140 0 +1024 ctx-lh-lateraloccipital_1 20 30 140 0 +1025 ctx-lh-lateraloccipital_2 20 30 127 0 +1026 ctx-lh-lateraloccipital_3 20 30 128 0 +1027 ctx-lh-lateraloccipital_4 20 30 129 0 +1028 ctx-lh-lateraloccipital_5 20 30 130 0 +1029 ctx-lh-lateralorbitofrontal_1 35 75 50 0 +1030 ctx-lh-lateralorbitofrontal_2 35 72 50 0 +1031 ctx-lh-lateralorbitofrontal_3 35 73 50 0 +1032 ctx-lh-lateralorbitofrontal_4 35 74 50 0 +1033 ctx-lh-lingual_1 225 140 140 0 +1034 ctx-lh-lingual_2 227 140 140 0 +1035 ctx-lh-lingual_3 228 140 140 0 +1036 ctx-lh-lingual_4 229 140 140 0 +1037 ctx-lh-medialorbitofrontal_1 200 35 75 0 +1038 ctx-lh-medialorbitofrontal_2 182 35 75 0 +1039 ctx-lh-middletemporal_1 160 100 50 0 +1040 ctx-lh-middletemporal_2 152 100 50 0 +1041 ctx-lh-middletemporal_3 153 100 50 0 +1042 ctx-lh-middletemporal_4 154 100 50 0 +1043 ctx-lh-parahippocampal_1 20 220 60 0 +1044 ctx-lh-paracentral_1 60 220 60 0 +1045 ctx-lh-paracentral_2 60 200 60 0 +1046 ctx-lh-parsopercularis_1 220 180 140 0 +1047 ctx-lh-parsopercularis_2 202 180 140 0 +1048 ctx-lh-parsorbitalis_1 20 100 50 0 +1049 ctx-lh-parstriangularis_1 220 60 20 0 +1050 ctx-lh-pericalcarine_1 120 100 60 0 +1051 ctx-lh-postcentral_1 220 20 20 0 +1052 ctx-lh-postcentral_2 219 20 20 0 +1053 ctx-lh-postcentral_3 221 20 20 0 +1054 ctx-lh-postcentral_4 222 20 20 0 +1055 ctx-lh-postcentral_5 223 20 20 0 +1056 ctx-lh-postcentral_6 224 20 20 0 +1057 ctx-lh-postcentral_7 220 6 20 0 +1058 ctx-lh-posteriorcingulate_1 220 180 220 0 +1059 ctx-lh-posteriorcingulate_2 220 180 202 0 +1060 ctx-lh-precentral_1 60 20 220 0 +1061 ctx-lh-precentral_2 60 20 211 0 +1062 ctx-lh-precentral_3 60 20 212 0 +1063 ctx-lh-precentral_4 60 20 213 0 +1064 ctx-lh-precentral_5 60 20 214 0 +1065 ctx-lh-precentral_6 60 20 215 0 +1066 ctx-lh-precentral_7 60 20 216 0 +1067 ctx-lh-precentral_8 60 20 217 0 +1068 ctx-lh-precuneus_1 160 140 180 0 +1069 ctx-lh-precuneus_2 160 140 162 0 +1070 ctx-lh-precuneus_3 160 140 163 0 +1071 ctx-lh-precuneus_4 160 140 164 0 +1072 ctx-lh-precuneus_5 160 140 165 0 +1073 ctx-lh-rostralanteriorcingulate_1 80 20 140 0 +1074 ctx-lh-rostralmiddlefrontal_1 75 50 125 0 +1075 ctx-lh-rostralmiddlefrontal_2 75 50 122 0 +1076 ctx-lh-rostralmiddlefrontal_3 75 50 123 0 +1077 ctx-lh-rostralmiddlefrontal_4 75 50 124 0 +1078 ctx-lh-rostralmiddlefrontal_5 75 50 126 0 +1079 ctx-lh-rostralmiddlefrontal_6 71 50 125 0 +1080 ctx-lh-superiorfrontal_1 20 220 160 0 +1081 ctx-lh-superiorfrontal_2 20 194 160 0 +1082 ctx-lh-superiorfrontal_3 20 195 160 0 +1083 ctx-lh-superiorfrontal_4 20 196 160 0 +1084 ctx-lh-superiorfrontal_5 20 197 160 0 +1085 ctx-lh-superiorfrontal_6 20 198 160 0 +1086 ctx-lh-superiorfrontal_7 20 199 160 0 +1087 ctx-lh-superiorfrontal_8 20 200 160 0 +1088 ctx-lh-superiorfrontal_9 20 201 160 0 +1089 ctx-lh-superiorparietal_1 20 180 140 0 +1090 ctx-lh-superiorparietal_2 20 162 140 0 +1091 ctx-lh-superiorparietal_3 20 163 140 0 +1092 ctx-lh-superiorparietal_4 20 164 140 0 +1093 ctx-lh-superiorparietal_5 20 165 140 0 +1094 ctx-lh-superiorparietal_6 20 166 140 0 +1095 ctx-lh-superiorparietal_7 20 167 140 0 +1096 ctx-lh-superiortemporal_1 140 220 220 0 +1097 ctx-lh-superiortemporal_2 140 220 202 0 +1098 ctx-lh-superiortemporal_3 140 220 203 0 +1099 ctx-lh-superiortemporal_4 140 220 204 0 +1100 ctx-lh-superiortemporal_5 140 220 205 0 +1101 ctx-lh-supramarginal_1 80 160 20 0 +1102 ctx-lh-supramarginal_2 80 152 20 0 +1103 ctx-lh-supramarginal_3 80 153 20 0 +1104 ctx-lh-supramarginal_4 80 154 20 0 +1105 ctx-lh-supramarginal_5 80 155 20 0 +1106 ctx-lh-frontalpole_1 100 0 100 0 +1107 ctx-lh-temporalpole_1 70 70 70 0 +1108 ctx-lh-transversetemporal_1 150 150 200 0 +1109 ctx-lh-insula_1 255 192 32 0 +1110 ctx-lh-insula_2 227 192 32 0 +1111 ctx-lh-insula_3 228 192 32 0 +1112 ctx-lh-insula_4 229 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-bankssts_1 25 100 40 0 +2003 ctx-rh-caudalanteriorcingulate_1 125 100 160 0 +2004 ctx-rh-caudalmiddlefrontal_1 100 25 0 0 +2005 ctx-rh-caudalmiddlefrontal_2 82 25 0 0 +2006 ctx-rh-caudalmiddlefrontal_3 83 25 0 0 +2007 ctx-rh-cuneus_1 220 20 100 0 +2008 ctx-rh-cuneus_2 202 20 100 0 +2009 ctx-rh-entorhinal_1 220 20 10 0 +2010 ctx-rh-fusiform_1 180 220 140 0 +2011 ctx-rh-fusiform_2 180 194 140 0 +2012 ctx-rh-fusiform_3 180 195 140 0 +2013 ctx-rh-fusiform_4 180 196 140 0 +2014 ctx-rh-inferiorparietal_1 220 60 220 0 +2015 ctx-rh-inferiorparietal_2 212 60 220 0 +2016 ctx-rh-inferiorparietal_3 213 60 220 0 +2017 ctx-rh-inferiorparietal_4 214 60 220 0 +2018 ctx-rh-inferiorparietal_5 215 60 220 0 +2019 ctx-rh-inferiorparietal_6 216 60 220 0 +2020 ctx-rh-inferiortemporal_1 180 40 120 0 +2021 ctx-rh-inferiortemporal_2 162 40 120 0 +2022 ctx-rh-inferiortemporal_3 163 40 120 0 +2023 ctx-rh-inferiortemporal_4 164 40 120 0 +2024 ctx-rh-isthmuscingulate_1 140 20 140 0 +2025 ctx-rh-lateraloccipital_1 20 30 140 0 +2026 ctx-rh-lateraloccipital_2 20 30 127 0 +2027 ctx-rh-lateraloccipital_3 20 30 128 0 +2028 ctx-rh-lateraloccipital_4 20 30 129 0 +2029 ctx-rh-lateraloccipital_5 20 30 130 0 +2030 ctx-rh-lateralorbitofrontal_1 35 75 50 0 +2031 ctx-rh-lateralorbitofrontal_2 35 72 50 0 +2032 ctx-rh-lateralorbitofrontal_3 35 73 50 0 +2033 ctx-rh-lateralorbitofrontal_4 35 74 50 0 +2034 ctx-rh-lingual_1 225 140 140 0 +2035 ctx-rh-lingual_2 227 140 140 0 +2036 ctx-rh-lingual_3 228 140 140 0 +2037 ctx-rh-medialorbitofrontal_1 200 35 75 0 +2038 ctx-rh-medialorbitofrontal_2 182 35 75 0 +2039 ctx-rh-medialorbitofrontal_3 183 35 75 0 +2040 ctx-rh-middletemporal_1 160 100 50 0 +2041 ctx-rh-middletemporal_2 152 100 50 0 +2042 ctx-rh-middletemporal_3 153 100 50 0 +2043 ctx-rh-middletemporal_4 154 100 50 0 +2044 ctx-rh-parahippocampal_1 20 220 60 0 +2045 ctx-rh-paracentral_1 60 220 60 0 +2046 ctx-rh-paracentral_2 60 200 60 0 +2047 ctx-rh-paracentral_3 60 201 60 0 +2048 ctx-rh-parsopercularis_1 220 180 140 0 +2049 ctx-rh-parsopercularis_2 202 180 140 0 +2050 ctx-rh-parsorbitalis_1 20 100 50 0 +2051 ctx-rh-parstriangularis_1 220 60 20 0 +2052 ctx-rh-parstriangularis_2 211 60 20 0 +2053 ctx-rh-pericalcarine_1 120 100 60 0 +2054 ctx-rh-pericalcarine_2 102 100 60 0 +2055 ctx-rh-postcentral_1 220 20 20 0 +2056 ctx-rh-postcentral_2 219 20 20 0 +2057 ctx-rh-postcentral_3 221 20 20 0 +2058 ctx-rh-postcentral_4 222 20 20 0 +2059 ctx-rh-postcentral_5 223 20 20 0 +2060 ctx-rh-posteriorcingulate_1 220 180 220 0 +2061 ctx-rh-posteriorcingulate_2 220 180 202 0 +2062 ctx-rh-precentral_1 60 20 220 0 +2063 ctx-rh-precentral_2 60 20 211 0 +2064 ctx-rh-precentral_3 60 20 212 0 +2065 ctx-rh-precentral_4 60 20 213 0 +2066 ctx-rh-precentral_5 60 20 214 0 +2067 ctx-rh-precentral_6 60 20 215 0 +2068 ctx-rh-precuneus_1 160 140 180 0 +2069 ctx-rh-precuneus_2 160 140 162 0 +2070 ctx-rh-precuneus_3 160 140 163 0 +2071 ctx-rh-precuneus_4 160 140 164 0 +2072 ctx-rh-precuneus_5 160 140 165 0 +2073 ctx-rh-rostralanteriorcingulate_1 80 20 140 0 +2074 ctx-rh-rostralmiddlefrontal_1 75 50 125 0 +2075 ctx-rh-rostralmiddlefrontal_2 75 50 122 0 +2076 ctx-rh-rostralmiddlefrontal_3 75 50 123 0 +2077 ctx-rh-rostralmiddlefrontal_4 75 50 124 0 +2078 ctx-rh-rostralmiddlefrontal_5 75 50 126 0 +2079 ctx-rh-rostralmiddlefrontal_6 71 50 125 0 +2080 ctx-rh-superiorfrontal_1 20 220 160 0 +2081 ctx-rh-superiorfrontal_2 20 194 160 0 +2082 ctx-rh-superiorfrontal_3 20 195 160 0 +2083 ctx-rh-superiorfrontal_4 20 196 160 0 +2084 ctx-rh-superiorfrontal_5 20 197 160 0 +2085 ctx-rh-superiorfrontal_6 20 198 160 0 +2086 ctx-rh-superiorfrontal_7 20 199 160 0 +2087 ctx-rh-superiorfrontal_8 20 200 160 0 +2088 ctx-rh-superiorparietal_1 20 180 140 0 +2089 ctx-rh-superiorparietal_2 20 162 140 0 +2090 ctx-rh-superiorparietal_3 20 163 140 0 +2091 ctx-rh-superiorparietal_4 20 164 140 0 +2092 ctx-rh-superiorparietal_5 20 165 140 0 +2093 ctx-rh-superiorparietal_6 20 166 140 0 +2094 ctx-rh-superiorparietal_7 20 167 140 0 +2095 ctx-rh-superiortemporal_1 140 220 220 0 +2096 ctx-rh-superiortemporal_2 140 220 202 0 +2097 ctx-rh-superiortemporal_3 140 220 203 0 +2098 ctx-rh-superiortemporal_4 140 220 204 0 +2099 ctx-rh-superiortemporal_5 140 220 205 0 +2100 ctx-rh-supramarginal_1 80 160 20 0 +2101 ctx-rh-supramarginal_2 80 152 20 0 +2102 ctx-rh-supramarginal_3 80 153 20 0 +2103 ctx-rh-supramarginal_4 80 154 20 0 +2104 ctx-rh-frontalpole_1 100 0 100 0 +2105 ctx-rh-temporalpole_1 70 70 70 0 +2106 ctx-rh-transversetemporal_1 150 150 200 0 +2107 ctx-rh-insula_1 255 192 32 0 +2108 ctx-rh-insula_2 227 192 32 0 +2109 ctx-rh-insula_3 228 192 32 0 \ No newline at end of file diff --git a/bin/macos/3.1.2/templates/lausanne250/lh.lausanne250.gcs b/bin/macos/3.1.2/templates/lausanne250/lh.lausanne250.gcs new file mode 100644 index 0000000..6fd9ed7 Binary files /dev/null and b/bin/macos/3.1.2/templates/lausanne250/lh.lausanne250.gcs differ diff --git a/bin/macos/3.1.2/templates/lausanne250/parcellate_lausanne250.sh b/bin/macos/3.1.2/templates/lausanne250/parcellate_lausanne250.sh new file mode 100755 index 0000000..3a88e1f --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne250/parcellate_lausanne250.sh @@ -0,0 +1,106 @@ +#!/bin/bash +# +# Parcellate lausanne250 atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=lausanne250 + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/macos/3.1.2/templates/lausanne250/rh.lausanne250.gcs b/bin/macos/3.1.2/templates/lausanne250/rh.lausanne250.gcs new file mode 100644 index 0000000..7f7f4ad Binary files /dev/null and b/bin/macos/3.1.2/templates/lausanne250/rh.lausanne250.gcs differ diff --git a/bin/macos/3.1.2/templates/lausanne500/ROIs_lausanne500.txt b/bin/macos/3.1.2/templates/lausanne500/ROIs_lausanne500.txt new file mode 100644 index 0000000..e4159b8 --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne500/ROIs_lausanne500.txt @@ -0,0 +1,448 @@ +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +1045 +1046 +1047 +1048 +1049 +1050 +1051 +1052 +1053 +1054 +1055 +1056 +1057 +1058 +1059 +1060 +1061 +1062 +1063 +1064 +1065 +1066 +1067 +1068 +1069 +1070 +1071 +1072 +1073 +1074 +1075 +1076 +1077 +1078 +1079 +1080 +1081 +1082 +1083 +1084 +1085 +1086 +1087 +1088 +1089 +1090 +1091 +1092 +1093 +1094 +1095 +1096 +1097 +1098 +1099 +1100 +1101 +1102 +1103 +1104 +1105 +1106 +1107 +1108 +1109 +1110 +1111 +1112 +1113 +1114 +1115 +1116 +1117 +1118 +1119 +1120 +1121 +1122 +1123 +1124 +1125 +1126 +1127 +1128 +1129 +1130 +1131 +1132 +1133 +1134 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b/bin/macos/3.1.2/templates/lausanne500/lausanne500.annot.ctab new file mode 100644 index 0000000..9929ba5 --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne500/lausanne500.annot.ctab @@ -0,0 +1,750 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-bankssts_1 25 100 40 0 +1003 ctx-lh-bankssts_2 25 77 40 0 +1004 ctx-lh-bankssts_3 25 78 40 0 +1005 ctx-lh-caudalanteriorcingulate_1 125 100 160 0 +1006 ctx-lh-caudalanteriorcingulate_2 125 100 142 0 +1007 ctx-lh-caudalmiddlefrontal_1 100 25 0 0 +1008 ctx-lh-caudalmiddlefrontal_2 82 25 0 0 +1009 ctx-lh-caudalmiddlefrontal_3 83 25 0 0 +1010 ctx-lh-caudalmiddlefrontal_4 84 25 0 0 +1011 ctx-lh-caudalmiddlefrontal_5 85 25 0 0 +1012 ctx-lh-caudalmiddlefrontal_6 86 25 0 0 +1013 ctx-lh-cuneus_1 220 20 100 0 +1014 ctx-lh-cuneus_2 202 20 100 0 +1015 ctx-lh-cuneus_3 203 20 100 0 +1016 ctx-lh-entorhinal_1 220 20 10 0 +1017 ctx-lh-fusiform_1 180 220 140 0 +1018 ctx-lh-fusiform_2 180 194 140 0 +1019 ctx-lh-fusiform_3 180 195 140 0 +1020 ctx-lh-fusiform_4 180 196 140 0 +1021 ctx-lh-fusiform_5 180 197 140 0 +1022 ctx-lh-fusiform_6 180 198 140 0 +1023 ctx-lh-fusiform_7 180 199 140 0 +1024 ctx-lh-fusiform_8 180 200 140 0 +1025 ctx-lh-inferiorparietal_1 220 60 220 0 +1026 ctx-lh-inferiorparietal_2 212 60 220 0 +1027 ctx-lh-inferiorparietal_3 213 60 220 0 +1028 ctx-lh-inferiorparietal_4 214 60 220 0 +1029 ctx-lh-inferiorparietal_5 215 60 220 0 +1030 ctx-lh-inferiorparietal_6 216 60 220 0 +1031 ctx-lh-inferiorparietal_7 217 60 220 0 +1032 ctx-lh-inferiorparietal_8 218 60 220 0 +1033 ctx-lh-inferiorparietal_9 219 60 220 0 +1034 ctx-lh-inferiorparietal_10 221 60 220 0 +1035 ctx-lh-inferiortemporal_1 180 40 120 0 +1036 ctx-lh-inferiortemporal_2 162 40 120 0 +1037 ctx-lh-inferiortemporal_3 163 40 120 0 +1038 ctx-lh-inferiortemporal_4 164 40 120 0 +1039 ctx-lh-inferiortemporal_5 165 40 120 0 +1040 ctx-lh-inferiortemporal_6 166 40 120 0 +1041 ctx-lh-inferiortemporal_7 167 40 120 0 +1042 ctx-lh-inferiortemporal_8 168 40 120 0 +1043 ctx-lh-isthmuscingulate_1 140 20 140 0 +1044 ctx-lh-isthmuscingulate_2 127 20 140 0 +1045 ctx-lh-isthmuscingulate_3 128 20 140 0 +1046 ctx-lh-lateraloccipital_1 20 30 140 0 +1047 ctx-lh-lateraloccipital_2 20 30 127 0 +1048 ctx-lh-lateraloccipital_3 20 30 128 0 +1049 ctx-lh-lateraloccipital_4 20 30 129 0 +1050 ctx-lh-lateraloccipital_5 20 30 130 0 +1051 ctx-lh-lateraloccipital_6 20 30 131 0 +1052 ctx-lh-lateraloccipital_7 20 30 132 0 +1053 ctx-lh-lateraloccipital_8 20 30 133 0 +1054 ctx-lh-lateraloccipital_9 20 30 134 0 +1055 ctx-lh-lateraloccipital_10 20 30 135 0 +1056 ctx-lh-lateraloccipital_11 20 30 136 0 +1057 ctx-lh-lateralorbitofrontal_1 35 75 50 0 +1058 ctx-lh-lateralorbitofrontal_2 35 72 50 0 +1059 ctx-lh-lateralorbitofrontal_3 35 73 50 0 +1060 ctx-lh-lateralorbitofrontal_4 35 74 50 0 +1061 ctx-lh-lateralorbitofrontal_5 35 76 50 0 +1062 ctx-lh-lateralorbitofrontal_6 35 75 41 0 +1063 ctx-lh-lateralorbitofrontal_7 35 75 42 0 +1064 ctx-lh-lingual_1 225 140 140 0 +1065 ctx-lh-lingual_2 227 140 140 0 +1066 ctx-lh-lingual_3 228 140 140 0 +1067 ctx-lh-lingual_4 229 140 140 0 +1068 ctx-lh-lingual_5 230 140 140 0 +1069 ctx-lh-lingual_6 231 140 140 0 +1070 ctx-lh-lingual_7 232 140 140 0 +1071 ctx-lh-lingual_8 233 140 140 0 +1072 ctx-lh-medialorbitofrontal_1 200 35 75 0 +1073 ctx-lh-medialorbitofrontal_2 182 35 75 0 +1074 ctx-lh-medialorbitofrontal_3 183 35 75 0 +1075 ctx-lh-medialorbitofrontal_4 184 35 75 0 +1076 ctx-lh-medialorbitofrontal_5 185 35 75 0 +1077 ctx-lh-middletemporal_1 160 100 50 0 +1078 ctx-lh-middletemporal_2 152 100 50 0 +1079 ctx-lh-middletemporal_3 153 100 50 0 +1080 ctx-lh-middletemporal_4 154 100 50 0 +1081 ctx-lh-middletemporal_5 155 100 50 0 +1082 ctx-lh-middletemporal_6 156 100 50 0 +1083 ctx-lh-middletemporal_7 157 100 50 0 +1084 ctx-lh-parahippocampal_1 20 220 60 0 +1085 ctx-lh-parahippocampal_2 20 194 60 0 +1086 ctx-lh-parahippocampal_3 20 195 60 0 +1087 ctx-lh-paracentral_1 60 220 60 0 +1088 ctx-lh-paracentral_2 60 200 60 0 +1089 ctx-lh-paracentral_3 60 201 60 0 +1090 ctx-lh-paracentral_4 60 202 60 0 +1091 ctx-lh-paracentral_5 60 203 60 0 +1092 ctx-lh-parsopercularis_1 220 180 140 0 +1093 ctx-lh-parsopercularis_2 202 180 140 0 +1094 ctx-lh-parsopercularis_3 203 180 140 0 +1095 ctx-lh-parsopercularis_4 204 180 140 0 +1096 ctx-lh-parsorbitalis_1 20 100 50 0 +1097 ctx-lh-parsorbitalis_2 20 77 50 0 +1098 ctx-lh-parstriangularis_1 220 60 20 0 +1099 ctx-lh-parstriangularis_2 212 60 20 0 +1100 ctx-lh-parstriangularis_3 213 60 20 0 +1101 ctx-lh-pericalcarine_1 120 100 60 0 +1102 ctx-lh-pericalcarine_2 102 100 60 0 +1103 ctx-lh-pericalcarine_3 103 100 60 0 +1104 ctx-lh-postcentral_1 220 20 20 0 +1105 ctx-lh-postcentral_2 219 20 20 0 +1106 ctx-lh-postcentral_3 221 20 20 0 +1107 ctx-lh-postcentral_4 222 20 20 0 +1108 ctx-lh-postcentral_5 223 20 20 0 +1109 ctx-lh-postcentral_6 224 20 20 0 +1110 ctx-lh-postcentral_7 220 6 20 0 +1111 ctx-lh-postcentral_8 220 7 20 0 +1112 ctx-lh-postcentral_9 220 8 20 0 +1113 ctx-lh-postcentral_10 220 9 20 0 +1114 ctx-lh-postcentral_11 220 10 20 0 +1115 ctx-lh-postcentral_12 220 11 20 0 +1116 ctx-lh-postcentral_13 220 12 20 0 +1117 ctx-lh-postcentral_14 220 13 20 0 +1118 ctx-lh-posteriorcingulate_1 220 180 220 0 +1119 ctx-lh-posteriorcingulate_2 220 180 202 0 +1120 ctx-lh-posteriorcingulate_3 220 180 203 0 +1121 ctx-lh-posteriorcingulate_4 220 180 204 0 +1122 ctx-lh-precentral_1 60 20 220 0 +1123 ctx-lh-precentral_2 60 20 211 0 +1124 ctx-lh-precentral_3 60 20 212 0 +1125 ctx-lh-precentral_4 60 20 213 0 +1126 ctx-lh-precentral_5 60 20 214 0 +1127 ctx-lh-precentral_6 60 20 215 0 +1128 ctx-lh-precentral_7 60 20 216 0 +1129 ctx-lh-precentral_8 60 20 217 0 +1130 ctx-lh-precentral_9 60 20 218 0 +1131 ctx-lh-precentral_10 60 20 219 0 +1132 ctx-lh-precentral_11 36 20 220 0 +1133 ctx-lh-precentral_12 37 20 220 0 +1134 ctx-lh-precentral_13 38 20 220 0 +1135 ctx-lh-precentral_14 39 20 220 0 +1136 ctx-lh-precentral_15 40 20 220 0 +1137 ctx-lh-precentral_16 41 20 220 0 +1138 ctx-lh-precuneus_1 160 140 180 0 +1139 ctx-lh-precuneus_2 160 140 162 0 +1140 ctx-lh-precuneus_3 160 140 163 0 +1141 ctx-lh-precuneus_4 160 140 164 0 +1142 ctx-lh-precuneus_5 160 140 165 0 +1143 ctx-lh-precuneus_6 160 140 166 0 +1144 ctx-lh-precuneus_7 160 140 167 0 +1145 ctx-lh-precuneus_8 160 140 168 0 +1146 ctx-lh-precuneus_9 160 140 169 0 +1147 ctx-lh-precuneus_10 160 140 170 0 +1148 ctx-lh-precuneus_11 160 140 171 0 +1149 ctx-lh-rostralanteriorcingulate_1 80 20 140 0 +1150 ctx-lh-rostralanteriorcingulate_2 80 20 127 0 +1151 ctx-lh-rostralmiddlefrontal_1 75 50 125 0 +1152 ctx-lh-rostralmiddlefrontal_2 75 50 122 0 +1153 ctx-lh-rostralmiddlefrontal_3 75 50 123 0 +1154 ctx-lh-rostralmiddlefrontal_4 75 50 124 0 +1155 ctx-lh-rostralmiddlefrontal_5 75 50 126 0 +1156 ctx-lh-rostralmiddlefrontal_6 71 50 125 0 +1157 ctx-lh-rostralmiddlefrontal_7 72 50 125 0 +1158 ctx-lh-rostralmiddlefrontal_8 73 50 125 0 +1159 ctx-lh-rostralmiddlefrontal_9 74 50 125 0 +1160 ctx-lh-rostralmiddlefrontal_10 76 50 125 0 +1161 ctx-lh-rostralmiddlefrontal_11 77 50 125 0 +1162 ctx-lh-rostralmiddlefrontal_12 78 50 125 0 +1163 ctx-lh-superiorfrontal_1 20 220 160 0 +1164 ctx-lh-superiorfrontal_2 20 194 160 0 +1165 ctx-lh-superiorfrontal_3 20 195 160 0 +1166 ctx-lh-superiorfrontal_4 20 196 160 0 +1167 ctx-lh-superiorfrontal_5 20 197 160 0 +1168 ctx-lh-superiorfrontal_6 20 198 160 0 +1169 ctx-lh-superiorfrontal_7 20 199 160 0 +1170 ctx-lh-superiorfrontal_8 20 200 160 0 +1171 ctx-lh-superiorfrontal_9 20 201 160 0 +1172 ctx-lh-superiorfrontal_10 20 202 160 0 +1173 ctx-lh-superiorfrontal_11 20 203 160 0 +1174 ctx-lh-superiorfrontal_12 20 204 160 0 +1175 ctx-lh-superiorfrontal_13 20 205 160 0 +1176 ctx-lh-superiorfrontal_14 20 206 160 0 +1177 ctx-lh-superiorfrontal_15 20 207 160 0 +1178 ctx-lh-superiorfrontal_16 20 208 160 0 +1179 ctx-lh-superiorfrontal_17 20 209 160 0 +1180 ctx-lh-superiorfrontal_18 20 210 160 0 +1181 ctx-lh-superiorparietal_1 20 180 140 0 +1182 ctx-lh-superiorparietal_2 20 162 140 0 +1183 ctx-lh-superiorparietal_3 20 163 140 0 +1184 ctx-lh-superiorparietal_4 20 164 140 0 +1185 ctx-lh-superiorparietal_5 20 165 140 0 +1186 ctx-lh-superiorparietal_6 20 166 140 0 +1187 ctx-lh-superiorparietal_7 20 167 140 0 +1188 ctx-lh-superiorparietal_8 20 168 140 0 +1189 ctx-lh-superiorparietal_9 20 169 140 0 +1190 ctx-lh-superiorparietal_10 20 170 140 0 +1191 ctx-lh-superiorparietal_11 20 171 140 0 +1192 ctx-lh-superiorparietal_12 20 172 140 0 +1193 ctx-lh-superiorparietal_13 20 173 140 0 +1194 ctx-lh-superiorparietal_14 20 174 140 0 +1195 ctx-lh-superiortemporal_1 140 220 220 0 +1196 ctx-lh-superiortemporal_2 140 220 202 0 +1197 ctx-lh-superiortemporal_3 140 220 203 0 +1198 ctx-lh-superiortemporal_4 140 220 204 0 +1199 ctx-lh-superiortemporal_5 140 220 205 0 +1200 ctx-lh-superiortemporal_6 140 220 206 0 +1201 ctx-lh-superiortemporal_7 140 220 207 0 +1202 ctx-lh-superiortemporal_8 140 220 208 0 +1203 ctx-lh-superiortemporal_9 140 220 209 0 +1204 ctx-lh-superiortemporal_10 140 220 210 0 +1205 ctx-lh-superiortemporal_11 140 220 211 0 +1206 ctx-lh-supramarginal_1 80 160 20 0 +1207 ctx-lh-supramarginal_2 80 152 20 0 +1208 ctx-lh-supramarginal_3 80 153 20 0 +1209 ctx-lh-supramarginal_4 80 154 20 0 +1210 ctx-lh-supramarginal_5 80 155 20 0 +1211 ctx-lh-supramarginal_6 80 156 20 0 +1212 ctx-lh-supramarginal_7 80 157 20 0 +1213 ctx-lh-supramarginal_8 80 158 20 0 +1214 ctx-lh-supramarginal_9 80 159 20 0 +1215 ctx-lh-supramarginal_10 80 161 20 0 +1216 ctx-lh-frontalpole_1 100 0 100 0 +1217 ctx-lh-temporalpole_1 70 70 70 0 +1218 ctx-lh-transversetemporal_1 150 150 200 0 +1219 ctx-lh-transversetemporal_2 150 150 182 0 +1220 ctx-lh-insula_1 255 192 32 0 +1221 ctx-lh-insula_2 227 192 32 0 +1222 ctx-lh-insula_3 228 192 32 0 +1223 ctx-lh-insula_4 229 192 32 0 +1224 ctx-lh-insula_5 230 192 32 0 +1225 ctx-lh-insula_6 231 192 32 0 +1226 ctx-lh-insula_7 232 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-bankssts_1 25 100 40 0 +2003 ctx-rh-bankssts_2 25 77 40 0 +2004 ctx-rh-bankssts_3 25 78 40 0 +2005 ctx-rh-caudalanteriorcingulate_1 125 100 160 0 +2006 ctx-rh-caudalanteriorcingulate_2 125 100 142 0 +2007 ctx-rh-caudalanteriorcingulate_3 125 100 143 0 +2008 ctx-rh-caudalmiddlefrontal_1 100 25 0 0 +2009 ctx-rh-caudalmiddlefrontal_2 82 25 0 0 +2010 ctx-rh-caudalmiddlefrontal_3 83 25 0 0 +2011 ctx-rh-caudalmiddlefrontal_4 84 25 0 0 +2012 ctx-rh-caudalmiddlefrontal_5 85 25 0 0 +2013 ctx-rh-cuneus_1 220 20 100 0 +2014 ctx-rh-cuneus_2 202 20 100 0 +2015 ctx-rh-cuneus_3 203 20 100 0 +2016 ctx-rh-cuneus_4 204 20 100 0 +2017 ctx-rh-entorhinal_1 220 20 10 0 +2018 ctx-rh-fusiform_1 180 220 140 0 +2019 ctx-rh-fusiform_2 180 194 140 0 +2020 ctx-rh-fusiform_3 180 195 140 0 +2021 ctx-rh-fusiform_4 180 196 140 0 +2022 ctx-rh-fusiform_5 180 197 140 0 +2023 ctx-rh-fusiform_6 180 198 140 0 +2024 ctx-rh-fusiform_7 180 199 140 0 +2025 ctx-rh-fusiform_8 180 200 140 0 +2026 ctx-rh-inferiorparietal_1 220 60 220 0 +2027 ctx-rh-inferiorparietal_2 212 60 220 0 +2028 ctx-rh-inferiorparietal_3 213 60 220 0 +2029 ctx-rh-inferiorparietal_4 214 60 220 0 +2030 ctx-rh-inferiorparietal_5 215 60 220 0 +2031 ctx-rh-inferiorparietal_6 216 60 220 0 +2032 ctx-rh-inferiorparietal_7 217 60 220 0 +2033 ctx-rh-inferiorparietal_8 218 60 220 0 +2034 ctx-rh-inferiorparietal_9 219 60 220 0 +2035 ctx-rh-inferiorparietal_10 221 60 220 0 +2036 ctx-rh-inferiorparietal_11 222 60 220 0 +2037 ctx-rh-inferiorparietal_12 223 60 220 0 +2038 ctx-rh-inferiortemporal_1 180 40 120 0 +2039 ctx-rh-inferiortemporal_2 162 40 120 0 +2040 ctx-rh-inferiortemporal_3 163 40 120 0 +2041 ctx-rh-inferiortemporal_4 164 40 120 0 +2042 ctx-rh-inferiortemporal_5 165 40 120 0 +2043 ctx-rh-inferiortemporal_6 166 40 120 0 +2044 ctx-rh-inferiortemporal_7 167 40 120 0 +2045 ctx-rh-isthmuscingulate_1 140 20 140 0 +2046 ctx-rh-isthmuscingulate_2 127 20 140 0 +2047 ctx-rh-lateraloccipital_1 20 30 140 0 +2048 ctx-rh-lateraloccipital_2 20 30 127 0 +2049 ctx-rh-lateraloccipital_3 20 30 128 0 +2050 ctx-rh-lateraloccipital_4 20 30 129 0 +2051 ctx-rh-lateraloccipital_5 20 30 130 0 +2052 ctx-rh-lateraloccipital_6 20 30 131 0 +2053 ctx-rh-lateraloccipital_7 20 30 132 0 +2054 ctx-rh-lateraloccipital_8 20 30 133 0 +2055 ctx-rh-lateraloccipital_9 20 30 134 0 +2056 ctx-rh-lateraloccipital_10 20 30 135 0 +2057 ctx-rh-lateralorbitofrontal_1 35 75 50 0 +2058 ctx-rh-lateralorbitofrontal_2 35 72 50 0 +2059 ctx-rh-lateralorbitofrontal_3 35 73 50 0 +2060 ctx-rh-lateralorbitofrontal_4 35 74 50 0 +2061 ctx-rh-lateralorbitofrontal_5 35 76 50 0 +2062 ctx-rh-lateralorbitofrontal_6 35 75 41 0 +2063 ctx-rh-lateralorbitofrontal_7 35 75 42 0 +2064 ctx-rh-lingual_1 225 140 140 0 +2065 ctx-rh-lingual_2 227 140 140 0 +2066 ctx-rh-lingual_3 228 140 140 0 +2067 ctx-rh-lingual_4 229 140 140 0 +2068 ctx-rh-lingual_5 230 140 140 0 +2069 ctx-rh-lingual_6 231 140 140 0 +2070 ctx-rh-lingual_7 232 140 140 0 +2071 ctx-rh-medialorbitofrontal_1 200 35 75 0 +2072 ctx-rh-medialorbitofrontal_2 182 35 75 0 +2073 ctx-rh-medialorbitofrontal_3 183 35 75 0 +2074 ctx-rh-medialorbitofrontal_4 184 35 75 0 +2075 ctx-rh-medialorbitofrontal_5 185 35 75 0 +2076 ctx-rh-middletemporal_1 160 100 50 0 +2077 ctx-rh-middletemporal_2 152 100 50 0 +2078 ctx-rh-middletemporal_3 153 100 50 0 +2079 ctx-rh-middletemporal_4 154 100 50 0 +2080 ctx-rh-middletemporal_5 155 100 50 0 +2081 ctx-rh-middletemporal_6 156 100 50 0 +2082 ctx-rh-middletemporal_7 157 100 50 0 +2083 ctx-rh-middletemporal_8 158 100 50 0 +2084 ctx-rh-middletemporal_9 159 100 50 0 +2085 ctx-rh-parahippocampal_1 20 220 60 0 +2086 ctx-rh-parahippocampal_2 20 194 60 0 +2087 ctx-rh-parahippocampal_3 20 195 60 0 +2088 ctx-rh-paracentral_1 60 220 60 0 +2089 ctx-rh-paracentral_2 60 200 60 0 +2090 ctx-rh-paracentral_3 60 201 60 0 +2091 ctx-rh-paracentral_4 60 202 60 0 +2092 ctx-rh-paracentral_5 60 203 60 0 +2093 ctx-rh-paracentral_6 60 204 60 0 +2094 ctx-rh-parsopercularis_1 220 180 140 0 +2095 ctx-rh-parsopercularis_2 202 180 140 0 +2096 ctx-rh-parsopercularis_3 203 180 140 0 +2097 ctx-rh-parsopercularis_4 204 180 140 0 +2098 ctx-rh-parsorbitalis_1 20 100 50 0 +2099 ctx-rh-parsorbitalis_2 20 77 50 0 +2100 ctx-rh-parstriangularis_1 220 60 20 0 +2101 ctx-rh-parstriangularis_2 211 60 20 0 +2102 ctx-rh-parstriangularis_3 212 60 20 0 +2103 ctx-rh-parstriangularis_4 213 60 20 0 +2104 ctx-rh-pericalcarine_1 120 100 60 0 +2105 ctx-rh-pericalcarine_2 102 100 60 0 +2106 ctx-rh-pericalcarine_3 103 100 60 0 +2107 ctx-rh-pericalcarine_4 104 100 60 0 +2108 ctx-rh-postcentral_1 220 20 20 0 +2109 ctx-rh-postcentral_2 219 20 20 0 +2110 ctx-rh-postcentral_3 221 20 20 0 +2111 ctx-rh-postcentral_4 222 20 20 0 +2112 ctx-rh-postcentral_5 223 20 20 0 +2113 ctx-rh-postcentral_6 224 20 20 0 +2114 ctx-rh-postcentral_7 220 6 20 0 +2115 ctx-rh-postcentral_8 220 7 20 0 +2116 ctx-rh-postcentral_9 220 8 20 0 +2117 ctx-rh-postcentral_10 220 9 20 0 +2118 ctx-rh-postcentral_11 220 10 20 0 +2119 ctx-rh-postcentral_12 220 11 20 0 +2120 ctx-rh-posteriorcingulate_1 220 180 220 0 +2121 ctx-rh-posteriorcingulate_2 220 180 202 0 +2122 ctx-rh-posteriorcingulate_3 220 180 203 0 +2123 ctx-rh-posteriorcingulate_4 220 180 204 0 +2124 ctx-rh-precentral_1 60 20 220 0 +2125 ctx-rh-precentral_2 60 20 211 0 +2126 ctx-rh-precentral_3 60 20 212 0 +2127 ctx-rh-precentral_4 60 20 213 0 +2128 ctx-rh-precentral_5 60 20 214 0 +2129 ctx-rh-precentral_6 60 20 215 0 +2130 ctx-rh-precentral_7 60 20 216 0 +2131 ctx-rh-precentral_8 60 20 217 0 +2132 ctx-rh-precentral_9 60 20 218 0 +2133 ctx-rh-precentral_10 60 20 219 0 +2134 ctx-rh-precentral_11 36 20 220 0 +2135 ctx-rh-precentral_12 37 20 220 0 +2136 ctx-rh-precentral_13 38 20 220 0 +2137 ctx-rh-precentral_14 39 20 220 0 +2138 ctx-rh-precentral_15 40 20 220 0 +2139 ctx-rh-precentral_16 41 20 220 0 +2140 ctx-rh-precuneus_1 160 140 180 0 +2141 ctx-rh-precuneus_2 160 140 162 0 +2142 ctx-rh-precuneus_3 160 140 163 0 +2143 ctx-rh-precuneus_4 160 140 164 0 +2144 ctx-rh-precuneus_5 160 140 165 0 +2145 ctx-rh-precuneus_6 160 140 166 0 +2146 ctx-rh-precuneus_7 160 140 167 0 +2147 ctx-rh-precuneus_8 160 140 168 0 +2148 ctx-rh-precuneus_9 160 140 169 0 +2149 ctx-rh-precuneus_10 160 140 170 0 +2150 ctx-rh-rostralanteriorcingulate_1 80 20 140 0 +2151 ctx-rh-rostralanteriorcingulate_2 80 20 127 0 +2152 ctx-rh-rostralmiddlefrontal_1 75 50 125 0 +2153 ctx-rh-rostralmiddlefrontal_2 75 50 122 0 +2154 ctx-rh-rostralmiddlefrontal_3 75 50 123 0 +2155 ctx-rh-rostralmiddlefrontal_4 75 50 124 0 +2156 ctx-rh-rostralmiddlefrontal_5 75 50 126 0 +2157 ctx-rh-rostralmiddlefrontal_6 71 50 125 0 +2158 ctx-rh-rostralmiddlefrontal_7 72 50 125 0 +2159 ctx-rh-rostralmiddlefrontal_8 73 50 125 0 +2160 ctx-rh-rostralmiddlefrontal_9 74 50 125 0 +2161 ctx-rh-rostralmiddlefrontal_10 76 50 125 0 +2162 ctx-rh-rostralmiddlefrontal_11 77 50 125 0 +2163 ctx-rh-rostralmiddlefrontal_12 78 50 125 0 +2164 ctx-rh-rostralmiddlefrontal_13 79 50 125 0 +2165 ctx-rh-superiorfrontal_1 20 220 160 0 +2166 ctx-rh-superiorfrontal_2 20 194 160 0 +2167 ctx-rh-superiorfrontal_3 20 195 160 0 +2168 ctx-rh-superiorfrontal_4 20 196 160 0 +2169 ctx-rh-superiorfrontal_5 20 197 160 0 +2170 ctx-rh-superiorfrontal_6 20 198 160 0 +2171 ctx-rh-superiorfrontal_7 20 199 160 0 +2172 ctx-rh-superiorfrontal_8 20 200 160 0 +2173 ctx-rh-superiorfrontal_9 20 201 160 0 +2174 ctx-rh-superiorfrontal_10 20 202 160 0 +2175 ctx-rh-superiorfrontal_11 20 203 160 0 +2176 ctx-rh-superiorfrontal_12 20 204 160 0 +2177 ctx-rh-superiorfrontal_13 20 205 160 0 +2178 ctx-rh-superiorfrontal_14 20 206 160 0 +2179 ctx-rh-superiorfrontal_15 20 207 160 0 +2180 ctx-rh-superiorfrontal_16 20 208 160 0 +2181 ctx-rh-superiorfrontal_17 20 209 160 0 +2182 ctx-rh-superiorparietal_1 20 180 140 0 +2183 ctx-rh-superiorparietal_2 20 162 140 0 +2184 ctx-rh-superiorparietal_3 20 163 140 0 +2185 ctx-rh-superiorparietal_4 20 164 140 0 +2186 ctx-rh-superiorparietal_5 20 165 140 0 +2187 ctx-rh-superiorparietal_6 20 166 140 0 +2188 ctx-rh-superiorparietal_7 20 167 140 0 +2189 ctx-rh-superiorparietal_8 20 168 140 0 +2190 ctx-rh-superiorparietal_9 20 169 140 0 +2191 ctx-rh-superiorparietal_10 20 170 140 0 +2192 ctx-rh-superiorparietal_11 20 171 140 0 +2193 ctx-rh-superiorparietal_12 20 172 140 0 +2194 ctx-rh-superiorparietal_13 20 173 140 0 +2195 ctx-rh-superiortemporal_1 140 220 220 0 +2196 ctx-rh-superiortemporal_2 140 220 202 0 +2197 ctx-rh-superiortemporal_3 140 220 203 0 +2198 ctx-rh-superiortemporal_4 140 220 204 0 +2199 ctx-rh-superiortemporal_5 140 220 205 0 +2200 ctx-rh-superiortemporal_6 140 220 206 0 +2201 ctx-rh-superiortemporal_7 140 220 207 0 +2202 ctx-rh-superiortemporal_8 140 220 208 0 +2203 ctx-rh-superiortemporal_9 140 220 209 0 +2204 ctx-rh-superiortemporal_10 140 220 210 0 +2205 ctx-rh-superiortemporal_11 140 220 211 0 +2206 ctx-rh-supramarginal_1 80 160 20 0 +2207 ctx-rh-supramarginal_2 80 152 20 0 +2208 ctx-rh-supramarginal_3 80 153 20 0 +2209 ctx-rh-supramarginal_4 80 154 20 0 +2210 ctx-rh-supramarginal_5 80 155 20 0 +2211 ctx-rh-supramarginal_6 80 156 20 0 +2212 ctx-rh-supramarginal_7 80 157 20 0 +2213 ctx-rh-supramarginal_8 80 158 20 0 +2214 ctx-rh-supramarginal_9 80 159 20 0 +2215 ctx-rh-frontalpole_1 100 0 100 0 +2216 ctx-rh-temporalpole_1 70 70 70 0 +2217 ctx-rh-transversetemporal_1 150 150 200 0 +2218 ctx-rh-insula_1 255 192 32 0 +2219 ctx-rh-insula_2 227 192 32 0 +2220 ctx-rh-insula_3 228 192 32 0 +2221 ctx-rh-insula_4 229 192 32 0 +2222 ctx-rh-insula_5 230 192 32 0 +2223 ctx-rh-insula_6 231 192 32 0 +2224 ctx-rh-insula_7 232 192 32 0 \ No newline at end of file diff --git a/bin/macos/3.1.2/templates/lausanne500/lh.lausanne500.gcs b/bin/macos/3.1.2/templates/lausanne500/lh.lausanne500.gcs new file mode 100644 index 0000000..ee015a2 Binary files /dev/null and b/bin/macos/3.1.2/templates/lausanne500/lh.lausanne500.gcs differ diff --git a/bin/macos/3.1.2/templates/lausanne500/parcellate_lausanne500.sh b/bin/macos/3.1.2/templates/lausanne500/parcellate_lausanne500.sh new file mode 100755 index 0000000..f8c0dda --- /dev/null +++ b/bin/macos/3.1.2/templates/lausanne500/parcellate_lausanne500.sh @@ -0,0 +1,106 @@ +#!/bin/bash +# +# Parcellate lausanne500 atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=lausanne500 + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/macos/3.1.2/templates/lausanne500/rh.lausanne500.gcs b/bin/macos/3.1.2/templates/lausanne500/rh.lausanne500.gcs new file mode 100644 index 0000000..968a488 Binary files /dev/null and b/bin/macos/3.1.2/templates/lausanne500/rh.lausanne500.gcs differ diff --git a/bin/macos/CATO-3.1.2-macos.zip b/bin/macos/CATO-3.1.2-macos.zip new file mode 100644 index 0000000..f7f6cb0 Binary files /dev/null and b/bin/macos/CATO-3.1.2-macos.zip differ diff --git a/bin/unix/3.1.2/LICENSE b/bin/unix/3.1.2/LICENSE new file mode 100755 index 0000000..b359b0b --- /dev/null +++ b/bin/unix/3.1.2/LICENSE @@ -0,0 +1,10 @@ +Unless otherwise specified by LICENSE(.txt) files in individual +directories, or within individual files or functions, all code is distributed under the MIT License: + +Copyright (c) 2020, CATO developers, All rights reserved. + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file diff --git a/bin/unix/3.1.2/VERSION b/bin/unix/3.1.2/VERSION new file mode 100644 index 0000000..7b9a810 --- /dev/null +++ b/bin/unix/3.1.2/VERSION @@ -0,0 +1,4 @@ +CATO 3.1.2 +Operating system: unix (GLNXA64) +Compiled on: 10-May-2021 23:00:43 +Compiled using: MATLAB Compiler 6.5 (R2017b) \ No newline at end of file diff --git a/bin/unix/3.1.2/functional_pipeline b/bin/unix/3.1.2/functional_pipeline new file mode 100755 index 0000000..3d5ce8b Binary files /dev/null and b/bin/unix/3.1.2/functional_pipeline differ diff --git a/bin/unix/3.1.2/functional_preprocessing/preprocess_default.sh b/bin/unix/3.1.2/functional_preprocessing/preprocess_default.sh new file mode 100755 index 0000000..ff323b1 --- /dev/null +++ b/bin/unix/3.1.2/functional_preprocessing/preprocess_default.sh @@ -0,0 +1,159 @@ +#!/bin/bash +# +# (Example) preprocessing script for functional MRI data: +# 1. Performs slice timing correction using FSL tool slicetimer if variable +# sliceTimingCorrection is TRUE. +# 2. Performs motion correction using FSL tool MCFLIRT. +# 3. Computes a rs-fMRI reference image by averaging all (motion corrected) +# rs-fMRI frames (using FSL). +# 4. Computes the registration matrix between the rs-fMRI reference image and +# the T1 image (using Freesurfer). +# 5. Registers the T1 parcellation to the reference rs-fMRI image (using +# Freesurfer). + +# https://google.github.io/styleguide/shellguide.html + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Usage +####################################### +usage() +{ + cat << EOF +(Example) preprocessing script for functional MRI data: + 1. Performs slice timing correction using FSL tool slicetimer if + variable sliceTimingCorrection is TRUE. + 2. Performs motion correction using FSL tool MCFLIRT. + 3. Computes a rs-fMRI reference image by averaging all (motion + corrected) rs-fMRI frames (using FSL). + 4. Computes the registration matrix between the rs-fMRI reference + image and the T1 image (using Freesurfer). + 5. Registers the T1 parcellation to the reference rs-fMRI image + (using Freesurfer). +EOF +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --fmriFile=*) + fmriFile=${1#*=} + shift + ;; + --fmriProcessedFile=*) + fmriProcessedFile=${1#*=} + shift + ;; + --slicetimerOptions=*) + slicetimerOptions=${1#*=} + shift + ;; + --sliceTimingCorrection=*) + sliceTimingCorrection=${1#*=} + shift + ;; + --fmriReferenceFile=*) + fmriReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --motionParametersFile=*) + motionParametersFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '$1'" + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR + +parse_input "$@" + +# TODO: convert MNC to NIFTI +cp "$fmriFile" "$fmriProcessedFile" + +# perform slice timing correction +if [ "$sliceTimingCorrection" = true ] ; then + slicetimer -i "$fmriProcessedFile" -o "${fmriProcessedFile/.nii.gz/_stc.nii.gz}" \ + $slicetimerOptions + mv "${fmriProcessedFile/.nii.gz/_stc.nii.gz}" "$fmriProcessedFile" +fi + +# perform motion correction +mcflirt -in "$fmriProcessedFile" -plots +mv "${fmriProcessedFile/.nii.gz/_mcf.nii.gz}" "$fmriProcessedFile" +mv "${fmriProcessedFile/.nii.gz/_mcf.par}" "$motionParametersFile" + +# create reference volume +fslmaths "$fmriProcessedFile" -Tmean "$fmriReferenceFile" + +# compute registration matrix +if [[ "$freesurferDir" =~ \ |\' ]] || [[ "$fmriReferenceFile" =~ \ |\' ]] || [[ "$registrationMatrixFile" =~ \ |\' ]]; then + echo "bbregister cannot handle filenames with spaces. Variable freesurferDir, fmriReferenceFile or registrationMatrixFile contains spaces." >&2 + exit 1 +fi + +bbregister --s "$freesurferDir" --mov "$fmriReferenceFile" --reg "$registrationMatrixFile" \ + --bold --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$fmriReferenceFile" \ + --reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO add registration of MTR weighted image + +exit 0 diff --git a/bin/unix/3.1.2/structural_pipeline b/bin/unix/3.1.2/structural_pipeline new file mode 100755 index 0000000..551583c Binary files /dev/null and b/bin/unix/3.1.2/structural_pipeline differ diff --git a/bin/unix/3.1.2/structural_preprocessing/preprocess_eddy.sh b/bin/unix/3.1.2/structural_preprocessing/preprocess_eddy.sh new file mode 100755 index 0000000..4b7c375 --- /dev/null +++ b/bin/unix/3.1.2/structural_preprocessing/preprocess_eddy.sh @@ -0,0 +1,197 @@ +#!/bin/bash +# +# (Example) preprocessing script that: +# 1. Runs FSL eddy to correct for eddy current distortions and motion artifacts in the DWI data. +# 2. Updates the b-vectors to adjust for the DWI corrections. +# 3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes. +# 4. Computes the registration matrix between DWI reference image and the T1 image using bbregister. +# 5. Registers the Freesurfer segmentation to the DWI reference image. + +# https://google.github.io/styleguide/shellguide.html + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Usage +####################################### +usage() +{ + echo "(Example) preprocessing script that:" + echo "1. Runs FSL eddy to correct for eddy current distortions and motion artifacts in the DWI data." + echo "2. Updates the b-vectors to adjust for the DWI corrections." + echo "3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes." + echo "4. Computes the registration matrix between DWI reference image and the T1 image using bbregister." + echo "5. Registers the Freesurfer segmentation to the DWI reference image." +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --b0Scans=*) + b0Scans=${1#*=} + shift + ;; + --dwiProcessedFile=*) + dwiProcessedFile=${1#*=} + shift + ;; + --dwiFile=*) + dwiFile=${1#*=} + shift + ;; + --dwiReferenceFile=*) + dwiReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + --processedBvecsFile=*) + processedBvecsFile=${1#*=} + shift + ;; + --processedBvalsFile=*) + processedBvalsFile=${1#*=} + shift + ;; + --acqpFile=*) + acqpFile=${1#*=} + shift + ;; + --indexFile=*) + indexFile=${1#*=} + shift + ;; + --eddyVersion=*) + eddyVersion=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '$1'" + shift + ;; + esac + done + +} + +computeReferenceB0(){ + + # use b0 scan(s) to create reference volume + for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiReferenceFile/.nii.gz/_indv_$i.nii.gz}" $((i- 1)) 1 + done + + fslmerge -t "$dwiReferenceFile" "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + fslmaths "$dwiReferenceFile" -Tmean "$dwiReferenceFile" + rm "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + + +} + +####################################### +# Run Eddy +####################################### +runEddy() { + + # Create index file for eddy + nScans=$(mri_info --nframes "$dwiProcessedFile" | tail -n1) + for i in $(eval echo {1..$nScans}); do + echo -n "1 "; + done > "$indexFile" + + $eddyVersion -v --imain="$dwiProcessedFile" \ + --mask="$brainMaskFile" \ + --acqp="$acqpFile" \ + --index="$indexFile" \ + --bvecs="$processedBvecsFile" --bvals="$processedBvalsFile" \ + --out="$dwiProcessedFile" + + # replace bvecs by their rotated counterparts + [ ! -f "${dwiProcessedFile}.eddy_rotated_bvecs" ] && + error "could not find rotated bvecs (use FSL 5.0.9 or higher)" + mv "${dwiProcessedFile}.eddy_rotated_bvecs" "$processedBvecsFile" + + # Clean eddy output + rm "$brainMaskFile" + +} + +####################################### +# Main function. +####################################### +trap error ERR + +parse_input "$@" + +# TODO: check FSL version + +# TODO: convert MNC to NIFTI +cp "$dwiFile" "$dwiProcessedFile" + +# Load b0-scans list and parse them into an array +b0Scans=(${b0Scans//,/ }) + +# Create a mask of the brain based on the b0-reference +computeReferenceB0 + +bet "$dwiReferenceFile" "$dwiProcessedFile" -m -n # creates ${dwiProcessedFile/.nii.gz/_mask.nii.gz} +brainMaskFile=${dwiProcessedFile/.nii.gz/_mask.nii.gz} +rm "$dwiReferenceFile" # we will create a new reference b0 after eddy correction + +runEddy + +# Create new eddy current and movement corrected reference b0-scan +computeReferenceB0 + +# Compute registration matrix from FS to subject space +bbregister --s "$freesurferDir" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \ + --dti --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# Register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$dwiReferenceFile" \ + --reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO: add registration of MTR weighted image + +exit 0 diff --git a/bin/unix/3.1.2/structural_preprocessing/preprocess_minimal.sh b/bin/unix/3.1.2/structural_preprocessing/preprocess_minimal.sh new file mode 100755 index 0000000..52e8ec8 --- /dev/null +++ b/bin/unix/3.1.2/structural_preprocessing/preprocess_minimal.sh @@ -0,0 +1,125 @@ +#!/bin/bash +# +# (Example) preprocessing script that: +# 1. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes. +# 2. Computes the registration matrix between DWI reference image and the T1 image using bbregister. +# 3. Registers the Freesurfer segmentation to the DWI reference image. + +# https://google.github.io/styleguide/shellguide.html + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Usage +####################################### +usage() +{ + echo "(Example) preprocessing script that:" + echo "1. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes." + echo "2. Computes the registration matrix between DWI reference image and the T1 image using bbregister." + echo "3. Registers the Freesurfer segmentation to the DWI reference image." +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --b0Scans=*) + b0Scans=${1#*=} + shift + ;; + --dwiProcessedFile=*) + dwiProcessedFile=${1#*=} + shift + ;; + --dwiFile=*) + dwiFile=${1#*=} + shift + ;; + --dwiReferenceFile=*) + dwiReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '$1'" + shift + ;; + esac +done +} + +####################################### +# Main function. +####################################### +trap error ERR + +parse_input "$@" + + +# TODO: include conversion MNC to NIFTI +cp "$dwiFile" "$dwiProcessedFile" + +# Load b0-scans list and parse them into an array +b0Scans=(${b0Scans//,/ }) + +# use b0 scan(s) to create reference volume +for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiReferenceFile/.nii.gz/_indv_$i.nii.gz}" $((i - 1)) 1 +done +fslmerge -t "$dwiReferenceFile" "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz +fslmaths "$dwiReferenceFile" -Tmean "$dwiReferenceFile" +rm "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + +# compute registration matrix +bbregister --s "$freesurferDir" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \ + --dti --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$dwiReferenceFile" \ + --reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO add registration of MTR weighted image + +exit 0 diff --git a/bin/unix/3.1.2/structural_preprocessing/preprocess_topup_eddy.sh b/bin/unix/3.1.2/structural_preprocessing/preprocess_topup_eddy.sh new file mode 100755 index 0000000..bf8e33f --- /dev/null +++ b/bin/unix/3.1.2/structural_preprocessing/preprocess_topup_eddy.sh @@ -0,0 +1,208 @@ +#!/bin/bash +# +# (Example) preprocessing script that: +# 1. Runs FSL eddy and FSL topup to correct for susceptibility induced distortions, eddy current distortions and motion artifacts in the DWI data. +# 2. Updates the b-vectors to adjust for the DWI corrections. +# 3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes. +# 4. Computes the registration matrix between DWI reference image and the T1 image using bbregister. +# 5. Registers the Freesurfer segmentation to the DWI reference image. + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 +} + +####################################### +# Usage +####################################### +usage() +{ + echo "(Example) preprocessing script that:" + echo "1. Runs FSL eddy and FSL topup to correct for susceptibility induced distortions, eddy current distortions and motion artifacts in the DWI data." + echo "2. Updates the b-vectors to adjust for the DWI corrections." + echo "3. Computes a DWI reference image based on the corrected diffusion-unweighted (b0) volumes." + echo "4. Computes the registration matrix between DWI reference image and the T1 image using bbregister." + echo "5. Registers the Freesurfer segmentation to the DWI reference image." +} + +####################################### +# Parse input +####################################### +parse_input() +{ + [[ $# -eq 0 ]] && set -- "--help" + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --b0Scans=*) + b0Scans=${1#*=} + shift + ;; + --dwiProcessedFile=*) + dwiProcessedFile=${1#*=} + shift + ;; + --dwiFiles=*) + dwiFiles=${1#*=} + shift + ;; + --dwiReferenceFile=*) + dwiReferenceFile=${1#*=} + shift + ;; + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --segmentationFile=*) + segmentationFile=${1#*=} + shift + ;; + --processedBvecsFile=*) + processedBvecsFile=${1#*=} + shift + ;; + --processedBvalsFile=*) + processedBvalsFile=${1#*=} + shift + ;; + --acqpFile=*) + acqpFile=${1#*=} + shift + ;; + --indexFile=*) + indexFile=${1#*=} + shift + ;; + --eddyVersion=*) + eddyVersion=${1#*=} + shift + ;; + -? | -h | -help | --help) + usage && exit + ;; + --*=*) + inputParam=${1:2}; + # echo Not used: $inputParam + shift + ;; + *) + error "Unkown input argument '${1}'" + shift + ;; + esac + done +} + +####################################### +# Parse input +####################################### +computeReferenceB0(){ + + # use b0 scan(s) to create reference volume + for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiReferenceFile/.nii.gz/_indv_$i.nii.gz}" $((i- 1)) 1 + done + + fslmerge -t "$dwiReferenceFile" "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + fslmaths "$dwiReferenceFile" -Tmean "$dwiReferenceFile" + rm "${dwiReferenceFile/.nii.gz/_indv_}"*.nii.gz + +} + +####################################### +# Main function +####################################### + +trap error ERR + +parse_input "$@" + +dwiFiles=(${dwiFiles//,/ }) +fslmerge -t "$dwiProcessedFile" "${dwiFiles[@]}" + +# TODO: check FSL version > 5.0.9 + +# Load b0-scans list and parse them into an array +b0Scans=(${b0Scans//,/ }) + +dwiB0ScansFile=${dwiProcessedFile/.nii.gz/_b0.nii.gz} +dwiB0UnwarpedScansFile=${dwiProcessedFile/.nii.gz/_b0_unwarped.nii.gz} +brainMaskFile=${dwiProcessedFile/.nii.gz/_mask.nii.gz} # DO NOT CHANGE: HARDCODED IN FSL + +# ------------------------------------- +# Topup +# ------------------------------------- + +# Extract b0-scan(s) and put them (temporary) in dwiReferenceFile +for i in ${b0Scans[@]}; do + fslroi "$dwiProcessedFile" "${dwiB0ScansFile/.nii.gz/_indv_$i.nii.gz}" $((i - 1)) 1 +done +fslmerge -t "$dwiB0ScansFile" "${dwiB0ScansFile/.nii.gz/_indv_}"*.nii.gz +rm "${dwiB0ScansFile/.nii.gz/_indv_}"*.nii.gz + +# Run topup +topup -v --imain="$dwiB0ScansFile" --config=b02b0.cnf \ +--datain="$acqpFile" --out="${dwiProcessedFile/.nii.gz/}" \ +--iout="$dwiB0UnwarpedScansFile" --subsamp=1 +rm "${dwiB0ScansFile/.nii.gz/}".{nii.gz,topup_log} + +# ------------------------------------- +# Eddy +# ------------------------------------- + +# Create reference b0-image from unwarped b0-scans +fslmaths "$dwiB0UnwarpedScansFile" -Tmean "$dwiReferenceFile" +bet "$dwiReferenceFile" "$dwiProcessedFile" -m -n # creates $brainMaskFile +rm "$dwiReferenceFile" "$dwiB0UnwarpedScansFile" + +# Run eddy current correction +$eddyVersion -v --imain="$dwiProcessedFile" \ + --mask="$brainMaskFile" \ + --acqp="$acqpFile" \ + --index="$indexFile" \ + --bvecs="$processedBvecsFile" --bvals="$processedBvalsFile" \ + --topup="${dwiProcessedFile/.nii.gz/}" \ + --out="$dwiProcessedFile" + +# clean up +# rm ${dwiProcessedFile/.nii.gz/_fieldcoef.nii.gz} ${dwiProcessedFile/.nii.gz/_movpar.txt} +rm "$brainMaskFile" + +mv "${dwiProcessedFile}".eddy_rotated_bvecs "$processedBvecsFile" + +# ------------------------------------- +# DWI and Freesurfer registration +# ------------------------------------- + +# Create new eddy current and movement corrected reference b0-scan +computeReferenceB0 + +# Compute registration matrix from FS to subject space +bbregister --s "$freesurferDir" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \ +--dti --init-fsl +rm "$registrationMatrixFile".{mincost,param,sum,log} + +# Register freesurfer segmentation to reference volume +mri_label2vol --seg "${freesurferDir}/mri/aseg.mgz" --temp "$dwiReferenceFile" \ +--reg "$registrationMatrixFile" --o "$segmentationFile" + +# TODO: add registration of MTR weighted image + +exit 0 diff --git a/bin/unix/3.1.2/templates/BB50human/BB50human.annot.ctab b/bin/unix/3.1.2/templates/BB50human/BB50human.annot.ctab new file mode 100755 index 0000000..d9cea91 --- /dev/null +++ b/bin/unix/3.1.2/templates/BB50human/BB50human.annot.ctab @@ -0,0 +1,78 @@ +1000 ctx-lh-FA 206 226 156 0 +1001 ctx-lh-FB 200 219 138 0 +1002 ctx-lh-FBA 200 200 120 0 +1003 ctx-lh-FC 187 204 115 0 +1004 ctx-lh-FCBm 85 193 170 0 +1005 ctx-lh-FDdelta 19 132 80 0 +1006 ctx-lh-FDL 27 240 160 0 +1007 ctx-lh-FDm 13 201 111 0 +1008 ctx-lh-FDp 69 168 123 0 +1009 ctx-lh-FE 27 178 138 0 +1010 ctx-lh-FF 49 172 192 0 +1011 ctx-lh-FG 61 127 118 0 +1012 ctx-lh-FH 77 135 106 0 +1013 ctx-lh-FL 80 145 146 0 +1014 ctx-lh-H 41 55 101 0 +1015 ctx-lh-IA 204 61 211 0 +1016 ctx-lh-IB 137 67 135 0 +1017 ctx-lh-LA 124 215 246 0 +1018 ctx-lh-LC1 0 133 185 0 +1019 ctx-lh-LC2 68 165 227 0 +1020 ctx-lh-LE 169 219 224 0 +1021 ctx-lh-unknown 50 50 50 0 +1022 ctx-lh-OA 253 252 187 0 +1023 ctx-lh-OB 251 250 146 0 +1024 ctx-lh-OC 247 222 71 0 +1025 ctx-lh-PB 247 67 148 0 +1026 ctx-lh-PC 239 87 150 0 +1027 ctx-lh-PEm 248 167 210 0 +1028 ctx-lh-PEp 250 150 200 0 +1029 ctx-lh-PF 250 180 224 0 +1030 ctx-lh-PFD 255 190 200 0 +1031 ctx-lh-PG 248 193 224 0 +1032 ctx-lh-PH 232 73 130 0 +1033 ctx-lh-TA 240 85 102 0 +1034 ctx-lh-TB 233 65 98 0 +1035 ctx-lh-TE1 235 181 136 0 +1036 ctx-lh-TE2 204 140 82 0 +1037 ctx-lh-TF 184 47 79 0 +1038 ctx-lh-TG 247 198 127 0 +2000 ctx-rh-FA 206 226 156 0 +2001 ctx-rh-FB 200 219 138 0 +2002 ctx-rh-FBA 200 200 120 0 +2003 ctx-rh-FC 187 204 115 0 +2004 ctx-rh-FCBm 85 193 170 0 +2005 ctx-rh-FDdelta 19 132 80 0 +2006 ctx-rh-FDL 27 240 160 0 +2007 ctx-rh-FDm 13 201 111 0 +2008 ctx-rh-FDp 69 168 123 0 +2009 ctx-rh-FE 27 178 138 0 +2010 ctx-rh-FF 49 172 192 0 +2011 ctx-rh-FG 61 127 118 0 +2012 ctx-rh-FH 77 135 106 0 +2013 ctx-rh-FL 80 145 146 0 +2014 ctx-rh-H 41 55 101 0 +2015 ctx-rh-IA 204 61 211 0 +2016 ctx-rh-IB 137 67 135 0 +2017 ctx-rh-LA 124 215 246 0 +2018 ctx-rh-LC1 0 133 185 0 +2019 ctx-rh-LC2 68 165 227 0 +2020 ctx-rh-LE 169 219 224 0 +2021 ctx-rh-unknown 50 50 50 0 +2022 ctx-rh-OA 253 252 187 0 +2023 ctx-rh-OB 251 250 146 0 +2024 ctx-rh-OC 247 222 71 0 +2025 ctx-rh-PB 247 67 148 0 +2026 ctx-rh-PC 239 87 150 0 +2027 ctx-rh-PEm 248 167 210 0 +2028 ctx-rh-PEp 250 150 200 0 +2029 ctx-rh-PF 250 180 224 0 +2030 ctx-rh-PFD 255 190 200 0 +2031 ctx-rh-PG 248 193 224 0 +2032 ctx-rh-PH 232 73 130 0 +2033 ctx-rh-TA 240 85 102 0 +2034 ctx-rh-TB 233 65 98 0 +2035 ctx-rh-TE1 235 181 136 0 +2036 ctx-rh-TE2 204 140 82 0 +2037 ctx-rh-TF 184 47 79 0 +2038 ctx-rh-TG 247 198 127 0 diff --git a/bin/unix/3.1.2/templates/BB50human/ROIs_BB50human.txt b/bin/unix/3.1.2/templates/BB50human/ROIs_BB50human.txt new file mode 100755 index 0000000..b0b12ea --- /dev/null +++ b/bin/unix/3.1.2/templates/BB50human/ROIs_BB50human.txt @@ -0,0 +1,78 @@ +1000 +1001 +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +2000 +2001 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 diff --git a/bin/unix/3.1.2/templates/BB50human/lh.BB50human.gcs b/bin/unix/3.1.2/templates/BB50human/lh.BB50human.gcs new file mode 100755 index 0000000..bbd6c51 Binary files /dev/null and b/bin/unix/3.1.2/templates/BB50human/lh.BB50human.gcs differ diff --git a/bin/unix/3.1.2/templates/BB50human/parcellate_BB50human.sh b/bin/unix/3.1.2/templates/BB50human/parcellate_BB50human.sh new file mode 100755 index 0000000..027e488 --- /dev/null +++ b/bin/unix/3.1.2/templates/BB50human/parcellate_BB50human.sh @@ -0,0 +1,105 @@ +#!/bin/bash +# +# Parcellate BB50human atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=BB50human + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/unix/3.1.2/templates/BB50human/rh.BB50human.gcs b/bin/unix/3.1.2/templates/BB50human/rh.BB50human.gcs new file mode 100755 index 0000000..98ba293 Binary files /dev/null and b/bin/unix/3.1.2/templates/BB50human/rh.BB50human.gcs differ diff --git a/bin/unix/3.1.2/templates/aparc/ROIs_aparc.txt b/bin/unix/3.1.2/templates/aparc/ROIs_aparc.txt new file mode 100755 index 0000000..7e3d0d7 --- /dev/null +++ b/bin/unix/3.1.2/templates/aparc/ROIs_aparc.txt @@ -0,0 +1,82 @@ +10 +11 +12 +13 +17 +18 +26 +49 +50 +51 +52 +53 +54 +58 +1001 +1002 +1003 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +2001 +2002 +2003 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 diff --git a/bin/unix/3.1.2/templates/aparc/aparc.annot.ctab b/bin/unix/3.1.2/templates/aparc/aparc.annot.ctab new file mode 100755 index 0000000..cc1ad96 --- /dev/null +++ b/bin/unix/3.1.2/templates/aparc/aparc.annot.ctab @@ -0,0 +1,1159 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-bankssts 25 100 40 0 +1002 ctx-lh-caudalanteriorcingulate 125 100 160 0 +1003 ctx-lh-caudalmiddlefrontal 100 25 0 0 +1004 ctx-lh-corpuscallosum 120 70 50 0 +1005 ctx-lh-cuneus 220 20 100 0 +1006 ctx-lh-entorhinal 220 20 10 0 +1007 ctx-lh-fusiform 180 220 140 0 +1008 ctx-lh-inferiorparietal 220 60 220 0 +1009 ctx-lh-inferiortemporal 180 40 120 0 +1010 ctx-lh-isthmuscingulate 140 20 140 0 +1011 ctx-lh-lateraloccipital 20 30 140 0 +1012 ctx-lh-lateralorbitofrontal 35 75 50 0 +1013 ctx-lh-lingual 225 140 140 0 +1014 ctx-lh-medialorbitofrontal 200 35 75 0 +1015 ctx-lh-middletemporal 160 100 50 0 +1016 ctx-lh-parahippocampal 20 220 60 0 +1017 ctx-lh-paracentral 60 220 60 0 +1018 ctx-lh-parsopercularis 220 180 140 0 +1019 ctx-lh-parsorbitalis 20 100 50 0 +1020 ctx-lh-parstriangularis 220 60 20 0 +1021 ctx-lh-pericalcarine 120 100 60 0 +1022 ctx-lh-postcentral 220 20 20 0 +1023 ctx-lh-posteriorcingulate 220 180 220 0 +1024 ctx-lh-precentral 60 20 220 0 +1025 ctx-lh-precuneus 160 140 180 0 +1026 ctx-lh-rostralanteriorcingulate 80 20 140 0 +1027 ctx-lh-rostralmiddlefrontal 75 50 125 0 +1028 ctx-lh-superiorfrontal 20 220 160 0 +1029 ctx-lh-superiorparietal 20 180 140 0 +1030 ctx-lh-superiortemporal 140 220 220 0 +1031 ctx-lh-supramarginal 80 160 20 0 +1032 ctx-lh-frontalpole 100 0 100 0 +1033 ctx-lh-temporalpole 70 70 70 0 +1034 ctx-lh-transversetemporal 150 150 200 0 +1035 ctx-lh-insula 255 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-bankssts 25 100 40 0 +2002 ctx-rh-caudalanteriorcingulate 125 100 160 0 +2003 ctx-rh-caudalmiddlefrontal 100 25 0 0 +2004 ctx-rh-corpuscallosum 120 70 50 0 +2005 ctx-rh-cuneus 220 20 100 0 +2006 ctx-rh-entorhinal 220 20 10 0 +2007 ctx-rh-fusiform 180 220 140 0 +2008 ctx-rh-inferiorparietal 220 60 220 0 +2009 ctx-rh-inferiortemporal 180 40 120 0 +2010 ctx-rh-isthmuscingulate 140 20 140 0 +2011 ctx-rh-lateraloccipital 20 30 140 0 +2012 ctx-rh-lateralorbitofrontal 35 75 50 0 +2013 ctx-rh-lingual 225 140 140 0 +2014 ctx-rh-medialorbitofrontal 200 35 75 0 +2015 ctx-rh-middletemporal 160 100 50 0 +2016 ctx-rh-parahippocampal 20 220 60 0 +2017 ctx-rh-paracentral 60 220 60 0 +2018 ctx-rh-parsopercularis 220 180 140 0 +2019 ctx-rh-parsorbitalis 20 100 50 0 +2020 ctx-rh-parstriangularis 220 60 20 0 +2021 ctx-rh-pericalcarine 120 100 60 0 +2022 ctx-rh-postcentral 220 20 20 0 +2023 ctx-rh-posteriorcingulate 220 180 220 0 +2024 ctx-rh-precentral 60 20 220 0 +2025 ctx-rh-precuneus 160 140 180 0 +2026 ctx-rh-rostralanteriorcingulate 80 20 140 0 +2027 ctx-rh-rostralmiddlefrontal 75 50 125 0 +2028 ctx-rh-superiorfrontal 20 220 160 0 +2029 ctx-rh-superiorparietal 20 180 140 0 +2030 ctx-rh-superiortemporal 140 220 220 0 +2031 ctx-rh-supramarginal 80 160 20 0 +2032 ctx-rh-frontalpole 100 0 100 0 +2033 ctx-rh-temporalpole 70 70 70 0 +2034 ctx-rh-transversetemporal 150 150 200 0 +2035 ctx-rh-insula 255 192 32 0 +3000 wm-lh-unknown 230 250 230 0 +3001 wm-lh-bankssts 230 155 215 0 +3002 wm-lh-caudalanteriorcingulate 130 155 95 0 +3003 wm-lh-caudalmiddlefrontal 155 230 255 0 +3004 wm-lh-corpuscallosum 135 185 205 0 +3005 wm-lh-cuneus 35 235 155 0 +3006 wm-lh-entorhinal 35 235 245 0 +3007 wm-lh-fusiform 75 35 115 0 +3008 wm-lh-inferiorparietal 35 195 35 0 +3009 wm-lh-inferiortemporal 75 215 135 0 +3010 wm-lh-isthmuscingulate 115 235 115 0 +3011 wm-lh-lateraloccipital 235 225 115 0 +3012 wm-lh-lateralorbitofrontal 220 180 205 0 +3013 wm-lh-lingual 30 115 115 0 +3014 wm-lh-medialorbitofrontal 55 220 180 0 +3015 wm-lh-middletemporal 95 155 205 0 +3016 wm-lh-parahippocampal 235 35 195 0 +3017 wm-lh-paracentral 195 35 195 0 +3018 wm-lh-parsopercularis 35 75 115 0 +3019 wm-lh-parsorbitalis 235 155 205 0 +3020 wm-lh-parstriangularis 35 195 235 0 +3021 wm-lh-pericalcarine 135 155 195 0 +3022 wm-lh-postcentral 35 235 235 0 +3023 wm-lh-posteriorcingulate 35 75 35 0 +3024 wm-lh-precentral 195 235 35 0 +3025 wm-lh-precuneus 95 115 75 0 +3026 wm-lh-rostralanteriorcingulate 175 235 115 0 +3027 wm-lh-rostralmiddlefrontal 180 205 130 0 +3028 wm-lh-superiorfrontal 235 35 95 0 +3029 wm-lh-superiorparietal 235 75 115 0 +3030 wm-lh-superiortemporal 115 35 35 0 +3031 wm-lh-supramarginal 175 95 235 0 +3032 wm-lh-frontalpole 155 255 155 0 +3033 wm-lh-temporalpole 185 185 185 0 +3034 wm-lh-transversetemporal 105 105 55 0 +3035 wm-lh-insula 254 191 31 0 +4000 wm-rh-unknown 230 250 230 0 +4001 wm-rh-bankssts 230 155 215 0 +4002 wm-rh-caudalanteriorcingulate 130 155 95 0 +4003 wm-rh-caudalmiddlefrontal 155 230 255 0 +4004 wm-rh-corpuscallosum 135 185 205 0 +4005 wm-rh-cuneus 35 235 155 0 +4006 wm-rh-entorhinal 35 235 245 0 +4007 wm-rh-fusiform 75 35 115 0 +4008 wm-rh-inferiorparietal 35 195 35 0 +4009 wm-rh-inferiortemporal 75 215 135 0 +4010 wm-rh-isthmuscingulate 115 235 115 0 +4011 wm-rh-lateraloccipital 235 225 115 0 +4012 wm-rh-lateralorbitofrontal 220 180 205 0 +4013 wm-rh-lingual 30 115 115 0 +4014 wm-rh-medialorbitofrontal 55 220 180 0 +4015 wm-rh-middletemporal 95 155 205 0 +4016 wm-rh-parahippocampal 235 35 195 0 +4017 wm-rh-paracentral 195 35 195 0 +4018 wm-rh-parsopercularis 35 75 115 0 +4019 wm-rh-parsorbitalis 235 155 205 0 +4020 wm-rh-parstriangularis 35 195 235 0 +4021 wm-rh-pericalcarine 135 155 195 0 +4022 wm-rh-postcentral 35 235 235 0 +4023 wm-rh-posteriorcingulate 35 75 35 0 +4024 wm-rh-precentral 195 235 35 0 +4025 wm-rh-precuneus 95 115 75 0 +4026 wm-rh-rostralanteriorcingulate 175 235 115 0 +4027 wm-rh-rostralmiddlefrontal 180 205 130 0 +4028 wm-rh-superiorfrontal 235 35 95 0 +4029 wm-rh-superiorparietal 235 75 115 0 +4030 wm-rh-superiortemporal 115 35 35 0 +4031 wm-rh-supramarginal 175 95 235 0 +4032 wm-rh-frontalpole 155 255 155 0 +4033 wm-rh-temporalpole 185 185 185 0 +4034 wm-rh-transversetemporal 105 105 55 0 +4035 wm-rh-insula 254 191 31 0 +1100 ctx-lh-Unknown 0 0 0 0 +1101 ctx-lh-Corpus_callosum 50 50 50 0 +1102 ctx-lh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +1103 ctx-lh-G_cingulate-Isthmus 60 25 25 0 +1104 ctx-lh-G_cingulate-Main_part 25 60 60 0 +1200 ctx-lh-G_cingulate-caudal_ACC 25 60 61 0 +1201 ctx-lh-G_cingulate-rostral_ACC 25 90 60 0 +1202 ctx-lh-G_cingulate-posterior 25 120 60 0 +1205 ctx-lh-S_cingulate-caudal_ACC 25 150 60 0 +1206 ctx-lh-S_cingulate-rostral_ACC 25 180 60 0 +1207 ctx-lh-S_cingulate-posterior 25 210 60 0 +1210 ctx-lh-S_pericallosal-caudal 25 150 90 0 +1211 ctx-lh-S_pericallosal-rostral 25 180 90 0 +1212 ctx-lh-S_pericallosal-posterior 25 210 90 0 +1105 ctx-lh-G_cuneus 180 20 20 0 +1106 ctx-lh-G_frontal_inf-Opercular_part 220 20 100 0 +1107 ctx-lh-G_frontal_inf-Orbital_part 140 60 60 0 +1108 ctx-lh-G_frontal_inf-Triangular_part 180 220 140 0 +1109 ctx-lh-G_frontal_middle 140 100 180 0 +1110 ctx-lh-G_frontal_superior 180 20 140 0 +1111 ctx-lh-G_frontomarginal 140 20 140 0 +1112 ctx-lh-G_insular_long 21 10 10 0 +1113 ctx-lh-G_insular_short 225 140 140 0 +1114 ctx-lh-G_and_S_occipital_inferior 23 60 180 0 +1115 ctx-lh-G_occipital_middle 180 60 180 0 +1116 ctx-lh-G_occipital_superior 20 220 60 0 +1117 ctx-lh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +1118 ctx-lh-G_occipit-temp_med-Lingual_part 220 180 140 0 +1119 ctx-lh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +1120 ctx-lh-G_orbital 220 60 20 0 +1121 ctx-lh-G_paracentral 60 100 60 0 +1122 ctx-lh-G_parietal_inferior-Angular_part 20 60 220 0 +1123 ctx-lh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +1124 ctx-lh-G_parietal_superior 220 180 220 0 +1125 ctx-lh-G_postcentral 20 180 140 0 +1126 ctx-lh-G_precentral 60 140 180 0 +1127 ctx-lh-G_precuneus 25 20 140 0 +1128 ctx-lh-G_rectus 20 60 100 0 +1129 ctx-lh-G_subcallosal 60 220 20 0 +1130 ctx-lh-G_subcentral 60 20 220 0 +1131 ctx-lh-G_temporal_inferior 220 220 100 0 +1132 ctx-lh-G_temporal_middle 180 60 60 0 +1133 ctx-lh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +1134 ctx-lh-G_temp_sup-Lateral_aspect 220 60 220 0 +1135 ctx-lh-G_temp_sup-Planum_polare 65 220 60 0 +1136 ctx-lh-G_temp_sup-Planum_tempolare 25 140 20 0 +1137 ctx-lh-G_and_S_transverse_frontopolar 13 0 250 0 +1138 ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +1139 ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +1140 ctx-lh-Lat_Fissure-post_sgt 61 60 100 0 +1141 ctx-lh-Medial_wall 25 25 25 0 +1142 ctx-lh-Pole_occipital 140 20 60 0 +1143 ctx-lh-Pole_temporal 220 180 20 0 +1144 ctx-lh-S_calcarine 63 180 180 0 +1145 ctx-lh-S_central 221 20 10 0 +1146 ctx-lh-S_central_insula 21 220 20 0 +1147 ctx-lh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +1148 ctx-lh-S_cingulate-Marginalis_part 221 20 100 0 +1149 ctx-lh-S_circular_insula_anterior 221 60 140 0 +1150 ctx-lh-S_circular_insula_inferior 221 20 220 0 +1151 ctx-lh-S_circular_insula_superior 61 220 220 0 +1152 ctx-lh-S_collateral_transverse_ant 100 200 200 0 +1153 ctx-lh-S_collateral_transverse_post 10 200 200 0 +1154 ctx-lh-S_frontal_inferior 221 220 20 0 +1155 ctx-lh-S_frontal_middle 141 20 100 0 +1156 ctx-lh-S_frontal_superior 61 220 100 0 +1157 ctx-lh-S_frontomarginal 21 220 60 0 +1158 ctx-lh-S_intermedius_primus-Jensen 141 60 20 0 +1159 ctx-lh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +1160 ctx-lh-S_occipital_anterior 61 20 180 0 +1161 ctx-lh-S_occipital_middle_and_Lunatus 101 60 220 0 +1162 ctx-lh-S_occipital_superior_and_transversalis 21 20 140 0 +1163 ctx-lh-S_occipito-temporal_lateral 221 140 20 0 +1164 ctx-lh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +1165 ctx-lh-S_orbital-H_shapped 101 20 20 0 +1166 ctx-lh-S_orbital_lateral 221 100 20 0 +1167 ctx-lh-S_orbital_medial-Or_olfactory 181 200 20 0 +1168 ctx-lh-S_paracentral 21 180 140 0 +1169 ctx-lh-S_parieto_occipital 101 100 180 0 +1170 ctx-lh-S_pericallosal 181 220 20 0 +1171 ctx-lh-S_postcentral 21 140 200 0 +1172 ctx-lh-S_precentral-Inferior-part 21 20 240 0 +1173 ctx-lh-S_precentral-Superior-part 21 20 200 0 +1174 ctx-lh-S_subcentral_ant 61 180 60 0 +1175 ctx-lh-S_subcentral_post 61 180 250 0 +1176 ctx-lh-S_suborbital 21 20 60 0 +1177 ctx-lh-S_subparietal 101 60 60 0 +1178 ctx-lh-S_supracingulate 21 220 220 0 +1179 ctx-lh-S_temporal_inferior 21 180 180 0 +1180 ctx-lh-S_temporal_superior 223 220 60 0 +1181 ctx-lh-S_temporal_transverse 221 60 60 0 +2100 ctx-rh-Unknown 0 0 0 0 +2101 ctx-rh-Corpus_callosum 50 50 50 0 +2102 ctx-rh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +2103 ctx-rh-G_cingulate-Isthmus 60 25 25 0 +2104 ctx-rh-G_cingulate-Main_part 25 60 60 0 +2105 ctx-rh-G_cuneus 180 20 20 0 +2106 ctx-rh-G_frontal_inf-Opercular_part 220 20 100 0 +2107 ctx-rh-G_frontal_inf-Orbital_part 140 60 60 0 +2108 ctx-rh-G_frontal_inf-Triangular_part 180 220 140 0 +2109 ctx-rh-G_frontal_middle 140 100 180 0 +2110 ctx-rh-G_frontal_superior 180 20 140 0 +2111 ctx-rh-G_frontomarginal 140 20 140 0 +2112 ctx-rh-G_insular_long 21 10 10 0 +2113 ctx-rh-G_insular_short 225 140 140 0 +2114 ctx-rh-G_and_S_occipital_inferior 23 60 180 0 +2115 ctx-rh-G_occipital_middle 180 60 180 0 +2116 ctx-rh-G_occipital_superior 20 220 60 0 +2117 ctx-rh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +2118 ctx-rh-G_occipit-temp_med-Lingual_part 220 180 140 0 +2119 ctx-rh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +2120 ctx-rh-G_orbital 220 60 20 0 +2121 ctx-rh-G_paracentral 60 100 60 0 +2122 ctx-rh-G_parietal_inferior-Angular_part 20 60 220 0 +2123 ctx-rh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +2124 ctx-rh-G_parietal_superior 220 180 220 0 +2125 ctx-rh-G_postcentral 20 180 140 0 +2126 ctx-rh-G_precentral 60 140 180 0 +2127 ctx-rh-G_precuneus 25 20 140 0 +2128 ctx-rh-G_rectus 20 60 100 0 +2129 ctx-rh-G_subcallosal 60 220 20 0 +2130 ctx-rh-G_subcentral 60 20 220 0 +2131 ctx-rh-G_temporal_inferior 220 220 100 0 +2132 ctx-rh-G_temporal_middle 180 60 60 0 +2133 ctx-rh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +2134 ctx-rh-G_temp_sup-Lateral_aspect 220 60 220 0 +2135 ctx-rh-G_temp_sup-Planum_polare 65 220 60 0 +2136 ctx-rh-G_temp_sup-Planum_tempolare 25 140 20 0 +2137 ctx-rh-G_and_S_transverse_frontopolar 13 0 250 0 +2138 ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +2139 ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +2140 ctx-rh-Lat_Fissure-post_sgt 61 60 100 0 +2141 ctx-rh-Medial_wall 25 25 25 0 +2142 ctx-rh-Pole_occipital 140 20 60 0 +2143 ctx-rh-Pole_temporal 220 180 20 0 +2144 ctx-rh-S_calcarine 63 180 180 0 +2145 ctx-rh-S_central 221 20 10 0 +2146 ctx-rh-S_central_insula 21 220 20 0 +2147 ctx-rh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +2148 ctx-rh-S_cingulate-Marginalis_part 221 20 100 0 +2149 ctx-rh-S_circular_insula_anterior 221 60 140 0 +2150 ctx-rh-S_circular_insula_inferior 221 20 220 0 +2151 ctx-rh-S_circular_insula_superior 61 220 220 0 +2152 ctx-rh-S_collateral_transverse_ant 100 200 200 0 +2153 ctx-rh-S_collateral_transverse_post 10 200 200 0 +2154 ctx-rh-S_frontal_inferior 221 220 20 0 +2155 ctx-rh-S_frontal_middle 141 20 100 0 +2156 ctx-rh-S_frontal_superior 61 220 100 0 +2157 ctx-rh-S_frontomarginal 21 220 60 0 +2158 ctx-rh-S_intermedius_primus-Jensen 141 60 20 0 +2159 ctx-rh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +2160 ctx-rh-S_occipital_anterior 61 20 180 0 +2161 ctx-rh-S_occipital_middle_and_Lunatus 101 60 220 0 +2162 ctx-rh-S_occipital_superior_and_transversalis 21 20 140 0 +2163 ctx-rh-S_occipito-temporal_lateral 221 140 20 0 +2164 ctx-rh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +2165 ctx-rh-S_orbital-H_shapped 101 20 20 0 +2166 ctx-rh-S_orbital_lateral 221 100 20 0 +2167 ctx-rh-S_orbital_medial-Or_olfactory 181 200 20 0 +2168 ctx-rh-S_paracentral 21 180 140 0 +2169 ctx-rh-S_parieto_occipital 101 100 180 0 +2170 ctx-rh-S_pericallosal 181 220 20 0 +2171 ctx-rh-S_postcentral 21 140 200 0 +2172 ctx-rh-S_precentral-Inferior-part 21 20 240 0 +2173 ctx-rh-S_precentral-Superior-part 21 20 200 0 +2174 ctx-rh-S_subcentral_ant 61 180 60 0 +2175 ctx-rh-S_subcentral_post 61 180 250 0 +2176 ctx-rh-S_suborbital 21 20 60 0 +2177 ctx-rh-S_subparietal 101 60 60 0 +2178 ctx-rh-S_supracingulate 21 220 220 0 +2179 ctx-rh-S_temporal_inferior 21 180 180 0 +2180 ctx-rh-S_temporal_superior 223 220 60 0 +2181 ctx-rh-S_temporal_transverse 221 60 60 0 +2200 ctx-rh-G_cingulate-caudal_ACC 25 60 61 0 +2201 ctx-rh-G_cingulate-rostral_ACC 25 90 60 0 +2202 ctx-rh-G_cingulate-posterior 25 120 60 0 +2205 ctx-rh-S_cingulate-caudal_ACC 25 150 60 0 +2206 ctx-rh-S_cingulate-rostral_ACC 25 180 60 0 +2207 ctx-rh-S_cingulate-posterior 25 210 60 0 +2210 ctx-rh-S_pericallosal-caudal 25 150 90 0 +2211 ctx-rh-S_pericallosal-rostral 25 180 90 0 +2212 ctx-rh-S_pericallosal-posterior 25 210 90 0 +3100 wm-lh-Unknown 0 0 0 0 +3101 wm-lh-Corpus_callosum 50 50 50 0 +3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +3103 wm-lh-G_cingulate-Isthmus 60 25 25 0 +3104 wm-lh-G_cingulate-Main_part 25 60 60 0 +3105 wm-lh-G_cuneus 180 20 20 0 +3106 wm-lh-G_frontal_inf-Opercular_part 220 20 100 0 +3107 wm-lh-G_frontal_inf-Orbital_part 140 60 60 0 +3108 wm-lh-G_frontal_inf-Triangular_part 180 220 140 0 +3109 wm-lh-G_frontal_middle 140 100 180 0 +3110 wm-lh-G_frontal_superior 180 20 140 0 +3111 wm-lh-G_frontomarginal 140 20 140 0 +3112 wm-lh-G_insular_long 21 10 10 0 +3113 wm-lh-G_insular_short 225 140 140 0 +3114 wm-lh-G_and_S_occipital_inferior 23 60 180 0 +3115 wm-lh-G_occipital_middle 180 60 180 0 +3116 wm-lh-G_occipital_superior 20 220 60 0 +3117 wm-lh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +3118 wm-lh-G_occipit-temp_med-Lingual_part 220 180 140 0 +3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +3120 wm-lh-G_orbital 220 60 20 0 +3121 wm-lh-G_paracentral 60 100 60 0 +3122 wm-lh-G_parietal_inferior-Angular_part 20 60 220 0 +3123 wm-lh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +3124 wm-lh-G_parietal_superior 220 180 220 0 +3125 wm-lh-G_postcentral 20 180 140 0 +3126 wm-lh-G_precentral 60 140 180 0 +3127 wm-lh-G_precuneus 25 20 140 0 +3128 wm-lh-G_rectus 20 60 100 0 +3129 wm-lh-G_subcallosal 60 220 20 0 +3130 wm-lh-G_subcentral 60 20 220 0 +3131 wm-lh-G_temporal_inferior 220 220 100 0 +3132 wm-lh-G_temporal_middle 180 60 60 0 +3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +3134 wm-lh-G_temp_sup-Lateral_aspect 220 60 220 0 +3135 wm-lh-G_temp_sup-Planum_polare 65 220 60 0 +3136 wm-lh-G_temp_sup-Planum_tempolare 25 140 20 0 +3137 wm-lh-G_and_S_transverse_frontopolar 13 0 250 0 +3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +3140 wm-lh-Lat_Fissure-post_sgt 61 60 100 0 +3141 wm-lh-Medial_wall 25 25 25 0 +3142 wm-lh-Pole_occipital 140 20 60 0 +3143 wm-lh-Pole_temporal 220 180 20 0 +3144 wm-lh-S_calcarine 63 180 180 0 +3145 wm-lh-S_central 221 20 10 0 +3146 wm-lh-S_central_insula 21 220 20 0 +3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +3148 wm-lh-S_cingulate-Marginalis_part 221 20 100 0 +3149 wm-lh-S_circular_insula_anterior 221 60 140 0 +3150 wm-lh-S_circular_insula_inferior 221 20 220 0 +3151 wm-lh-S_circular_insula_superior 61 220 220 0 +3152 wm-lh-S_collateral_transverse_ant 100 200 200 0 +3153 wm-lh-S_collateral_transverse_post 10 200 200 0 +3154 wm-lh-S_frontal_inferior 221 220 20 0 +3155 wm-lh-S_frontal_middle 141 20 100 0 +3156 wm-lh-S_frontal_superior 61 220 100 0 +3157 wm-lh-S_frontomarginal 21 220 60 0 +3158 wm-lh-S_intermedius_primus-Jensen 141 60 20 0 +3159 wm-lh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +3160 wm-lh-S_occipital_anterior 61 20 180 0 +3161 wm-lh-S_occipital_middle_and_Lunatus 101 60 220 0 +3162 wm-lh-S_occipital_superior_and_transversalis 21 20 140 0 +3163 wm-lh-S_occipito-temporal_lateral 221 140 20 0 +3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +3165 wm-lh-S_orbital-H_shapped 101 20 20 0 +3166 wm-lh-S_orbital_lateral 221 100 20 0 +3167 wm-lh-S_orbital_medial-Or_olfactory 181 200 20 0 +3168 wm-lh-S_paracentral 21 180 140 0 +3169 wm-lh-S_parieto_occipital 101 100 180 0 +3170 wm-lh-S_pericallosal 181 220 20 0 +3171 wm-lh-S_postcentral 21 140 200 0 +3172 wm-lh-S_precentral-Inferior-part 21 20 240 0 +3173 wm-lh-S_precentral-Superior-part 21 20 200 0 +3174 wm-lh-S_subcentral_ant 61 180 60 0 +3175 wm-lh-S_subcentral_post 61 180 250 0 +3176 wm-lh-S_suborbital 21 20 60 0 +3177 wm-lh-S_subparietal 101 60 60 0 +3178 wm-lh-S_supracingulate 21 220 220 0 +3179 wm-lh-S_temporal_inferior 21 180 180 0 +3180 wm-lh-S_temporal_superior 223 220 60 0 +3181 wm-lh-S_temporal_transverse 221 60 60 0 +4100 wm-rh-Unknown 0 0 0 0 +4101 wm-rh-Corpus_callosum 50 50 50 0 +4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 180 20 30 0 +4103 wm-rh-G_cingulate-Isthmus 60 25 25 0 +4104 wm-rh-G_cingulate-Main_part 25 60 60 0 +4105 wm-rh-G_cuneus 180 20 20 0 +4106 wm-rh-G_frontal_inf-Opercular_part 220 20 100 0 +4107 wm-rh-G_frontal_inf-Orbital_part 140 60 60 0 +4108 wm-rh-G_frontal_inf-Triangular_part 180 220 140 0 +4109 wm-rh-G_frontal_middle 140 100 180 0 +4110 wm-rh-G_frontal_superior 180 20 140 0 +4111 wm-rh-G_frontomarginal 140 20 140 0 +4112 wm-rh-G_insular_long 21 10 10 0 +4113 wm-rh-G_insular_short 225 140 140 0 +4114 wm-rh-G_and_S_occipital_inferior 23 60 180 0 +4115 wm-rh-G_occipital_middle 180 60 180 0 +4116 wm-rh-G_occipital_superior 20 220 60 0 +4117 wm-rh-G_occipit-temp_lat-Or_fusiform 60 20 140 0 +4118 wm-rh-G_occipit-temp_med-Lingual_part 220 180 140 0 +4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 65 100 20 0 +4120 wm-rh-G_orbital 220 60 20 0 +4121 wm-rh-G_paracentral 60 100 60 0 +4122 wm-rh-G_parietal_inferior-Angular_part 20 60 220 0 +4123 wm-rh-G_parietal_inferior-Supramarginal_part 100 100 60 0 +4124 wm-rh-G_parietal_superior 220 180 220 0 +4125 wm-rh-G_postcentral 20 180 140 0 +4126 wm-rh-G_precentral 60 140 180 0 +4127 wm-rh-G_precuneus 25 20 140 0 +4128 wm-rh-G_rectus 20 60 100 0 +4129 wm-rh-G_subcallosal 60 220 20 0 +4130 wm-rh-G_subcentral 60 20 220 0 +4131 wm-rh-G_temporal_inferior 220 220 100 0 +4132 wm-rh-G_temporal_middle 180 60 60 0 +4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 60 60 220 0 +4134 wm-rh-G_temp_sup-Lateral_aspect 220 60 220 0 +4135 wm-rh-G_temp_sup-Planum_polare 65 220 60 0 +4136 wm-rh-G_temp_sup-Planum_tempolare 25 140 20 0 +4137 wm-rh-G_and_S_transverse_frontopolar 13 0 250 0 +4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 61 20 220 0 +4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 61 20 60 0 +4140 wm-rh-Lat_Fissure-post_sgt 61 60 100 0 +4141 wm-rh-Medial_wall 25 25 25 0 +4142 wm-rh-Pole_occipital 140 20 60 0 +4143 wm-rh-Pole_temporal 220 180 20 0 +4144 wm-rh-S_calcarine 63 180 180 0 +4145 wm-rh-S_central 221 20 10 0 +4146 wm-rh-S_central_insula 21 220 20 0 +4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 183 100 20 0 +4148 wm-rh-S_cingulate-Marginalis_part 221 20 100 0 +4149 wm-rh-S_circular_insula_anterior 221 60 140 0 +4150 wm-rh-S_circular_insula_inferior 221 20 220 0 +4151 wm-rh-S_circular_insula_superior 61 220 220 0 +4152 wm-rh-S_collateral_transverse_ant 100 200 200 0 +4153 wm-rh-S_collateral_transverse_post 10 200 200 0 +4154 wm-rh-S_frontal_inferior 221 220 20 0 +4155 wm-rh-S_frontal_middle 141 20 100 0 +4156 wm-rh-S_frontal_superior 61 220 100 0 +4157 wm-rh-S_frontomarginal 21 220 60 0 +4158 wm-rh-S_intermedius_primus-Jensen 141 60 20 0 +4159 wm-rh-S_intraparietal-and_Parietal_transverse 143 20 220 0 +4160 wm-rh-S_occipital_anterior 61 20 180 0 +4161 wm-rh-S_occipital_middle_and_Lunatus 101 60 220 0 +4162 wm-rh-S_occipital_superior_and_transversalis 21 20 140 0 +4163 wm-rh-S_occipito-temporal_lateral 221 140 20 0 +4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 141 100 220 0 +4165 wm-rh-S_orbital-H_shapped 101 20 20 0 +4166 wm-rh-S_orbital_lateral 221 100 20 0 +4167 wm-rh-S_orbital_medial-Or_olfactory 181 200 20 0 +4168 wm-rh-S_paracentral 21 180 140 0 +4169 wm-rh-S_parieto_occipital 101 100 180 0 +4170 wm-rh-S_pericallosal 181 220 20 0 +4171 wm-rh-S_postcentral 21 140 200 0 +4172 wm-rh-S_precentral-Inferior-part 21 20 240 0 +4173 wm-rh-S_precentral-Superior-part 21 20 200 0 +4174 wm-rh-S_subcentral_ant 61 180 60 0 +4175 wm-rh-S_subcentral_post 61 180 250 0 +4176 wm-rh-S_suborbital 21 20 60 0 +4177 wm-rh-S_subparietal 101 60 60 0 +4178 wm-rh-S_supracingulate 21 220 220 0 +4179 wm-rh-S_temporal_inferior 21 180 180 0 +4180 wm-rh-S_temporal_superior 223 220 60 0 +4181 wm-rh-S_temporal_transverse 221 60 60 0 +5001 Left-UnsegmentedWhiteMatter 20 30 40 0 +5002 Right-UnsegmentedWhiteMatter 20 30 40 0 +5100 fmajor 204 102 102 0 +5101 fminor 204 102 102 0 +5102 lh.atr 255 255 102 0 +5103 lh.cab 153 204 0 0 +5104 lh.ccg 0 153 153 0 +5105 lh.cst 204 153 255 0 +5106 lh.ilf 255 153 51 0 +5107 lh.slfp 204 204 204 0 +5108 lh.slft 153 255 255 0 +5109 lh.unc 102 153 255 0 +5110 rh.atr 255 255 102 0 +5111 rh.cab 153 204 0 0 +5112 rh.ccg 0 153 153 0 +5113 rh.cst 204 153 255 0 +5114 rh.ilf 255 153 51 0 +5115 rh.slfp 204 204 204 0 +5116 rh.slft 153 255 255 0 +5117 rh.unc 102 153 255 0 +6000 CST-orig 0 255 0 0 +6001 CST-hammer 255 255 0 0 +6002 CST-CVS 0 255 255 0 +6003 CST-flirt 0 0 255 0 +6010 Left-SLF1 236 16 231 0 +6020 Right-SLF1 237 18 232 0 +6030 Left-SLF3 236 13 227 0 +6040 Right-SLF3 236 17 228 0 +6050 Left-CST 1 255 1 0 +6060 Right-CST 2 255 1 0 +6070 Left-SLF2 236 14 230 0 +6080 Right-SLF2 237 14 230 0 +7001 Lateral-nucleus 72 132 181 0 +7002 Basolateral-nucleus 243 243 243 0 +7003 Basal-nucleus 207 63 79 0 +7004 Centromedial-nucleus 121 20 135 0 +7005 Central-nucleus 197 60 248 0 +7006 Medial-nucleus 2 149 2 0 +7007 Cortical-nucleus 221 249 166 0 +7008 Accessory-Basal-nucleus 232 146 35 0 +7009 Corticoamygdaloid-transitio 20 60 120 0 +7010 Anterior-amygdaloid-area-AAA 250 250 0 0 +7011 Fusion-amygdala-HP-FAH 122 187 222 0 +7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 +7013 Endopiriform-nucleus 10 49 255 0 +7014 Lateral-nucleus-olfactory-tract 205 184 144 0 +7015 Paralaminar-nucleus 45 205 165 0 +7016 Intercalated-nucleus 117 160 175 0 +7017 Prepiriform-cortex 221 217 21 0 +7018 Periamygdaloid-cortex 20 60 120 0 +7019 Envelope-Amygdala 141 21 100 0 +7020 Extranuclear-Amydala 225 140 141 0 +7100 Brainstem-inferior-colliculus 42 201 168 0 +7101 Brainstem-cochlear-nucleus 168 104 162 0 +8001 Thalamus-Anterior 74 130 181 0 +8002 Thalamus-Ventral-anterior 242 241 240 0 +8003 Thalamus-Lateral-dorsal 206 65 78 0 +8004 Thalamus-Lateral-posterior 120 21 133 0 +8005 Thalamus-Ventral-lateral 195 61 246 0 +8006 Thalamus-Ventral-posterior-medial 3 147 6 0 +8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 +8008 Thalamus-intralaminar 232 146 33 0 +8009 Thalamus-centromedian 4 114 14 0 +8010 Thalamus-mediodorsal 121 184 220 0 +8011 Thalamus-medial 235 11 175 0 +8012 Thalamus-pulvinar 12 46 250 0 +8013 Thalamus-lateral-geniculate 203 182 143 0 +8014 Thalamus-medial-geniculate 42 204 167 0 +11100 ctx_lh_Unknown 0 0 0 0 +11101 ctx_lh_G_and_S_frontomargin 23 220 60 0 +11102 ctx_lh_G_and_S_occipital_inf 23 60 180 0 +11103 ctx_lh_G_and_S_paracentral 63 100 60 0 +11104 ctx_lh_G_and_S_subcentral 63 20 220 0 +11105 ctx_lh_G_and_S_transv_frontopol 13 0 250 0 +11106 ctx_lh_G_and_S_cingul-Ant 26 60 0 0 +11107 ctx_lh_G_and_S_cingul-Mid-Ant 26 60 75 0 +11108 ctx_lh_G_and_S_cingul-Mid-Post 26 60 150 0 +11109 ctx_lh_G_cingul-Post-dorsal 25 60 250 0 +11110 ctx_lh_G_cingul-Post-ventral 60 25 25 0 +11111 ctx_lh_G_cuneus 180 20 20 0 +11112 ctx_lh_G_front_inf-Opercular 220 20 100 0 +11113 ctx_lh_G_front_inf-Orbital 140 60 60 0 +11114 ctx_lh_G_front_inf-Triangul 180 220 140 0 +11115 ctx_lh_G_front_middle 140 100 180 0 +11116 ctx_lh_G_front_sup 180 20 140 0 +11117 ctx_lh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +11118 ctx_lh_G_insular_short 225 140 140 0 +11119 ctx_lh_G_occipital_middle 180 60 180 0 +11120 ctx_lh_G_occipital_sup 20 220 60 0 +11121 ctx_lh_G_oc-temp_lat-fusifor 60 20 140 0 +11122 ctx_lh_G_oc-temp_med-Lingual 220 180 140 0 +11123 ctx_lh_G_oc-temp_med-Parahip 65 100 20 0 +11124 ctx_lh_G_orbital 220 60 20 0 +11125 ctx_lh_G_pariet_inf-Angular 20 60 220 0 +11126 ctx_lh_G_pariet_inf-Supramar 100 100 60 0 +11127 ctx_lh_G_parietal_sup 220 180 220 0 +11128 ctx_lh_G_postcentral 20 180 140 0 +11129 ctx_lh_G_precentral 60 140 180 0 +11130 ctx_lh_G_precuneus 25 20 140 0 +11131 ctx_lh_G_rectus 20 60 100 0 +11132 ctx_lh_G_subcallosal 60 220 20 0 +11133 ctx_lh_G_temp_sup-G_T_transv 60 60 220 0 +11134 ctx_lh_G_temp_sup-Lateral 220 60 220 0 +11135 ctx_lh_G_temp_sup-Plan_polar 65 220 60 0 +11136 ctx_lh_G_temp_sup-Plan_tempo 25 140 20 0 +11137 ctx_lh_G_temporal_inf 220 220 100 0 +11138 ctx_lh_G_temporal_middle 180 60 60 0 +11139 ctx_lh_Lat_Fis-ant-Horizont 61 20 220 0 +11140 ctx_lh_Lat_Fis-ant-Vertical 61 20 60 0 +11141 ctx_lh_Lat_Fis-post 61 60 100 0 +11142 ctx_lh_Medial_wall 25 25 25 0 +11143 ctx_lh_Pole_occipital 140 20 60 0 +11144 ctx_lh_Pole_temporal 220 180 20 0 +11145 ctx_lh_S_calcarine 63 180 180 0 +11146 ctx_lh_S_central 221 20 10 0 +11147 ctx_lh_S_cingul-Marginalis 221 20 100 0 +11148 ctx_lh_S_circular_insula_ant 221 60 140 0 +11149 ctx_lh_S_circular_insula_inf 221 20 220 0 +11150 ctx_lh_S_circular_insula_sup 61 220 220 0 +11151 ctx_lh_S_collat_transv_ant 100 200 200 0 +11152 ctx_lh_S_collat_transv_post 10 200 200 0 +11153 ctx_lh_S_front_inf 221 220 20 0 +11154 ctx_lh_S_front_middle 141 20 100 0 +11155 ctx_lh_S_front_sup 61 220 100 0 +11156 ctx_lh_S_interm_prim-Jensen 141 60 20 0 +11157 ctx_lh_S_intrapariet_and_P_trans 143 20 220 0 +11158 ctx_lh_S_oc_middle_and_Lunatus 101 60 220 0 +11159 ctx_lh_S_oc_sup_and_transversal 21 20 140 0 +11160 ctx_lh_S_occipital_ant 61 20 180 0 +11161 ctx_lh_S_oc-temp_lat 221 140 20 0 +11162 ctx_lh_S_oc-temp_med_and_Lingual 141 100 220 0 +11163 ctx_lh_S_orbital_lateral 221 100 20 0 +11164 ctx_lh_S_orbital_med-olfact 181 200 20 0 +11165 ctx_lh_S_orbital-H_Shaped 101 20 20 0 +11166 ctx_lh_S_parieto_occipital 101 100 180 0 +11167 ctx_lh_S_pericallosal 181 220 20 0 +11168 ctx_lh_S_postcentral 21 140 200 0 +11169 ctx_lh_S_precentral-inf-part 21 20 240 0 +11170 ctx_lh_S_precentral-sup-part 21 20 200 0 +11171 ctx_lh_S_suborbital 21 20 60 0 +11172 ctx_lh_S_subparietal 101 60 60 0 +11173 ctx_lh_S_temporal_inf 21 180 180 0 +11174 ctx_lh_S_temporal_sup 223 220 60 0 +11175 ctx_lh_S_temporal_transverse 221 60 60 0 +12100 ctx_rh_Unknown 0 0 0 0 +12101 ctx_rh_G_and_S_frontomargin 23 220 60 0 +12102 ctx_rh_G_and_S_occipital_inf 23 60 180 0 +12103 ctx_rh_G_and_S_paracentral 63 100 60 0 +12104 ctx_rh_G_and_S_subcentral 63 20 220 0 +12105 ctx_rh_G_and_S_transv_frontopol 13 0 250 0 +12106 ctx_rh_G_and_S_cingul-Ant 26 60 0 0 +12107 ctx_rh_G_and_S_cingul-Mid-Ant 26 60 75 0 +12108 ctx_rh_G_and_S_cingul-Mid-Post 26 60 150 0 +12109 ctx_rh_G_cingul-Post-dorsal 25 60 250 0 +12110 ctx_rh_G_cingul-Post-ventral 60 25 25 0 +12111 ctx_rh_G_cuneus 180 20 20 0 +12112 ctx_rh_G_front_inf-Opercular 220 20 100 0 +12113 ctx_rh_G_front_inf-Orbital 140 60 60 0 +12114 ctx_rh_G_front_inf-Triangul 180 220 140 0 +12115 ctx_rh_G_front_middle 140 100 180 0 +12116 ctx_rh_G_front_sup 180 20 140 0 +12117 ctx_rh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +12118 ctx_rh_G_insular_short 225 140 140 0 +12119 ctx_rh_G_occipital_middle 180 60 180 0 +12120 ctx_rh_G_occipital_sup 20 220 60 0 +12121 ctx_rh_G_oc-temp_lat-fusifor 60 20 140 0 +12122 ctx_rh_G_oc-temp_med-Lingual 220 180 140 0 +12123 ctx_rh_G_oc-temp_med-Parahip 65 100 20 0 +12124 ctx_rh_G_orbital 220 60 20 0 +12125 ctx_rh_G_pariet_inf-Angular 20 60 220 0 +12126 ctx_rh_G_pariet_inf-Supramar 100 100 60 0 +12127 ctx_rh_G_parietal_sup 220 180 220 0 +12128 ctx_rh_G_postcentral 20 180 140 0 +12129 ctx_rh_G_precentral 60 140 180 0 +12130 ctx_rh_G_precuneus 25 20 140 0 +12131 ctx_rh_G_rectus 20 60 100 0 +12132 ctx_rh_G_subcallosal 60 220 20 0 +12133 ctx_rh_G_temp_sup-G_T_transv 60 60 220 0 +12134 ctx_rh_G_temp_sup-Lateral 220 60 220 0 +12135 ctx_rh_G_temp_sup-Plan_polar 65 220 60 0 +12136 ctx_rh_G_temp_sup-Plan_tempo 25 140 20 0 +12137 ctx_rh_G_temporal_inf 220 220 100 0 +12138 ctx_rh_G_temporal_middle 180 60 60 0 +12139 ctx_rh_Lat_Fis-ant-Horizont 61 20 220 0 +12140 ctx_rh_Lat_Fis-ant-Vertical 61 20 60 0 +12141 ctx_rh_Lat_Fis-post 61 60 100 0 +12142 ctx_rh_Medial_wall 25 25 25 0 +12143 ctx_rh_Pole_occipital 140 20 60 0 +12144 ctx_rh_Pole_temporal 220 180 20 0 +12145 ctx_rh_S_calcarine 63 180 180 0 +12146 ctx_rh_S_central 221 20 10 0 +12147 ctx_rh_S_cingul-Marginalis 221 20 100 0 +12148 ctx_rh_S_circular_insula_ant 221 60 140 0 +12149 ctx_rh_S_circular_insula_inf 221 20 220 0 +12150 ctx_rh_S_circular_insula_sup 61 220 220 0 +12151 ctx_rh_S_collat_transv_ant 100 200 200 0 +12152 ctx_rh_S_collat_transv_post 10 200 200 0 +12153 ctx_rh_S_front_inf 221 220 20 0 +12154 ctx_rh_S_front_middle 141 20 100 0 +12155 ctx_rh_S_front_sup 61 220 100 0 +12156 ctx_rh_S_interm_prim-Jensen 141 60 20 0 +12157 ctx_rh_S_intrapariet_and_P_trans 143 20 220 0 +12158 ctx_rh_S_oc_middle_and_Lunatus 101 60 220 0 +12159 ctx_rh_S_oc_sup_and_transversal 21 20 140 0 +12160 ctx_rh_S_occipital_ant 61 20 180 0 +12161 ctx_rh_S_oc-temp_lat 221 140 20 0 +12162 ctx_rh_S_oc-temp_med_and_Lingual 141 100 220 0 +12163 ctx_rh_S_orbital_lateral 221 100 20 0 +12164 ctx_rh_S_orbital_med-olfact 181 200 20 0 +12165 ctx_rh_S_orbital-H_Shaped 101 20 20 0 +12166 ctx_rh_S_parieto_occipital 101 100 180 0 +12167 ctx_rh_S_pericallosal 181 220 20 0 +12168 ctx_rh_S_postcentral 21 140 200 0 +12169 ctx_rh_S_precentral-inf-part 21 20 240 0 +12170 ctx_rh_S_precentral-sup-part 21 20 200 0 +12171 ctx_rh_S_suborbital 21 20 60 0 +12172 ctx_rh_S_subparietal 101 60 60 0 +12173 ctx_rh_S_temporal_inf 21 180 180 0 +12174 ctx_rh_S_temporal_sup 223 220 60 0 +12175 ctx_rh_S_temporal_transverse 221 60 60 0 +13100 wm_lh_Unknown 0 0 0 0 +13101 wm_lh_G_and_S_frontomargin 23 220 60 0 +13102 wm_lh_G_and_S_occipital_inf 23 60 180 0 +13103 wm_lh_G_and_S_paracentral 63 100 60 0 +13104 wm_lh_G_and_S_subcentral 63 20 220 0 +13105 wm_lh_G_and_S_transv_frontopol 13 0 250 0 +13106 wm_lh_G_and_S_cingul-Ant 26 60 0 0 +13107 wm_lh_G_and_S_cingul-Mid-Ant 26 60 75 0 +13108 wm_lh_G_and_S_cingul-Mid-Post 26 60 150 0 +13109 wm_lh_G_cingul-Post-dorsal 25 60 250 0 +13110 wm_lh_G_cingul-Post-ventral 60 25 25 0 +13111 wm_lh_G_cuneus 180 20 20 0 +13112 wm_lh_G_front_inf-Opercular 220 20 100 0 +13113 wm_lh_G_front_inf-Orbital 140 60 60 0 +13114 wm_lh_G_front_inf-Triangul 180 220 140 0 +13115 wm_lh_G_front_middle 140 100 180 0 +13116 wm_lh_G_front_sup 180 20 140 0 +13117 wm_lh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +13118 wm_lh_G_insular_short 225 140 140 0 +13119 wm_lh_G_occipital_middle 180 60 180 0 +13120 wm_lh_G_occipital_sup 20 220 60 0 +13121 wm_lh_G_oc-temp_lat-fusifor 60 20 140 0 +13122 wm_lh_G_oc-temp_med-Lingual 220 180 140 0 +13123 wm_lh_G_oc-temp_med-Parahip 65 100 20 0 +13124 wm_lh_G_orbital 220 60 20 0 +13125 wm_lh_G_pariet_inf-Angular 20 60 220 0 +13126 wm_lh_G_pariet_inf-Supramar 100 100 60 0 +13127 wm_lh_G_parietal_sup 220 180 220 0 +13128 wm_lh_G_postcentral 20 180 140 0 +13129 wm_lh_G_precentral 60 140 180 0 +13130 wm_lh_G_precuneus 25 20 140 0 +13131 wm_lh_G_rectus 20 60 100 0 +13132 wm_lh_G_subcallosal 60 220 20 0 +13133 wm_lh_G_temp_sup-G_T_transv 60 60 220 0 +13134 wm_lh_G_temp_sup-Lateral 220 60 220 0 +13135 wm_lh_G_temp_sup-Plan_polar 65 220 60 0 +13136 wm_lh_G_temp_sup-Plan_tempo 25 140 20 0 +13137 wm_lh_G_temporal_inf 220 220 100 0 +13138 wm_lh_G_temporal_middle 180 60 60 0 +13139 wm_lh_Lat_Fis-ant-Horizont 61 20 220 0 +13140 wm_lh_Lat_Fis-ant-Vertical 61 20 60 0 +13141 wm_lh_Lat_Fis-post 61 60 100 0 +13142 wm_lh_Medial_wall 25 25 25 0 +13143 wm_lh_Pole_occipital 140 20 60 0 +13144 wm_lh_Pole_temporal 220 180 20 0 +13145 wm_lh_S_calcarine 63 180 180 0 +13146 wm_lh_S_central 221 20 10 0 +13147 wm_lh_S_cingul-Marginalis 221 20 100 0 +13148 wm_lh_S_circular_insula_ant 221 60 140 0 +13149 wm_lh_S_circular_insula_inf 221 20 220 0 +13150 wm_lh_S_circular_insula_sup 61 220 220 0 +13151 wm_lh_S_collat_transv_ant 100 200 200 0 +13152 wm_lh_S_collat_transv_post 10 200 200 0 +13153 wm_lh_S_front_inf 221 220 20 0 +13154 wm_lh_S_front_middle 141 20 100 0 +13155 wm_lh_S_front_sup 61 220 100 0 +13156 wm_lh_S_interm_prim-Jensen 141 60 20 0 +13157 wm_lh_S_intrapariet_and_P_trans 143 20 220 0 +13158 wm_lh_S_oc_middle_and_Lunatus 101 60 220 0 +13159 wm_lh_S_oc_sup_and_transversal 21 20 140 0 +13160 wm_lh_S_occipital_ant 61 20 180 0 +13161 wm_lh_S_oc-temp_lat 221 140 20 0 +13162 wm_lh_S_oc-temp_med_and_Lingual 141 100 220 0 +13163 wm_lh_S_orbital_lateral 221 100 20 0 +13164 wm_lh_S_orbital_med-olfact 181 200 20 0 +13165 wm_lh_S_orbital-H_Shaped 101 20 20 0 +13166 wm_lh_S_parieto_occipital 101 100 180 0 +13167 wm_lh_S_pericallosal 181 220 20 0 +13168 wm_lh_S_postcentral 21 140 200 0 +13169 wm_lh_S_precentral-inf-part 21 20 240 0 +13170 wm_lh_S_precentral-sup-part 21 20 200 0 +13171 wm_lh_S_suborbital 21 20 60 0 +13172 wm_lh_S_subparietal 101 60 60 0 +13173 wm_lh_S_temporal_inf 21 180 180 0 +13174 wm_lh_S_temporal_sup 223 220 60 0 +13175 wm_lh_S_temporal_transverse 221 60 60 0 +14100 wm_rh_Unknown 0 0 0 0 +14101 wm_rh_G_and_S_frontomargin 23 220 60 0 +14102 wm_rh_G_and_S_occipital_inf 23 60 180 0 +14103 wm_rh_G_and_S_paracentral 63 100 60 0 +14104 wm_rh_G_and_S_subcentral 63 20 220 0 +14105 wm_rh_G_and_S_transv_frontopol 13 0 250 0 +14106 wm_rh_G_and_S_cingul-Ant 26 60 0 0 +14107 wm_rh_G_and_S_cingul-Mid-Ant 26 60 75 0 +14108 wm_rh_G_and_S_cingul-Mid-Post 26 60 150 0 +14109 wm_rh_G_cingul-Post-dorsal 25 60 250 0 +14110 wm_rh_G_cingul-Post-ventral 60 25 25 0 +14111 wm_rh_G_cuneus 180 20 20 0 +14112 wm_rh_G_front_inf-Opercular 220 20 100 0 +14113 wm_rh_G_front_inf-Orbital 140 60 60 0 +14114 wm_rh_G_front_inf-Triangul 180 220 140 0 +14115 wm_rh_G_front_middle 140 100 180 0 +14116 wm_rh_G_front_sup 180 20 140 0 +14117 wm_rh_G_Ins_lg_and_S_cent_ins 23 10 10 0 +14118 wm_rh_G_insular_short 225 140 140 0 +14119 wm_rh_G_occipital_middle 180 60 180 0 +14120 wm_rh_G_occipital_sup 20 220 60 0 +14121 wm_rh_G_oc-temp_lat-fusifor 60 20 140 0 +14122 wm_rh_G_oc-temp_med-Lingual 220 180 140 0 +14123 wm_rh_G_oc-temp_med-Parahip 65 100 20 0 +14124 wm_rh_G_orbital 220 60 20 0 +14125 wm_rh_G_pariet_inf-Angular 20 60 220 0 +14126 wm_rh_G_pariet_inf-Supramar 100 100 60 0 +14127 wm_rh_G_parietal_sup 220 180 220 0 +14128 wm_rh_G_postcentral 20 180 140 0 +14129 wm_rh_G_precentral 60 140 180 0 +14130 wm_rh_G_precuneus 25 20 140 0 +14131 wm_rh_G_rectus 20 60 100 0 +14132 wm_rh_G_subcallosal 60 220 20 0 +14133 wm_rh_G_temp_sup-G_T_transv 60 60 220 0 +14134 wm_rh_G_temp_sup-Lateral 220 60 220 0 +14135 wm_rh_G_temp_sup-Plan_polar 65 220 60 0 +14136 wm_rh_G_temp_sup-Plan_tempo 25 140 20 0 +14137 wm_rh_G_temporal_inf 220 220 100 0 +14138 wm_rh_G_temporal_middle 180 60 60 0 +14139 wm_rh_Lat_Fis-ant-Horizont 61 20 220 0 +14140 wm_rh_Lat_Fis-ant-Vertical 61 20 60 0 +14141 wm_rh_Lat_Fis-post 61 60 100 0 +14142 wm_rh_Medial_wall 25 25 25 0 +14143 wm_rh_Pole_occipital 140 20 60 0 +14144 wm_rh_Pole_temporal 220 180 20 0 +14145 wm_rh_S_calcarine 63 180 180 0 +14146 wm_rh_S_central 221 20 10 0 +14147 wm_rh_S_cingul-Marginalis 221 20 100 0 +14148 wm_rh_S_circular_insula_ant 221 60 140 0 +14149 wm_rh_S_circular_insula_inf 221 20 220 0 +14150 wm_rh_S_circular_insula_sup 61 220 220 0 +14151 wm_rh_S_collat_transv_ant 100 200 200 0 +14152 wm_rh_S_collat_transv_post 10 200 200 0 +14153 wm_rh_S_front_inf 221 220 20 0 +14154 wm_rh_S_front_middle 141 20 100 0 +14155 wm_rh_S_front_sup 61 220 100 0 +14156 wm_rh_S_interm_prim-Jensen 141 60 20 0 +14157 wm_rh_S_intrapariet_and_P_trans 143 20 220 0 +14158 wm_rh_S_oc_middle_and_Lunatus 101 60 220 0 +14159 wm_rh_S_oc_sup_and_transversal 21 20 140 0 +14160 wm_rh_S_occipital_ant 61 20 180 0 +14161 wm_rh_S_oc-temp_lat 221 140 20 0 +14162 wm_rh_S_oc-temp_med_and_Lingual 141 100 220 0 +14163 wm_rh_S_orbital_lateral 221 100 20 0 +14164 wm_rh_S_orbital_med-olfact 181 200 20 0 +14165 wm_rh_S_orbital-H_Shaped 101 20 20 0 +14166 wm_rh_S_parieto_occipital 101 100 180 0 +14167 wm_rh_S_pericallosal 181 220 20 0 +14168 wm_rh_S_postcentral 21 140 200 0 +14169 wm_rh_S_precentral-inf-part 21 20 240 0 +14170 wm_rh_S_precentral-sup-part 21 20 200 0 +14171 wm_rh_S_suborbital 21 20 60 0 +14172 wm_rh_S_subparietal 101 60 60 0 +14173 wm_rh_S_temporal_inf 21 180 180 0 +14174 wm_rh_S_temporal_sup 223 220 60 0 +14175 wm_rh_S_temporal_transverse 221 60 60 0 diff --git a/bin/unix/3.1.2/templates/aparc/parcellate_aparc.sh b/bin/unix/3.1.2/templates/aparc/parcellate_aparc.sh new file mode 100755 index 0000000..4715be4 --- /dev/null +++ b/bin/unix/3.1.2/templates/aparc/parcellate_aparc.sh @@ -0,0 +1,77 @@ +#!/bin/bash +# +# Parcellate aparc atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + + + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +subjectDir=$(pwd) +freesurferDir=${subjectDir}/${freesurferDir} + +# Create parcellation +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/aparc+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + + +exit 0 diff --git a/bin/unix/3.1.2/templates/economo/ROIs_economo.txt b/bin/unix/3.1.2/templates/economo/ROIs_economo.txt new file mode 100755 index 0000000..f0aa163 --- /dev/null +++ b/bin/unix/3.1.2/templates/economo/ROIs_economo.txt @@ -0,0 +1,87 @@ +4 +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 +2039 +2040 +2041 +2042 +2043 +2044 diff --git a/bin/unix/3.1.2/templates/economo/economo.annot.ctab b/bin/unix/3.1.2/templates/economo/economo.annot.ctab new file mode 100755 index 0000000..3f0209a --- /dev/null +++ b/bin/unix/3.1.2/templates/economo/economo.annot.ctab @@ -0,0 +1,388 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-FA 206 226 156 0 +1003 ctx-lh-FB 200 219 138 0 +1004 ctx-lh-FC 187 204 115 0 +1005 ctx-lh-FCBm 85 193 170 0 +1006 ctx-lh-FD 13 201 111 0 +1007 ctx-lh-FDdelta 19 132 80 0 +1008 ctx-lh-FDT 69 168 123 0 +1009 ctx-lh-FE 27 178 138 0 +1010 ctx-lh-FF 49 172 192 0 +1011 ctx-lh-FG 61 127 118 0 +1012 ctx-lh-FH 77 135 106 0 +1013 ctx-lh-FJK 29 154 135 0 +1014 ctx-lh-FLMN 80 145 146 0 +1015 ctx-lh-HA 41 55 101 0 +1016 ctx-lh-HB 50 72 127 0 +1017 ctx-lh-HC 60 87 146 0 +1018 ctx-lh-IA 204 61 211 0 +1019 ctx-lh-IB 137 67 135 0 +1020 ctx-lh-LA1 124 215 246 0 +1021 ctx-lh-LA2 162 221 249 0 +1022 ctx-lh-LC1 0 133 185 0 +1023 ctx-lh-LC2 68 165 227 0 +1024 ctx-lh-LC3 118 179 215 0 +1025 ctx-lh-LD 122 212 215 0 +1026 ctx-lh-LE 169 219 224 0 +1027 ctx-lh-OA 253 252 187 0 +1028 ctx-lh-OB 251 250 146 0 +1029 ctx-lh-OC 247 222 71 0 +1030 ctx-lh-PA 230 42 133 0 +1031 ctx-lh-PB 247 67 148 0 +1032 ctx-lh-PC 239 87 150 0 +1033 ctx-lh-PD 188 53 121 0 +1034 ctx-lh-PE 248 167 210 0 +1035 ctx-lh-PF 250 180 224 0 +1036 ctx-lh-PG 248 193 224 0 +1037 ctx-lh-PH 232 73 130 0 +1038 ctx-lh-TA 240 85 102 0 +1039 ctx-lh-TB 233 65 98 0 +1040 ctx-lh-TC 239 64 107 0 +1041 ctx-lh-TD 245 79 113 0 +1042 ctx-lh-TE 235 181 136 0 +1043 ctx-lh-TF 184 47 79 0 +1044 ctx-lh-TG 247 198 127 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-FA 206 226 156 0 +2003 ctx-rh-FB 200 219 138 0 +2004 ctx-rh-FC 187 204 115 0 +2005 ctx-rh-FCBm 85 193 170 0 +2006 ctx-rh-FD 13 201 111 0 +2007 ctx-rh-FDdelta 19 132 80 0 +2008 ctx-rh-FDT 69 168 123 0 +2009 ctx-rh-FE 27 178 138 0 +2010 ctx-rh-FF 49 172 192 0 +2011 ctx-rh-FG 61 127 118 0 +2012 ctx-rh-FH 77 135 106 0 +2013 ctx-rh-FJK 29 154 135 0 +2014 ctx-rh-FLMN 80 145 146 0 +2015 ctx-rh-HA 41 55 101 0 +2016 ctx-rh-HB 50 72 127 0 +2017 ctx-rh-HC 60 87 146 0 +2018 ctx-rh-IA 204 61 211 0 +2019 ctx-rh-IB 137 67 135 0 +2020 ctx-rh-LA1 124 215 246 0 +2021 ctx-rh-LA2 162 221 249 0 +2022 ctx-rh-LC1 0 133 185 0 +2023 ctx-rh-LC2 68 165 227 0 +2024 ctx-rh-LC3 118 179 215 0 +2025 ctx-rh-LD 122 212 215 0 +2026 ctx-rh-LE 169 219 224 0 +2027 ctx-rh-OA 253 252 187 0 +2028 ctx-rh-OB 251 250 146 0 +2029 ctx-rh-OC 247 222 71 0 +2030 ctx-rh-PA 230 42 133 0 +2031 ctx-rh-PB 247 67 148 0 +2032 ctx-rh-PC 239 87 150 0 +2033 ctx-rh-PD 188 53 121 0 +2034 ctx-rh-PE 248 167 210 0 +2035 ctx-rh-PF 250 180 224 0 +2036 ctx-rh-PG 248 193 224 0 +2037 ctx-rh-PH 232 73 130 0 +2038 ctx-rh-TA 240 85 102 0 +2039 ctx-rh-TB 233 65 98 0 +2040 ctx-rh-TC 239 64 107 0 +2041 ctx-rh-TD 245 79 113 0 +2042 ctx-rh-TE 235 181 136 0 +2043 ctx-rh-TF 184 47 79 0 +2044 ctx-rh-TG 247 198 127 0 diff --git a/bin/unix/3.1.2/templates/economo/lh.economo.gcs b/bin/unix/3.1.2/templates/economo/lh.economo.gcs new file mode 100755 index 0000000..b22869e Binary files /dev/null and b/bin/unix/3.1.2/templates/economo/lh.economo.gcs differ diff --git a/bin/unix/3.1.2/templates/economo/parcellate_economo.sh b/bin/unix/3.1.2/templates/economo/parcellate_economo.sh new file mode 100755 index 0000000..f89b886 --- /dev/null +++ b/bin/unix/3.1.2/templates/economo/parcellate_economo.sh @@ -0,0 +1,105 @@ +#!/bin/bash +# +# Parcellate economo atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=economo + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/unix/3.1.2/templates/economo/rh.economo.gcs b/bin/unix/3.1.2/templates/economo/rh.economo.gcs new file mode 100755 index 0000000..d69797f Binary files /dev/null and b/bin/unix/3.1.2/templates/economo/rh.economo.gcs differ diff --git a/bin/unix/3.1.2/templates/lausanne120/ROIs_lausanne120.txt b/bin/unix/3.1.2/templates/lausanne120/ROIs_lausanne120.txt new file mode 100755 index 0000000..e75cf39 --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne120/ROIs_lausanne120.txt @@ -0,0 +1,114 @@ +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +1045 +1046 +1047 +1048 +1049 +1050 +1051 +1052 +1053 +1054 +1055 +1056 +1057 +1058 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 +2039 +2040 +2041 +2042 +2043 +2044 +2045 +2046 +2047 +2048 +2049 +2050 +2051 +2052 +2053 +2054 +2055 +2056 +2057 +2058 diff --git a/bin/unix/3.1.2/templates/lausanne120/lausanne120.annot.ctab b/bin/unix/3.1.2/templates/lausanne120/lausanne120.annot.ctab new file mode 100755 index 0000000..d29710f --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne120/lausanne120.annot.ctab @@ -0,0 +1,416 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-bankssts_1 25 100 40 0 +1003 ctx-lh-caudalanteriorcingulate_1 125 100 160 0 +1004 ctx-lh-caudalmiddlefrontal_1 100 25 0 0 +1005 ctx-lh-cuneus_1 220 20 100 0 +1006 ctx-lh-entorhinal_1 220 20 10 0 +1007 ctx-lh-fusiform_1 180 220 140 0 +1008 ctx-lh-fusiform_2 180 194 140 0 +1009 ctx-lh-inferiorparietal_1 220 60 220 0 +1010 ctx-lh-inferiorparietal_2 212 60 220 0 +1011 ctx-lh-inferiortemporal_1 180 40 120 0 +1012 ctx-lh-inferiortemporal_2 162 40 120 0 +1013 ctx-lh-isthmuscingulate_1 140 20 140 0 +1014 ctx-lh-lateraloccipital_1 20 30 140 0 +1015 ctx-lh-lateraloccipital_2 20 30 127 0 +1016 ctx-lh-lateralorbitofrontal_1 35 75 50 0 +1017 ctx-lh-lateralorbitofrontal_2 35 72 50 0 +1018 ctx-lh-lingual_1 225 140 140 0 +1019 ctx-lh-lingual_2 227 140 140 0 +1020 ctx-lh-medialorbitofrontal_1 200 35 75 0 +1021 ctx-lh-middletemporal_1 160 100 50 0 +1022 ctx-lh-middletemporal_2 152 100 50 0 +1023 ctx-lh-parahippocampal_1 20 220 60 0 +1024 ctx-lh-paracentral_1 60 220 60 0 +1025 ctx-lh-parsopercularis_1 220 180 140 0 +1026 ctx-lh-parsorbitalis_1 20 100 50 0 +1027 ctx-lh-parstriangularis_1 220 60 20 0 +1028 ctx-lh-pericalcarine_1 120 100 60 0 +1029 ctx-lh-postcentral_1 220 20 20 0 +1030 ctx-lh-postcentral_2 219 20 20 0 +1031 ctx-lh-postcentral_3 221 20 20 0 +1032 ctx-lh-posteriorcingulate_1 220 180 220 0 +1033 ctx-lh-precentral_1 60 20 220 0 +1034 ctx-lh-precentral_2 60 20 211 0 +1035 ctx-lh-precentral_3 60 20 212 0 +1036 ctx-lh-precentral_4 60 20 213 0 +1037 ctx-lh-precuneus_1 160 140 180 0 +1038 ctx-lh-precuneus_2 160 140 162 0 +1039 ctx-lh-rostralanteriorcingulate_1 80 20 140 0 +1040 ctx-lh-rostralmiddlefrontal_1 75 50 125 0 +1041 ctx-lh-rostralmiddlefrontal_2 75 50 122 0 +1042 ctx-lh-rostralmiddlefrontal_3 75 50 123 0 +1043 ctx-lh-superiorfrontal_1 20 220 160 0 +1044 ctx-lh-superiorfrontal_2 20 194 160 0 +1045 ctx-lh-superiorfrontal_3 20 195 160 0 +1046 ctx-lh-superiorfrontal_4 20 196 160 0 +1047 ctx-lh-superiorparietal_1 20 180 140 0 +1048 ctx-lh-superiorparietal_2 20 162 140 0 +1049 ctx-lh-superiorparietal_3 20 163 140 0 +1050 ctx-lh-superiortemporal_1 140 220 220 0 +1051 ctx-lh-superiortemporal_2 140 220 202 0 +1052 ctx-lh-supramarginal_1 80 160 20 0 +1053 ctx-lh-supramarginal_2 80 152 20 0 +1054 ctx-lh-frontalpole_1 100 0 100 0 +1055 ctx-lh-temporalpole_1 70 70 70 0 +1056 ctx-lh-transversetemporal_1 150 150 200 0 +1057 ctx-lh-insula_1 255 192 32 0 +1058 ctx-lh-insula_2 227 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-bankssts_1 25 100 40 0 +2003 ctx-rh-caudalanteriorcingulate_1 125 100 160 0 +2004 ctx-rh-caudalmiddlefrontal_1 100 25 0 0 +2005 ctx-rh-cuneus_1 220 20 100 0 +2006 ctx-rh-entorhinal_1 220 20 10 0 +2007 ctx-rh-fusiform_1 180 220 140 0 +2008 ctx-rh-fusiform_2 180 194 140 0 +2009 ctx-rh-inferiorparietal_1 220 60 220 0 +2010 ctx-rh-inferiorparietal_2 212 60 220 0 +2011 ctx-rh-inferiorparietal_3 213 60 220 0 +2012 ctx-rh-inferiortemporal_1 180 40 120 0 +2013 ctx-rh-inferiortemporal_2 162 40 120 0 +2014 ctx-rh-isthmuscingulate_1 140 20 140 0 +2015 ctx-rh-lateraloccipital_1 20 30 140 0 +2016 ctx-rh-lateraloccipital_2 20 30 127 0 +2017 ctx-rh-lateraloccipital_3 20 30 128 0 +2018 ctx-rh-lateralorbitofrontal_1 35 75 50 0 +2019 ctx-rh-lateralorbitofrontal_2 35 72 50 0 +2020 ctx-rh-lingual_1 225 140 140 0 +2021 ctx-rh-lingual_2 227 140 140 0 +2022 ctx-rh-medialorbitofrontal_1 200 35 75 0 +2023 ctx-rh-medialorbitofrontal_2 182 35 75 0 +2024 ctx-rh-middletemporal_1 160 100 50 0 +2025 ctx-rh-middletemporal_2 152 100 50 0 +2026 ctx-rh-parahippocampal_1 20 220 60 0 +2027 ctx-rh-paracentral_1 60 220 60 0 +2028 ctx-rh-parsopercularis_1 220 180 140 0 +2029 ctx-rh-parsorbitalis_1 20 100 50 0 +2030 ctx-rh-parstriangularis_1 220 60 20 0 +2031 ctx-rh-pericalcarine_1 120 100 60 0 +2032 ctx-rh-postcentral_1 220 20 20 0 +2033 ctx-rh-postcentral_2 219 20 20 0 +2034 ctx-rh-posteriorcingulate_1 220 180 220 0 +2035 ctx-rh-precentral_1 60 20 220 0 +2036 ctx-rh-precentral_2 60 20 211 0 +2037 ctx-rh-precentral_3 60 20 212 0 +2038 ctx-rh-precuneus_1 160 140 180 0 +2039 ctx-rh-precuneus_2 160 140 162 0 +2040 ctx-rh-rostralanteriorcingulate_1 80 20 140 0 +2041 ctx-rh-rostralmiddlefrontal_1 75 50 125 0 +2042 ctx-rh-rostralmiddlefrontal_2 75 50 122 0 +2043 ctx-rh-superiorfrontal_1 20 220 160 0 +2044 ctx-rh-superiorfrontal_2 20 194 160 0 +2045 ctx-rh-superiorfrontal_3 20 195 160 0 +2046 ctx-rh-superiorfrontal_4 20 196 160 0 +2047 ctx-rh-superiorparietal_1 20 180 140 0 +2048 ctx-rh-superiorparietal_2 20 162 140 0 +2049 ctx-rh-superiorparietal_3 20 163 140 0 +2050 ctx-rh-superiortemporal_1 140 220 220 0 +2051 ctx-rh-superiortemporal_2 140 220 202 0 +2052 ctx-rh-supramarginal_1 80 160 20 0 +2053 ctx-rh-supramarginal_2 80 152 20 0 +2054 ctx-rh-frontalpole_1 100 0 100 0 +2055 ctx-rh-temporalpole_1 70 70 70 0 +2056 ctx-rh-transversetemporal_1 150 150 200 0 +2057 ctx-rh-insula_1 255 192 32 0 +2058 ctx-rh-insula_2 227 192 32 0 \ No newline at end of file diff --git a/bin/unix/3.1.2/templates/lausanne120/lh.lausanne120.gcs b/bin/unix/3.1.2/templates/lausanne120/lh.lausanne120.gcs new file mode 100755 index 0000000..fa9a3a8 Binary files /dev/null and b/bin/unix/3.1.2/templates/lausanne120/lh.lausanne120.gcs differ diff --git a/bin/unix/3.1.2/templates/lausanne120/parcellate_lausanne120.sh b/bin/unix/3.1.2/templates/lausanne120/parcellate_lausanne120.sh new file mode 100755 index 0000000..4acd611 --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne120/parcellate_lausanne120.sh @@ -0,0 +1,106 @@ +#!/bin/bash +# +# Parcellate lausanne120 atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=lausanne120 + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/unix/3.1.2/templates/lausanne120/rh.lausanne120.gcs b/bin/unix/3.1.2/templates/lausanne120/rh.lausanne120.gcs new file mode 100755 index 0000000..fa23595 Binary files /dev/null and b/bin/unix/3.1.2/templates/lausanne120/rh.lausanne120.gcs differ diff --git a/bin/unix/3.1.2/templates/lausanne250/ROIs_lausanne250.txt b/bin/unix/3.1.2/templates/lausanne250/ROIs_lausanne250.txt new file mode 100755 index 0000000..ccdd7f1 --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne250/ROIs_lausanne250.txt @@ -0,0 +1,219 @@ +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +1045 +1046 +1047 +1048 +1049 +1050 +1051 +1052 +1053 +1054 +1055 +1056 +1057 +1058 +1059 +1060 +1061 +1062 +1063 +1064 +1065 +1066 +1067 +1068 +1069 +1070 +1071 +1072 +1073 +1074 +1075 +1076 +1077 +1078 +1079 +1080 +1081 +1082 +1083 +1084 +1085 +1086 +1087 +1088 +1089 +1090 +1091 +1092 +1093 +1094 +1095 +1096 +1097 +1098 +1099 +1100 +1101 +1102 +1103 +1104 +1105 +1106 +1107 +1108 +1109 +1110 +1111 +1112 +2002 +2003 +2004 +2005 +2006 +2007 +2008 +2009 +2010 +2011 +2012 +2013 +2014 +2015 +2016 +2017 +2018 +2019 +2020 +2021 +2022 +2023 +2024 +2025 +2026 +2027 +2028 +2029 +2030 +2031 +2032 +2033 +2034 +2035 +2036 +2037 +2038 +2039 +2040 +2041 +2042 +2043 +2044 +2045 +2046 +2047 +2048 +2049 +2050 +2051 +2052 +2053 +2054 +2055 +2056 +2057 +2058 +2059 +2060 +2061 +2062 +2063 +2064 +2065 +2066 +2067 +2068 +2069 +2070 +2071 +2072 +2073 +2074 +2075 +2076 +2077 +2078 +2079 +2080 +2081 +2082 +2083 +2084 +2085 +2086 +2087 +2088 +2089 +2090 +2091 +2092 +2093 +2094 +2095 +2096 +2097 +2098 +2099 +2100 +2101 +2102 +2103 +2104 +2105 +2106 +2107 +2108 +2109 diff --git a/bin/unix/3.1.2/templates/lausanne250/lausanne250.annot.ctab b/bin/unix/3.1.2/templates/lausanne250/lausanne250.annot.ctab new file mode 100755 index 0000000..b487c97 --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne250/lausanne250.annot.ctab @@ -0,0 +1,521 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 +999 SUSPICIOUS 255 100 100 0 +1000 ctx-lh-unknown 25 5 25 0 +1001 ctx-lh-corpuscallosum 120 70 50 0 +1002 ctx-lh-bankssts_1 25 100 40 0 +1003 ctx-lh-bankssts_2 25 77 40 0 +1004 ctx-lh-caudalanteriorcingulate_1 125 100 160 0 +1005 ctx-lh-caudalmiddlefrontal_1 100 25 0 0 +1006 ctx-lh-caudalmiddlefrontal_2 82 25 0 0 +1007 ctx-lh-caudalmiddlefrontal_3 83 25 0 0 +1008 ctx-lh-cuneus_1 220 20 100 0 +1009 ctx-lh-entorhinal_1 220 20 10 0 +1010 ctx-lh-fusiform_1 180 220 140 0 +1011 ctx-lh-fusiform_2 180 194 140 0 +1012 ctx-lh-fusiform_3 180 195 140 0 +1013 ctx-lh-fusiform_4 180 196 140 0 +1014 ctx-lh-inferiorparietal_1 220 60 220 0 +1015 ctx-lh-inferiorparietal_2 212 60 220 0 +1016 ctx-lh-inferiorparietal_3 213 60 220 0 +1017 ctx-lh-inferiorparietal_4 214 60 220 0 +1018 ctx-lh-inferiorparietal_5 215 60 220 0 +1019 ctx-lh-inferiortemporal_1 180 40 120 0 +1020 ctx-lh-inferiortemporal_2 162 40 120 0 +1021 ctx-lh-inferiortemporal_3 163 40 120 0 +1022 ctx-lh-inferiortemporal_4 164 40 120 0 +1023 ctx-lh-isthmuscingulate_1 140 20 140 0 +1024 ctx-lh-lateraloccipital_1 20 30 140 0 +1025 ctx-lh-lateraloccipital_2 20 30 127 0 +1026 ctx-lh-lateraloccipital_3 20 30 128 0 +1027 ctx-lh-lateraloccipital_4 20 30 129 0 +1028 ctx-lh-lateraloccipital_5 20 30 130 0 +1029 ctx-lh-lateralorbitofrontal_1 35 75 50 0 +1030 ctx-lh-lateralorbitofrontal_2 35 72 50 0 +1031 ctx-lh-lateralorbitofrontal_3 35 73 50 0 +1032 ctx-lh-lateralorbitofrontal_4 35 74 50 0 +1033 ctx-lh-lingual_1 225 140 140 0 +1034 ctx-lh-lingual_2 227 140 140 0 +1035 ctx-lh-lingual_3 228 140 140 0 +1036 ctx-lh-lingual_4 229 140 140 0 +1037 ctx-lh-medialorbitofrontal_1 200 35 75 0 +1038 ctx-lh-medialorbitofrontal_2 182 35 75 0 +1039 ctx-lh-middletemporal_1 160 100 50 0 +1040 ctx-lh-middletemporal_2 152 100 50 0 +1041 ctx-lh-middletemporal_3 153 100 50 0 +1042 ctx-lh-middletemporal_4 154 100 50 0 +1043 ctx-lh-parahippocampal_1 20 220 60 0 +1044 ctx-lh-paracentral_1 60 220 60 0 +1045 ctx-lh-paracentral_2 60 200 60 0 +1046 ctx-lh-parsopercularis_1 220 180 140 0 +1047 ctx-lh-parsopercularis_2 202 180 140 0 +1048 ctx-lh-parsorbitalis_1 20 100 50 0 +1049 ctx-lh-parstriangularis_1 220 60 20 0 +1050 ctx-lh-pericalcarine_1 120 100 60 0 +1051 ctx-lh-postcentral_1 220 20 20 0 +1052 ctx-lh-postcentral_2 219 20 20 0 +1053 ctx-lh-postcentral_3 221 20 20 0 +1054 ctx-lh-postcentral_4 222 20 20 0 +1055 ctx-lh-postcentral_5 223 20 20 0 +1056 ctx-lh-postcentral_6 224 20 20 0 +1057 ctx-lh-postcentral_7 220 6 20 0 +1058 ctx-lh-posteriorcingulate_1 220 180 220 0 +1059 ctx-lh-posteriorcingulate_2 220 180 202 0 +1060 ctx-lh-precentral_1 60 20 220 0 +1061 ctx-lh-precentral_2 60 20 211 0 +1062 ctx-lh-precentral_3 60 20 212 0 +1063 ctx-lh-precentral_4 60 20 213 0 +1064 ctx-lh-precentral_5 60 20 214 0 +1065 ctx-lh-precentral_6 60 20 215 0 +1066 ctx-lh-precentral_7 60 20 216 0 +1067 ctx-lh-precentral_8 60 20 217 0 +1068 ctx-lh-precuneus_1 160 140 180 0 +1069 ctx-lh-precuneus_2 160 140 162 0 +1070 ctx-lh-precuneus_3 160 140 163 0 +1071 ctx-lh-precuneus_4 160 140 164 0 +1072 ctx-lh-precuneus_5 160 140 165 0 +1073 ctx-lh-rostralanteriorcingulate_1 80 20 140 0 +1074 ctx-lh-rostralmiddlefrontal_1 75 50 125 0 +1075 ctx-lh-rostralmiddlefrontal_2 75 50 122 0 +1076 ctx-lh-rostralmiddlefrontal_3 75 50 123 0 +1077 ctx-lh-rostralmiddlefrontal_4 75 50 124 0 +1078 ctx-lh-rostralmiddlefrontal_5 75 50 126 0 +1079 ctx-lh-rostralmiddlefrontal_6 71 50 125 0 +1080 ctx-lh-superiorfrontal_1 20 220 160 0 +1081 ctx-lh-superiorfrontal_2 20 194 160 0 +1082 ctx-lh-superiorfrontal_3 20 195 160 0 +1083 ctx-lh-superiorfrontal_4 20 196 160 0 +1084 ctx-lh-superiorfrontal_5 20 197 160 0 +1085 ctx-lh-superiorfrontal_6 20 198 160 0 +1086 ctx-lh-superiorfrontal_7 20 199 160 0 +1087 ctx-lh-superiorfrontal_8 20 200 160 0 +1088 ctx-lh-superiorfrontal_9 20 201 160 0 +1089 ctx-lh-superiorparietal_1 20 180 140 0 +1090 ctx-lh-superiorparietal_2 20 162 140 0 +1091 ctx-lh-superiorparietal_3 20 163 140 0 +1092 ctx-lh-superiorparietal_4 20 164 140 0 +1093 ctx-lh-superiorparietal_5 20 165 140 0 +1094 ctx-lh-superiorparietal_6 20 166 140 0 +1095 ctx-lh-superiorparietal_7 20 167 140 0 +1096 ctx-lh-superiortemporal_1 140 220 220 0 +1097 ctx-lh-superiortemporal_2 140 220 202 0 +1098 ctx-lh-superiortemporal_3 140 220 203 0 +1099 ctx-lh-superiortemporal_4 140 220 204 0 +1100 ctx-lh-superiortemporal_5 140 220 205 0 +1101 ctx-lh-supramarginal_1 80 160 20 0 +1102 ctx-lh-supramarginal_2 80 152 20 0 +1103 ctx-lh-supramarginal_3 80 153 20 0 +1104 ctx-lh-supramarginal_4 80 154 20 0 +1105 ctx-lh-supramarginal_5 80 155 20 0 +1106 ctx-lh-frontalpole_1 100 0 100 0 +1107 ctx-lh-temporalpole_1 70 70 70 0 +1108 ctx-lh-transversetemporal_1 150 150 200 0 +1109 ctx-lh-insula_1 255 192 32 0 +1110 ctx-lh-insula_2 227 192 32 0 +1111 ctx-lh-insula_3 228 192 32 0 +1112 ctx-lh-insula_4 229 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-bankssts_1 25 100 40 0 +2003 ctx-rh-caudalanteriorcingulate_1 125 100 160 0 +2004 ctx-rh-caudalmiddlefrontal_1 100 25 0 0 +2005 ctx-rh-caudalmiddlefrontal_2 82 25 0 0 +2006 ctx-rh-caudalmiddlefrontal_3 83 25 0 0 +2007 ctx-rh-cuneus_1 220 20 100 0 +2008 ctx-rh-cuneus_2 202 20 100 0 +2009 ctx-rh-entorhinal_1 220 20 10 0 +2010 ctx-rh-fusiform_1 180 220 140 0 +2011 ctx-rh-fusiform_2 180 194 140 0 +2012 ctx-rh-fusiform_3 180 195 140 0 +2013 ctx-rh-fusiform_4 180 196 140 0 +2014 ctx-rh-inferiorparietal_1 220 60 220 0 +2015 ctx-rh-inferiorparietal_2 212 60 220 0 +2016 ctx-rh-inferiorparietal_3 213 60 220 0 +2017 ctx-rh-inferiorparietal_4 214 60 220 0 +2018 ctx-rh-inferiorparietal_5 215 60 220 0 +2019 ctx-rh-inferiorparietal_6 216 60 220 0 +2020 ctx-rh-inferiortemporal_1 180 40 120 0 +2021 ctx-rh-inferiortemporal_2 162 40 120 0 +2022 ctx-rh-inferiortemporal_3 163 40 120 0 +2023 ctx-rh-inferiortemporal_4 164 40 120 0 +2024 ctx-rh-isthmuscingulate_1 140 20 140 0 +2025 ctx-rh-lateraloccipital_1 20 30 140 0 +2026 ctx-rh-lateraloccipital_2 20 30 127 0 +2027 ctx-rh-lateraloccipital_3 20 30 128 0 +2028 ctx-rh-lateraloccipital_4 20 30 129 0 +2029 ctx-rh-lateraloccipital_5 20 30 130 0 +2030 ctx-rh-lateralorbitofrontal_1 35 75 50 0 +2031 ctx-rh-lateralorbitofrontal_2 35 72 50 0 +2032 ctx-rh-lateralorbitofrontal_3 35 73 50 0 +2033 ctx-rh-lateralorbitofrontal_4 35 74 50 0 +2034 ctx-rh-lingual_1 225 140 140 0 +2035 ctx-rh-lingual_2 227 140 140 0 +2036 ctx-rh-lingual_3 228 140 140 0 +2037 ctx-rh-medialorbitofrontal_1 200 35 75 0 +2038 ctx-rh-medialorbitofrontal_2 182 35 75 0 +2039 ctx-rh-medialorbitofrontal_3 183 35 75 0 +2040 ctx-rh-middletemporal_1 160 100 50 0 +2041 ctx-rh-middletemporal_2 152 100 50 0 +2042 ctx-rh-middletemporal_3 153 100 50 0 +2043 ctx-rh-middletemporal_4 154 100 50 0 +2044 ctx-rh-parahippocampal_1 20 220 60 0 +2045 ctx-rh-paracentral_1 60 220 60 0 +2046 ctx-rh-paracentral_2 60 200 60 0 +2047 ctx-rh-paracentral_3 60 201 60 0 +2048 ctx-rh-parsopercularis_1 220 180 140 0 +2049 ctx-rh-parsopercularis_2 202 180 140 0 +2050 ctx-rh-parsorbitalis_1 20 100 50 0 +2051 ctx-rh-parstriangularis_1 220 60 20 0 +2052 ctx-rh-parstriangularis_2 211 60 20 0 +2053 ctx-rh-pericalcarine_1 120 100 60 0 +2054 ctx-rh-pericalcarine_2 102 100 60 0 +2055 ctx-rh-postcentral_1 220 20 20 0 +2056 ctx-rh-postcentral_2 219 20 20 0 +2057 ctx-rh-postcentral_3 221 20 20 0 +2058 ctx-rh-postcentral_4 222 20 20 0 +2059 ctx-rh-postcentral_5 223 20 20 0 +2060 ctx-rh-posteriorcingulate_1 220 180 220 0 +2061 ctx-rh-posteriorcingulate_2 220 180 202 0 +2062 ctx-rh-precentral_1 60 20 220 0 +2063 ctx-rh-precentral_2 60 20 211 0 +2064 ctx-rh-precentral_3 60 20 212 0 +2065 ctx-rh-precentral_4 60 20 213 0 +2066 ctx-rh-precentral_5 60 20 214 0 +2067 ctx-rh-precentral_6 60 20 215 0 +2068 ctx-rh-precuneus_1 160 140 180 0 +2069 ctx-rh-precuneus_2 160 140 162 0 +2070 ctx-rh-precuneus_3 160 140 163 0 +2071 ctx-rh-precuneus_4 160 140 164 0 +2072 ctx-rh-precuneus_5 160 140 165 0 +2073 ctx-rh-rostralanteriorcingulate_1 80 20 140 0 +2074 ctx-rh-rostralmiddlefrontal_1 75 50 125 0 +2075 ctx-rh-rostralmiddlefrontal_2 75 50 122 0 +2076 ctx-rh-rostralmiddlefrontal_3 75 50 123 0 +2077 ctx-rh-rostralmiddlefrontal_4 75 50 124 0 +2078 ctx-rh-rostralmiddlefrontal_5 75 50 126 0 +2079 ctx-rh-rostralmiddlefrontal_6 71 50 125 0 +2080 ctx-rh-superiorfrontal_1 20 220 160 0 +2081 ctx-rh-superiorfrontal_2 20 194 160 0 +2082 ctx-rh-superiorfrontal_3 20 195 160 0 +2083 ctx-rh-superiorfrontal_4 20 196 160 0 +2084 ctx-rh-superiorfrontal_5 20 197 160 0 +2085 ctx-rh-superiorfrontal_6 20 198 160 0 +2086 ctx-rh-superiorfrontal_7 20 199 160 0 +2087 ctx-rh-superiorfrontal_8 20 200 160 0 +2088 ctx-rh-superiorparietal_1 20 180 140 0 +2089 ctx-rh-superiorparietal_2 20 162 140 0 +2090 ctx-rh-superiorparietal_3 20 163 140 0 +2091 ctx-rh-superiorparietal_4 20 164 140 0 +2092 ctx-rh-superiorparietal_5 20 165 140 0 +2093 ctx-rh-superiorparietal_6 20 166 140 0 +2094 ctx-rh-superiorparietal_7 20 167 140 0 +2095 ctx-rh-superiortemporal_1 140 220 220 0 +2096 ctx-rh-superiortemporal_2 140 220 202 0 +2097 ctx-rh-superiortemporal_3 140 220 203 0 +2098 ctx-rh-superiortemporal_4 140 220 204 0 +2099 ctx-rh-superiortemporal_5 140 220 205 0 +2100 ctx-rh-supramarginal_1 80 160 20 0 +2101 ctx-rh-supramarginal_2 80 152 20 0 +2102 ctx-rh-supramarginal_3 80 153 20 0 +2103 ctx-rh-supramarginal_4 80 154 20 0 +2104 ctx-rh-frontalpole_1 100 0 100 0 +2105 ctx-rh-temporalpole_1 70 70 70 0 +2106 ctx-rh-transversetemporal_1 150 150 200 0 +2107 ctx-rh-insula_1 255 192 32 0 +2108 ctx-rh-insula_2 227 192 32 0 +2109 ctx-rh-insula_3 228 192 32 0 \ No newline at end of file diff --git a/bin/unix/3.1.2/templates/lausanne250/lh.lausanne250.gcs b/bin/unix/3.1.2/templates/lausanne250/lh.lausanne250.gcs new file mode 100755 index 0000000..6fd9ed7 Binary files /dev/null and b/bin/unix/3.1.2/templates/lausanne250/lh.lausanne250.gcs differ diff --git a/bin/unix/3.1.2/templates/lausanne250/parcellate_lausanne250.sh b/bin/unix/3.1.2/templates/lausanne250/parcellate_lausanne250.sh new file mode 100755 index 0000000..3a88e1f --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne250/parcellate_lausanne250.sh @@ -0,0 +1,106 @@ +#!/bin/bash +# +# Parcellate lausanne250 atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=lausanne250 + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/unix/3.1.2/templates/lausanne250/rh.lausanne250.gcs b/bin/unix/3.1.2/templates/lausanne250/rh.lausanne250.gcs new file mode 100755 index 0000000..7f7f4ad Binary files /dev/null and b/bin/unix/3.1.2/templates/lausanne250/rh.lausanne250.gcs differ diff --git a/bin/unix/3.1.2/templates/lausanne500/ROIs_lausanne500.txt b/bin/unix/3.1.2/templates/lausanne500/ROIs_lausanne500.txt new file mode 100755 index 0000000..e4159b8 --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne500/ROIs_lausanne500.txt @@ -0,0 +1,448 @@ +1002 +1003 +1004 +1005 +1006 +1007 +1008 +1009 +1010 +1011 +1012 +1013 +1014 +1015 +1016 +1017 +1018 +1019 +1020 +1021 +1022 +1023 +1024 +1025 +1026 +1027 +1028 +1029 +1030 +1031 +1032 +1033 +1034 +1035 +1036 +1037 +1038 +1039 +1040 +1041 +1042 +1043 +1044 +1045 +1046 +1047 +1048 +1049 +1050 +1051 +1052 +1053 +1054 +1055 +1056 +1057 +1058 +1059 +1060 +1061 +1062 +1063 +1064 +1065 +1066 +1067 +1068 +1069 +1070 +1071 +1072 +1073 +1074 +1075 +1076 +1077 +1078 +1079 +1080 +1081 +1082 +1083 +1084 +1085 +1086 +1087 +1088 +1089 +1090 +1091 +1092 +1093 +1094 +1095 +1096 +1097 +1098 +1099 +1100 +1101 +1102 +1103 +1104 +1105 +1106 +1107 +1108 +1109 +1110 +1111 +1112 +1113 +1114 +1115 +1116 +1117 +1118 +1119 +1120 +1121 +1122 +1123 +1124 +1125 +1126 +1127 +1128 +1129 +1130 +1131 +1132 +1133 +1134 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b/bin/unix/3.1.2/templates/lausanne500/lausanne500.annot.ctab new file mode 100755 index 0000000..9929ba5 --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne500/lausanne500.annot.ctab @@ -0,0 +1,750 @@ +0 Unknown 0 0 0 0 +1 Left-Cerebral-Exterior 70 130 180 0 +2 Left-Cerebral-White-Matter 245 245 245 0 +3 Left-Cerebral-Cortex 205 62 78 0 +4 Left-Lateral-Ventricle 120 18 134 0 +5 Left-Inf-Lat-Vent 196 58 250 0 +6 Left-Cerebellum-Exterior 0 148 0 0 +7 Left-Cerebellum-White-Matter 220 248 164 0 +8 Left-Cerebellum-Cortex 230 148 34 0 +9 Left-Thalamus 0 118 14 0 +10 Left-Thalamus-Proper 0 118 14 0 +11 Left-Caudate 122 186 220 0 +12 Left-Putamen 236 13 176 0 +13 Left-Pallidum 12 48 255 0 +14 3rd-Ventricle 204 182 142 0 +15 4th-Ventricle 42 204 164 0 +16 Brain-Stem 119 159 176 0 +17 Left-Hippocampus 220 216 20 0 +18 Left-Amygdala 103 255 255 0 +19 Left-Insula 80 196 98 0 +20 Left-Operculum 60 58 210 0 +21 Line-1 60 58 210 0 +22 Line-2 60 58 210 0 +23 Line-3 60 58 210 0 +24 CSF 60 60 60 0 +25 Left-Lesion 255 165 0 0 +26 Left-Accumbens-area 255 165 0 0 +27 Left-Substancia-Nigra 0 255 127 0 +28 Left-VentralDC 165 42 42 0 +29 Left-undetermined 135 206 235 0 +30 Left-vessel 160 32 240 0 +31 Left-choroid-plexus 0 200 200 0 +32 Left-F3orb 100 50 100 0 +33 Left-lOg 135 50 74 0 +34 Left-aOg 122 135 50 0 +35 Left-mOg 51 50 135 0 +36 Left-pOg 74 155 60 0 +37 Left-Stellate 120 62 43 0 +38 Left-Porg 74 155 60 0 +39 Left-Aorg 122 135 50 0 +40 Right-Cerebral-Exterior 70 130 180 0 +41 Right-Cerebral-White-Matter 0 225 0 0 +42 Right-Cerebral-Cortex 205 62 78 0 +43 Right-Lateral-Ventricle 120 18 134 0 +44 Right-Inf-Lat-Vent 196 58 250 0 +45 Right-Cerebellum-Exterior 0 148 0 0 +46 Right-Cerebellum-White-Matter 220 248 164 0 +47 Right-Cerebellum-Cortex 230 148 34 0 +48 Right-Thalamus 0 118 14 0 +49 Right-Thalamus-Proper 0 118 14 0 +50 Right-Caudate 122 186 220 0 +51 Right-Putamen 236 13 176 0 +52 Right-Pallidum 13 48 255 0 +53 Right-Hippocampus 220 216 20 0 +54 Right-Amygdala 103 255 255 0 +55 Right-Insula 80 196 98 0 +56 Right-Operculum 60 58 210 0 +57 Right-Lesion 255 165 0 0 +58 Right-Accumbens-area 255 165 0 0 +59 Right-Substancia-Nigra 0 255 127 0 +60 Right-VentralDC 165 42 42 0 +61 Right-undetermined 135 206 235 0 +62 Right-vessel 160 32 240 0 +63 Right-choroid-plexus 0 200 221 0 +64 Right-F3orb 100 50 100 0 +65 Right-lOg 135 50 74 0 +66 Right-aOg 122 135 50 0 +67 Right-mOg 51 50 135 0 +68 Right-pOg 74 155 60 0 +69 Right-Stellate 120 62 43 0 +70 Right-Porg 74 155 60 0 +71 Right-Aorg 122 135 50 0 +72 5th-Ventricle 120 190 150 0 +73 Left-Interior 122 135 50 0 +74 Right-Interior 122 135 50 0 +75 Left-Lateral-Ventricles 120 18 134 0 +76 Right-Lateral-Ventricles 120 18 134 0 +77 WM-hypointensities 200 70 255 0 +78 Left-WM-hypointensities 255 148 10 0 +79 Right-WM-hypointensities 255 148 10 0 +80 non-WM-hypointensities 164 108 226 0 +81 Left-non-WM-hypointensities 164 108 226 0 +82 Right-non-WM-hypointensities 164 108 226 0 +83 Left-F1 255 218 185 0 +84 Right-F1 255 218 185 0 +85 Optic-Chiasm 234 169 30 0 +86 Corpus_Callosum 250 255 50 0 +96 Left-Amygdala-Anterior 205 10 125 0 +97 Right-Amygdala-Anterior 205 10 125 0 +98 Dura 160 32 240 0 +100 Left-wm-intensity-abnormality 124 140 178 0 +101 Left-caudate-intensity-abnormality 125 140 178 0 +102 Left-putamen-intensity-abnormality 126 140 178 0 +103 Left-accumbens-intensity-abnormality 127 140 178 0 +104 Left-pallidum-intensity-abnormality 124 141 178 0 +105 Left-amygdala-intensity-abnormality 124 142 178 0 +106 Left-hippocampus-intensity-abnormality 124 143 178 0 +107 Left-thalamus-intensity-abnormality 124 144 178 0 +108 Left-VDC-intensity-abnormality 124 140 179 0 +109 Right-wm-intensity-abnormality 124 140 178 0 +110 Right-caudate-intensity-abnormality 125 140 178 0 +111 Right-putamen-intensity-abnormality 126 140 178 0 +112 Right-accumbens-intensity-abnormality 127 140 178 0 +113 Right-pallidum-intensity-abnormality 124 141 178 0 +114 Right-amygdala-intensity-abnormality 124 142 178 0 +115 Right-hippocampus-intensity-abnormality 124 143 178 0 +116 Right-thalamus-intensity-abnormality 124 144 178 0 +117 Right-VDC-intensity-abnormality 124 140 179 0 +118 Epidermis 255 20 147 0 +119 Conn-Tissue 205 179 139 0 +120 SC-Fat/Muscle 238 238 209 0 +121 Cranium 200 200 200 0 +122 CSF-SA 74 255 74 0 +123 Muscle 238 0 0 0 +124 Ear 0 0 139 0 +125 Adipose 173 255 47 0 +126 Spinal-Cord 133 203 229 0 +127 Soft-Tissue 26 237 57 0 +128 Nerve 34 139 34 0 +129 Bone 30 144 255 0 +130 Air 147 19 173 0 +131 Orbital-Fat 238 59 59 0 +132 Tongue 221 39 200 0 +133 Nasal-Structures 238 174 238 0 +134 Globe 255 0 0 0 +135 Teeth 72 61 139 0 +136 Left-Caudate/Putamen 21 39 132 0 +137 Right-Caudate/Putamen 21 39 132 0 +138 Left-Claustrum 65 135 20 0 +139 Right-Claustrum 65 135 20 0 +140 Cornea 134 4 160 0 +142 Diploe 221 226 68 0 +143 Vitreous-Humor 255 255 254 0 +144 Lens 52 209 226 0 +145 Aqueous-Humor 239 160 223 0 +146 Outer-Table 70 130 180 0 +147 Inner-Table 70 130 181 0 +148 Periosteum 139 121 94 0 +149 Endosteum 224 224 224 0 +150 R/C/S 255 0 0 0 +151 Iris 205 205 0 0 +152 SC-Adipose/Muscle 238 238 209 0 +153 SC-Tissue 139 121 94 0 +154 Orbital-Adipose 238 59 59 0 +155 Left-IntCapsule-Ant 238 59 59 0 +156 Right-IntCapsule-Ant 238 59 59 0 +157 Left-IntCapsule-Pos 62 10 205 0 +158 Right-IntCapsule-Pos 62 10 205 0 +159 Left-Cerebral-WM-unmyelinated 0 118 14 0 +160 Right-Cerebral-WM-unmyelinated 0 118 14 0 +161 Left-Cerebral-WM-myelinated 220 216 21 0 +162 Right-Cerebral-WM-myelinated 220 216 21 0 +163 Left-Subcortical-Gray-Matter 122 186 220 0 +164 Right-Subcortical-Gray-Matter 122 186 220 0 +165 Skull 255 165 0 0 +166 Posterior-fossa 14 48 255 0 +167 Scalp 166 42 42 0 +168 Hematoma 121 18 134 0 +170 brainstem 119 159 176 0 +171 DCG 119 0 176 0 +172 Vermis 119 100 176 0 +173 Midbrain 119 200 176 0 +174 Pons 119 159 100 0 +175 Medulla 119 159 200 0 +180 Left-Cortical-Dysplasia 73 61 139 0 +181 Right-Cortical-Dysplasia 73 62 139 0 +193 Left-hippocampal_fissure 0 196 255 0 +194 Left-CADG-head 255 164 164 0 +195 Left-subiculum 196 196 0 0 +196 Left-fimbria 0 100 255 0 +197 Right-hippocampal_fissure 128 196 164 0 +198 Right-CADG-head 0 126 75 0 +199 Right-subiculum 128 96 64 0 +200 Right-fimbria 0 50 128 0 +201 alveus 255 204 153 0 +202 perforant_pathway 255 128 128 0 +203 parasubiculum 255 255 0 0 +204 presubiculum 64 0 64 0 +205 subiculum 0 0 255 0 +206 CA1 255 0 0 0 +207 CA2 128 128 255 0 +208 CA3 0 128 0 0 +209 CA4 196 160 128 0 +210 GC-DG 32 200 255 0 +211 HATA 128 255 128 0 +212 fimbria 204 153 204 0 +213 lateral_ventricle 121 17 136 0 +214 molecular_layer_HP 128 0 0 0 +215 hippocampal_fissure 128 32 255 0 +216 entorhinal_cortex 255 204 102 0 +217 molecular_layer_subiculum 128 128 128 0 +218 Amygdala 104 255 255 0 +219 Cerebral_White_Matter 0 226 0 0 +220 Cerebral_Cortex 205 63 78 0 +221 Inf_Lat_Vent 197 58 250 0 +222 Perirhinal 33 150 250 0 +223 Cerebral_White_Matter_Edge 226 0 0 0 +224 Background 100 100 100 0 +225 Ectorhinal 197 150 250 0 +250 Fornix 255 0 0 0 +251 CC_Posterior 0 0 64 0 +252 CC_Mid_Posterior 0 0 112 0 +253 CC_Central 0 0 160 0 +254 CC_Mid_Anterior 0 0 208 0 +255 CC_Anterior 0 0 255 0 +256 Voxel-Unchanged 0 0 0 0 +331 Aorta 255 0 0 0 +332 Left-Common-IliacA 255 80 0 0 +333 Right-Common-IliacA 255 160 0 0 +334 Left-External-IliacA 255 255 0 0 +335 Right-External-IliacA 0 255 0 0 +336 Left-Internal-IliacA 255 0 160 0 +337 Right-Internal-IliacA 255 0 255 0 +338 Left-Lateral-SacralA 255 50 80 0 +339 Right-Lateral-SacralA 80 255 50 0 +340 Left-ObturatorA 160 255 50 0 +341 Right-ObturatorA 160 200 255 0 +342 Left-Internal-PudendalA 0 255 160 0 +343 Right-Internal-PudendalA 0 0 255 0 +344 Left-UmbilicalA 80 50 255 0 +345 Right-UmbilicalA 160 0 255 0 +346 Left-Inf-RectalA 255 210 0 0 +347 Right-Inf-RectalA 0 160 255 0 +348 Left-Common-IliacV 255 200 80 0 +349 Right-Common-IliacV 255 200 160 0 +350 Left-External-IliacV 255 80 200 0 +351 Right-External-IliacV 255 160 200 0 +352 Left-Internal-IliacV 30 255 80 0 +353 Right-Internal-IliacV 80 200 255 0 +354 Left-ObturatorV 80 255 200 0 +355 Right-ObturatorV 195 255 200 0 +356 Left-Internal-PudendalV 120 200 20 0 +357 Right-Internal-PudendalV 170 10 200 0 +358 Pos-Lymph 20 130 180 0 +359 Neg-Lymph 20 180 130 0 +400 V1 206 62 78 0 +401 V2 121 18 134 0 +402 BA44 199 58 250 0 +403 BA45 1 148 0 0 +404 BA4a 221 248 164 0 +405 BA4p 231 148 34 0 +406 BA6 1 118 14 0 +407 BA2 120 118 14 0 +408 BA1_old 123 186 221 0 +409 BAun2 238 13 177 0 +410 BA1 123 186 220 0 +411 BA2b 138 13 206 0 +412 BA3a 238 130 176 0 +413 BA3b 218 230 76 0 +414 MT 38 213 176 0 +415 AIPS_AIP_l 1 225 176 0 +416 AIPS_AIP_r 1 225 176 0 +417 AIPS_VIP_l 200 2 100 0 +418 AIPS_VIP_r 200 2 100 0 +419 IPL_PFcm_l 5 200 90 0 +420 IPL_PFcm_r 5 200 90 0 +421 IPL_PF_l 100 5 200 0 +422 IPL_PFm_l 25 255 100 0 +423 IPL_PFm_r 25 255 100 0 +424 IPL_PFop_l 230 7 100 0 +425 IPL_PFop_r 230 7 100 0 +426 IPL_PF_r 100 5 200 0 +427 IPL_PFt_l 150 10 200 0 +428 IPL_PFt_r 150 10 200 0 +429 IPL_PGa_l 175 10 176 0 +430 IPL_PGa_r 175 10 176 0 +431 IPL_PGp_l 10 100 255 0 +432 IPL_PGp_r 10 100 255 0 +433 Visual_V3d_l 150 45 70 0 +434 Visual_V3d_r 150 45 70 0 +435 Visual_V4_l 45 200 15 0 +436 Visual_V4_r 45 200 15 0 +437 Visual_V5_b 227 45 100 0 +438 Visual_VP_l 227 45 100 0 +439 Visual_VP_r 227 45 100 0 +500 right_CA2/3 17 85 136 0 +501 right_alveus 119 187 102 0 +502 right_CA1 204 68 34 0 +503 right_fimbria 204 0 255 0 +504 right_presubiculum 221 187 17 0 +505 right_hippocampal_fissure 153 221 238 0 +506 right_CA4/DG 51 17 17 0 +507 right_subiculum 0 119 85 0 +508 right_fornix 20 100 200 0 +550 left_CA2/3 17 85 137 0 +551 left_alveus 119 187 103 0 +552 left_CA1 204 68 35 0 +553 left_fimbria 204 0 254 0 +554 left_presubiculum 221 187 16 0 +555 left_hippocampal_fissure 153 221 239 0 +556 left_CA4/DG 51 17 18 0 +557 left_subiculum 0 119 86 0 +558 left_fornix 20 100 201 0 +600 Tumor 254 254 254 0 +701 CSF-FSL-FAST 120 18 134 0 +702 GrayMatter-FSL-FAST 205 62 78 0 +703 WhiteMatter-FSL-FAST 0 225 0 0 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ctx-lh-fusiform_8 180 200 140 0 +1025 ctx-lh-inferiorparietal_1 220 60 220 0 +1026 ctx-lh-inferiorparietal_2 212 60 220 0 +1027 ctx-lh-inferiorparietal_3 213 60 220 0 +1028 ctx-lh-inferiorparietal_4 214 60 220 0 +1029 ctx-lh-inferiorparietal_5 215 60 220 0 +1030 ctx-lh-inferiorparietal_6 216 60 220 0 +1031 ctx-lh-inferiorparietal_7 217 60 220 0 +1032 ctx-lh-inferiorparietal_8 218 60 220 0 +1033 ctx-lh-inferiorparietal_9 219 60 220 0 +1034 ctx-lh-inferiorparietal_10 221 60 220 0 +1035 ctx-lh-inferiortemporal_1 180 40 120 0 +1036 ctx-lh-inferiortemporal_2 162 40 120 0 +1037 ctx-lh-inferiortemporal_3 163 40 120 0 +1038 ctx-lh-inferiortemporal_4 164 40 120 0 +1039 ctx-lh-inferiortemporal_5 165 40 120 0 +1040 ctx-lh-inferiortemporal_6 166 40 120 0 +1041 ctx-lh-inferiortemporal_7 167 40 120 0 +1042 ctx-lh-inferiortemporal_8 168 40 120 0 +1043 ctx-lh-isthmuscingulate_1 140 20 140 0 +1044 ctx-lh-isthmuscingulate_2 127 20 140 0 +1045 ctx-lh-isthmuscingulate_3 128 20 140 0 +1046 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ctx-lh-lingual_6 231 140 140 0 +1070 ctx-lh-lingual_7 232 140 140 0 +1071 ctx-lh-lingual_8 233 140 140 0 +1072 ctx-lh-medialorbitofrontal_1 200 35 75 0 +1073 ctx-lh-medialorbitofrontal_2 182 35 75 0 +1074 ctx-lh-medialorbitofrontal_3 183 35 75 0 +1075 ctx-lh-medialorbitofrontal_4 184 35 75 0 +1076 ctx-lh-medialorbitofrontal_5 185 35 75 0 +1077 ctx-lh-middletemporal_1 160 100 50 0 +1078 ctx-lh-middletemporal_2 152 100 50 0 +1079 ctx-lh-middletemporal_3 153 100 50 0 +1080 ctx-lh-middletemporal_4 154 100 50 0 +1081 ctx-lh-middletemporal_5 155 100 50 0 +1082 ctx-lh-middletemporal_6 156 100 50 0 +1083 ctx-lh-middletemporal_7 157 100 50 0 +1084 ctx-lh-parahippocampal_1 20 220 60 0 +1085 ctx-lh-parahippocampal_2 20 194 60 0 +1086 ctx-lh-parahippocampal_3 20 195 60 0 +1087 ctx-lh-paracentral_1 60 220 60 0 +1088 ctx-lh-paracentral_2 60 200 60 0 +1089 ctx-lh-paracentral_3 60 201 60 0 +1090 ctx-lh-paracentral_4 60 202 60 0 +1091 ctx-lh-paracentral_5 60 203 60 0 +1092 ctx-lh-parsopercularis_1 220 180 140 0 +1093 ctx-lh-parsopercularis_2 202 180 140 0 +1094 ctx-lh-parsopercularis_3 203 180 140 0 +1095 ctx-lh-parsopercularis_4 204 180 140 0 +1096 ctx-lh-parsorbitalis_1 20 100 50 0 +1097 ctx-lh-parsorbitalis_2 20 77 50 0 +1098 ctx-lh-parstriangularis_1 220 60 20 0 +1099 ctx-lh-parstriangularis_2 212 60 20 0 +1100 ctx-lh-parstriangularis_3 213 60 20 0 +1101 ctx-lh-pericalcarine_1 120 100 60 0 +1102 ctx-lh-pericalcarine_2 102 100 60 0 +1103 ctx-lh-pericalcarine_3 103 100 60 0 +1104 ctx-lh-postcentral_1 220 20 20 0 +1105 ctx-lh-postcentral_2 219 20 20 0 +1106 ctx-lh-postcentral_3 221 20 20 0 +1107 ctx-lh-postcentral_4 222 20 20 0 +1108 ctx-lh-postcentral_5 223 20 20 0 +1109 ctx-lh-postcentral_6 224 20 20 0 +1110 ctx-lh-postcentral_7 220 6 20 0 +1111 ctx-lh-postcentral_8 220 7 20 0 +1112 ctx-lh-postcentral_9 220 8 20 0 +1113 ctx-lh-postcentral_10 220 9 20 0 +1114 ctx-lh-postcentral_11 220 10 20 0 +1115 ctx-lh-postcentral_12 220 11 20 0 +1116 ctx-lh-postcentral_13 220 12 20 0 +1117 ctx-lh-postcentral_14 220 13 20 0 +1118 ctx-lh-posteriorcingulate_1 220 180 220 0 +1119 ctx-lh-posteriorcingulate_2 220 180 202 0 +1120 ctx-lh-posteriorcingulate_3 220 180 203 0 +1121 ctx-lh-posteriorcingulate_4 220 180 204 0 +1122 ctx-lh-precentral_1 60 20 220 0 +1123 ctx-lh-precentral_2 60 20 211 0 +1124 ctx-lh-precentral_3 60 20 212 0 +1125 ctx-lh-precentral_4 60 20 213 0 +1126 ctx-lh-precentral_5 60 20 214 0 +1127 ctx-lh-precentral_6 60 20 215 0 +1128 ctx-lh-precentral_7 60 20 216 0 +1129 ctx-lh-precentral_8 60 20 217 0 +1130 ctx-lh-precentral_9 60 20 218 0 +1131 ctx-lh-precentral_10 60 20 219 0 +1132 ctx-lh-precentral_11 36 20 220 0 +1133 ctx-lh-precentral_12 37 20 220 0 +1134 ctx-lh-precentral_13 38 20 220 0 +1135 ctx-lh-precentral_14 39 20 220 0 +1136 ctx-lh-precentral_15 40 20 220 0 +1137 ctx-lh-precentral_16 41 20 220 0 +1138 ctx-lh-precuneus_1 160 140 180 0 +1139 ctx-lh-precuneus_2 160 140 162 0 +1140 ctx-lh-precuneus_3 160 140 163 0 +1141 ctx-lh-precuneus_4 160 140 164 0 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0 +1164 ctx-lh-superiorfrontal_2 20 194 160 0 +1165 ctx-lh-superiorfrontal_3 20 195 160 0 +1166 ctx-lh-superiorfrontal_4 20 196 160 0 +1167 ctx-lh-superiorfrontal_5 20 197 160 0 +1168 ctx-lh-superiorfrontal_6 20 198 160 0 +1169 ctx-lh-superiorfrontal_7 20 199 160 0 +1170 ctx-lh-superiorfrontal_8 20 200 160 0 +1171 ctx-lh-superiorfrontal_9 20 201 160 0 +1172 ctx-lh-superiorfrontal_10 20 202 160 0 +1173 ctx-lh-superiorfrontal_11 20 203 160 0 +1174 ctx-lh-superiorfrontal_12 20 204 160 0 +1175 ctx-lh-superiorfrontal_13 20 205 160 0 +1176 ctx-lh-superiorfrontal_14 20 206 160 0 +1177 ctx-lh-superiorfrontal_15 20 207 160 0 +1178 ctx-lh-superiorfrontal_16 20 208 160 0 +1179 ctx-lh-superiorfrontal_17 20 209 160 0 +1180 ctx-lh-superiorfrontal_18 20 210 160 0 +1181 ctx-lh-superiorparietal_1 20 180 140 0 +1182 ctx-lh-superiorparietal_2 20 162 140 0 +1183 ctx-lh-superiorparietal_3 20 163 140 0 +1184 ctx-lh-superiorparietal_4 20 164 140 0 +1185 ctx-lh-superiorparietal_5 20 165 140 0 +1186 ctx-lh-superiorparietal_6 20 166 140 0 +1187 ctx-lh-superiorparietal_7 20 167 140 0 +1188 ctx-lh-superiorparietal_8 20 168 140 0 +1189 ctx-lh-superiorparietal_9 20 169 140 0 +1190 ctx-lh-superiorparietal_10 20 170 140 0 +1191 ctx-lh-superiorparietal_11 20 171 140 0 +1192 ctx-lh-superiorparietal_12 20 172 140 0 +1193 ctx-lh-superiorparietal_13 20 173 140 0 +1194 ctx-lh-superiorparietal_14 20 174 140 0 +1195 ctx-lh-superiortemporal_1 140 220 220 0 +1196 ctx-lh-superiortemporal_2 140 220 202 0 +1197 ctx-lh-superiortemporal_3 140 220 203 0 +1198 ctx-lh-superiortemporal_4 140 220 204 0 +1199 ctx-lh-superiortemporal_5 140 220 205 0 +1200 ctx-lh-superiortemporal_6 140 220 206 0 +1201 ctx-lh-superiortemporal_7 140 220 207 0 +1202 ctx-lh-superiortemporal_8 140 220 208 0 +1203 ctx-lh-superiortemporal_9 140 220 209 0 +1204 ctx-lh-superiortemporal_10 140 220 210 0 +1205 ctx-lh-superiortemporal_11 140 220 211 0 +1206 ctx-lh-supramarginal_1 80 160 20 0 +1207 ctx-lh-supramarginal_2 80 152 20 0 +1208 ctx-lh-supramarginal_3 80 153 20 0 +1209 ctx-lh-supramarginal_4 80 154 20 0 +1210 ctx-lh-supramarginal_5 80 155 20 0 +1211 ctx-lh-supramarginal_6 80 156 20 0 +1212 ctx-lh-supramarginal_7 80 157 20 0 +1213 ctx-lh-supramarginal_8 80 158 20 0 +1214 ctx-lh-supramarginal_9 80 159 20 0 +1215 ctx-lh-supramarginal_10 80 161 20 0 +1216 ctx-lh-frontalpole_1 100 0 100 0 +1217 ctx-lh-temporalpole_1 70 70 70 0 +1218 ctx-lh-transversetemporal_1 150 150 200 0 +1219 ctx-lh-transversetemporal_2 150 150 182 0 +1220 ctx-lh-insula_1 255 192 32 0 +1221 ctx-lh-insula_2 227 192 32 0 +1222 ctx-lh-insula_3 228 192 32 0 +1223 ctx-lh-insula_4 229 192 32 0 +1224 ctx-lh-insula_5 230 192 32 0 +1225 ctx-lh-insula_6 231 192 32 0 +1226 ctx-lh-insula_7 232 192 32 0 +2000 ctx-rh-unknown 25 5 25 0 +2001 ctx-rh-corpuscallosum 120 70 50 0 +2002 ctx-rh-bankssts_1 25 100 40 0 +2003 ctx-rh-bankssts_2 25 77 40 0 +2004 ctx-rh-bankssts_3 25 78 40 0 +2005 ctx-rh-caudalanteriorcingulate_1 125 100 160 0 +2006 ctx-rh-caudalanteriorcingulate_2 125 100 142 0 +2007 ctx-rh-caudalanteriorcingulate_3 125 100 143 0 +2008 ctx-rh-caudalmiddlefrontal_1 100 25 0 0 +2009 ctx-rh-caudalmiddlefrontal_2 82 25 0 0 +2010 ctx-rh-caudalmiddlefrontal_3 83 25 0 0 +2011 ctx-rh-caudalmiddlefrontal_4 84 25 0 0 +2012 ctx-rh-caudalmiddlefrontal_5 85 25 0 0 +2013 ctx-rh-cuneus_1 220 20 100 0 +2014 ctx-rh-cuneus_2 202 20 100 0 +2015 ctx-rh-cuneus_3 203 20 100 0 +2016 ctx-rh-cuneus_4 204 20 100 0 +2017 ctx-rh-entorhinal_1 220 20 10 0 +2018 ctx-rh-fusiform_1 180 220 140 0 +2019 ctx-rh-fusiform_2 180 194 140 0 +2020 ctx-rh-fusiform_3 180 195 140 0 +2021 ctx-rh-fusiform_4 180 196 140 0 +2022 ctx-rh-fusiform_5 180 197 140 0 +2023 ctx-rh-fusiform_6 180 198 140 0 +2024 ctx-rh-fusiform_7 180 199 140 0 +2025 ctx-rh-fusiform_8 180 200 140 0 +2026 ctx-rh-inferiorparietal_1 220 60 220 0 +2027 ctx-rh-inferiorparietal_2 212 60 220 0 +2028 ctx-rh-inferiorparietal_3 213 60 220 0 +2029 ctx-rh-inferiorparietal_4 214 60 220 0 +2030 ctx-rh-inferiorparietal_5 215 60 220 0 +2031 ctx-rh-inferiorparietal_6 216 60 220 0 +2032 ctx-rh-inferiorparietal_7 217 60 220 0 +2033 ctx-rh-inferiorparietal_8 218 60 220 0 +2034 ctx-rh-inferiorparietal_9 219 60 220 0 +2035 ctx-rh-inferiorparietal_10 221 60 220 0 +2036 ctx-rh-inferiorparietal_11 222 60 220 0 +2037 ctx-rh-inferiorparietal_12 223 60 220 0 +2038 ctx-rh-inferiortemporal_1 180 40 120 0 +2039 ctx-rh-inferiortemporal_2 162 40 120 0 +2040 ctx-rh-inferiortemporal_3 163 40 120 0 +2041 ctx-rh-inferiortemporal_4 164 40 120 0 +2042 ctx-rh-inferiortemporal_5 165 40 120 0 +2043 ctx-rh-inferiortemporal_6 166 40 120 0 +2044 ctx-rh-inferiortemporal_7 167 40 120 0 +2045 ctx-rh-isthmuscingulate_1 140 20 140 0 +2046 ctx-rh-isthmuscingulate_2 127 20 140 0 +2047 ctx-rh-lateraloccipital_1 20 30 140 0 +2048 ctx-rh-lateraloccipital_2 20 30 127 0 +2049 ctx-rh-lateraloccipital_3 20 30 128 0 +2050 ctx-rh-lateraloccipital_4 20 30 129 0 +2051 ctx-rh-lateraloccipital_5 20 30 130 0 +2052 ctx-rh-lateraloccipital_6 20 30 131 0 +2053 ctx-rh-lateraloccipital_7 20 30 132 0 +2054 ctx-rh-lateraloccipital_8 20 30 133 0 +2055 ctx-rh-lateraloccipital_9 20 30 134 0 +2056 ctx-rh-lateraloccipital_10 20 30 135 0 +2057 ctx-rh-lateralorbitofrontal_1 35 75 50 0 +2058 ctx-rh-lateralorbitofrontal_2 35 72 50 0 +2059 ctx-rh-lateralorbitofrontal_3 35 73 50 0 +2060 ctx-rh-lateralorbitofrontal_4 35 74 50 0 +2061 ctx-rh-lateralorbitofrontal_5 35 76 50 0 +2062 ctx-rh-lateralorbitofrontal_6 35 75 41 0 +2063 ctx-rh-lateralorbitofrontal_7 35 75 42 0 +2064 ctx-rh-lingual_1 225 140 140 0 +2065 ctx-rh-lingual_2 227 140 140 0 +2066 ctx-rh-lingual_3 228 140 140 0 +2067 ctx-rh-lingual_4 229 140 140 0 +2068 ctx-rh-lingual_5 230 140 140 0 +2069 ctx-rh-lingual_6 231 140 140 0 +2070 ctx-rh-lingual_7 232 140 140 0 +2071 ctx-rh-medialorbitofrontal_1 200 35 75 0 +2072 ctx-rh-medialorbitofrontal_2 182 35 75 0 +2073 ctx-rh-medialorbitofrontal_3 183 35 75 0 +2074 ctx-rh-medialorbitofrontal_4 184 35 75 0 +2075 ctx-rh-medialorbitofrontal_5 185 35 75 0 +2076 ctx-rh-middletemporal_1 160 100 50 0 +2077 ctx-rh-middletemporal_2 152 100 50 0 +2078 ctx-rh-middletemporal_3 153 100 50 0 +2079 ctx-rh-middletemporal_4 154 100 50 0 +2080 ctx-rh-middletemporal_5 155 100 50 0 +2081 ctx-rh-middletemporal_6 156 100 50 0 +2082 ctx-rh-middletemporal_7 157 100 50 0 +2083 ctx-rh-middletemporal_8 158 100 50 0 +2084 ctx-rh-middletemporal_9 159 100 50 0 +2085 ctx-rh-parahippocampal_1 20 220 60 0 +2086 ctx-rh-parahippocampal_2 20 194 60 0 +2087 ctx-rh-parahippocampal_3 20 195 60 0 +2088 ctx-rh-paracentral_1 60 220 60 0 +2089 ctx-rh-paracentral_2 60 200 60 0 +2090 ctx-rh-paracentral_3 60 201 60 0 +2091 ctx-rh-paracentral_4 60 202 60 0 +2092 ctx-rh-paracentral_5 60 203 60 0 +2093 ctx-rh-paracentral_6 60 204 60 0 +2094 ctx-rh-parsopercularis_1 220 180 140 0 +2095 ctx-rh-parsopercularis_2 202 180 140 0 +2096 ctx-rh-parsopercularis_3 203 180 140 0 +2097 ctx-rh-parsopercularis_4 204 180 140 0 +2098 ctx-rh-parsorbitalis_1 20 100 50 0 +2099 ctx-rh-parsorbitalis_2 20 77 50 0 +2100 ctx-rh-parstriangularis_1 220 60 20 0 +2101 ctx-rh-parstriangularis_2 211 60 20 0 +2102 ctx-rh-parstriangularis_3 212 60 20 0 +2103 ctx-rh-parstriangularis_4 213 60 20 0 +2104 ctx-rh-pericalcarine_1 120 100 60 0 +2105 ctx-rh-pericalcarine_2 102 100 60 0 +2106 ctx-rh-pericalcarine_3 103 100 60 0 +2107 ctx-rh-pericalcarine_4 104 100 60 0 +2108 ctx-rh-postcentral_1 220 20 20 0 +2109 ctx-rh-postcentral_2 219 20 20 0 +2110 ctx-rh-postcentral_3 221 20 20 0 +2111 ctx-rh-postcentral_4 222 20 20 0 +2112 ctx-rh-postcentral_5 223 20 20 0 +2113 ctx-rh-postcentral_6 224 20 20 0 +2114 ctx-rh-postcentral_7 220 6 20 0 +2115 ctx-rh-postcentral_8 220 7 20 0 +2116 ctx-rh-postcentral_9 220 8 20 0 +2117 ctx-rh-postcentral_10 220 9 20 0 +2118 ctx-rh-postcentral_11 220 10 20 0 +2119 ctx-rh-postcentral_12 220 11 20 0 +2120 ctx-rh-posteriorcingulate_1 220 180 220 0 +2121 ctx-rh-posteriorcingulate_2 220 180 202 0 +2122 ctx-rh-posteriorcingulate_3 220 180 203 0 +2123 ctx-rh-posteriorcingulate_4 220 180 204 0 +2124 ctx-rh-precentral_1 60 20 220 0 +2125 ctx-rh-precentral_2 60 20 211 0 +2126 ctx-rh-precentral_3 60 20 212 0 +2127 ctx-rh-precentral_4 60 20 213 0 +2128 ctx-rh-precentral_5 60 20 214 0 +2129 ctx-rh-precentral_6 60 20 215 0 +2130 ctx-rh-precentral_7 60 20 216 0 +2131 ctx-rh-precentral_8 60 20 217 0 +2132 ctx-rh-precentral_9 60 20 218 0 +2133 ctx-rh-precentral_10 60 20 219 0 +2134 ctx-rh-precentral_11 36 20 220 0 +2135 ctx-rh-precentral_12 37 20 220 0 +2136 ctx-rh-precentral_13 38 20 220 0 +2137 ctx-rh-precentral_14 39 20 220 0 +2138 ctx-rh-precentral_15 40 20 220 0 +2139 ctx-rh-precentral_16 41 20 220 0 +2140 ctx-rh-precuneus_1 160 140 180 0 +2141 ctx-rh-precuneus_2 160 140 162 0 +2142 ctx-rh-precuneus_3 160 140 163 0 +2143 ctx-rh-precuneus_4 160 140 164 0 +2144 ctx-rh-precuneus_5 160 140 165 0 +2145 ctx-rh-precuneus_6 160 140 166 0 +2146 ctx-rh-precuneus_7 160 140 167 0 +2147 ctx-rh-precuneus_8 160 140 168 0 +2148 ctx-rh-precuneus_9 160 140 169 0 +2149 ctx-rh-precuneus_10 160 140 170 0 +2150 ctx-rh-rostralanteriorcingulate_1 80 20 140 0 +2151 ctx-rh-rostralanteriorcingulate_2 80 20 127 0 +2152 ctx-rh-rostralmiddlefrontal_1 75 50 125 0 +2153 ctx-rh-rostralmiddlefrontal_2 75 50 122 0 +2154 ctx-rh-rostralmiddlefrontal_3 75 50 123 0 +2155 ctx-rh-rostralmiddlefrontal_4 75 50 124 0 +2156 ctx-rh-rostralmiddlefrontal_5 75 50 126 0 +2157 ctx-rh-rostralmiddlefrontal_6 71 50 125 0 +2158 ctx-rh-rostralmiddlefrontal_7 72 50 125 0 +2159 ctx-rh-rostralmiddlefrontal_8 73 50 125 0 +2160 ctx-rh-rostralmiddlefrontal_9 74 50 125 0 +2161 ctx-rh-rostralmiddlefrontal_10 76 50 125 0 +2162 ctx-rh-rostralmiddlefrontal_11 77 50 125 0 +2163 ctx-rh-rostralmiddlefrontal_12 78 50 125 0 +2164 ctx-rh-rostralmiddlefrontal_13 79 50 125 0 +2165 ctx-rh-superiorfrontal_1 20 220 160 0 +2166 ctx-rh-superiorfrontal_2 20 194 160 0 +2167 ctx-rh-superiorfrontal_3 20 195 160 0 +2168 ctx-rh-superiorfrontal_4 20 196 160 0 +2169 ctx-rh-superiorfrontal_5 20 197 160 0 +2170 ctx-rh-superiorfrontal_6 20 198 160 0 +2171 ctx-rh-superiorfrontal_7 20 199 160 0 +2172 ctx-rh-superiorfrontal_8 20 200 160 0 +2173 ctx-rh-superiorfrontal_9 20 201 160 0 +2174 ctx-rh-superiorfrontal_10 20 202 160 0 +2175 ctx-rh-superiorfrontal_11 20 203 160 0 +2176 ctx-rh-superiorfrontal_12 20 204 160 0 +2177 ctx-rh-superiorfrontal_13 20 205 160 0 +2178 ctx-rh-superiorfrontal_14 20 206 160 0 +2179 ctx-rh-superiorfrontal_15 20 207 160 0 +2180 ctx-rh-superiorfrontal_16 20 208 160 0 +2181 ctx-rh-superiorfrontal_17 20 209 160 0 +2182 ctx-rh-superiorparietal_1 20 180 140 0 +2183 ctx-rh-superiorparietal_2 20 162 140 0 +2184 ctx-rh-superiorparietal_3 20 163 140 0 +2185 ctx-rh-superiorparietal_4 20 164 140 0 +2186 ctx-rh-superiorparietal_5 20 165 140 0 +2187 ctx-rh-superiorparietal_6 20 166 140 0 +2188 ctx-rh-superiorparietal_7 20 167 140 0 +2189 ctx-rh-superiorparietal_8 20 168 140 0 +2190 ctx-rh-superiorparietal_9 20 169 140 0 +2191 ctx-rh-superiorparietal_10 20 170 140 0 +2192 ctx-rh-superiorparietal_11 20 171 140 0 +2193 ctx-rh-superiorparietal_12 20 172 140 0 +2194 ctx-rh-superiorparietal_13 20 173 140 0 +2195 ctx-rh-superiortemporal_1 140 220 220 0 +2196 ctx-rh-superiortemporal_2 140 220 202 0 +2197 ctx-rh-superiortemporal_3 140 220 203 0 +2198 ctx-rh-superiortemporal_4 140 220 204 0 +2199 ctx-rh-superiortemporal_5 140 220 205 0 +2200 ctx-rh-superiortemporal_6 140 220 206 0 +2201 ctx-rh-superiortemporal_7 140 220 207 0 +2202 ctx-rh-superiortemporal_8 140 220 208 0 +2203 ctx-rh-superiortemporal_9 140 220 209 0 +2204 ctx-rh-superiortemporal_10 140 220 210 0 +2205 ctx-rh-superiortemporal_11 140 220 211 0 +2206 ctx-rh-supramarginal_1 80 160 20 0 +2207 ctx-rh-supramarginal_2 80 152 20 0 +2208 ctx-rh-supramarginal_3 80 153 20 0 +2209 ctx-rh-supramarginal_4 80 154 20 0 +2210 ctx-rh-supramarginal_5 80 155 20 0 +2211 ctx-rh-supramarginal_6 80 156 20 0 +2212 ctx-rh-supramarginal_7 80 157 20 0 +2213 ctx-rh-supramarginal_8 80 158 20 0 +2214 ctx-rh-supramarginal_9 80 159 20 0 +2215 ctx-rh-frontalpole_1 100 0 100 0 +2216 ctx-rh-temporalpole_1 70 70 70 0 +2217 ctx-rh-transversetemporal_1 150 150 200 0 +2218 ctx-rh-insula_1 255 192 32 0 +2219 ctx-rh-insula_2 227 192 32 0 +2220 ctx-rh-insula_3 228 192 32 0 +2221 ctx-rh-insula_4 229 192 32 0 +2222 ctx-rh-insula_5 230 192 32 0 +2223 ctx-rh-insula_6 231 192 32 0 +2224 ctx-rh-insula_7 232 192 32 0 \ No newline at end of file diff --git a/bin/unix/3.1.2/templates/lausanne500/lh.lausanne500.gcs b/bin/unix/3.1.2/templates/lausanne500/lh.lausanne500.gcs new file mode 100755 index 0000000..ee015a2 Binary files /dev/null and b/bin/unix/3.1.2/templates/lausanne500/lh.lausanne500.gcs differ diff --git a/bin/unix/3.1.2/templates/lausanne500/parcellate_lausanne500.sh b/bin/unix/3.1.2/templates/lausanne500/parcellate_lausanne500.sh new file mode 100755 index 0000000..f8c0dda --- /dev/null +++ b/bin/unix/3.1.2/templates/lausanne500/parcellate_lausanne500.sh @@ -0,0 +1,106 @@ +#!/bin/bash +# +# Parcellate lausanne500 atlas + +# set -x +set -e + +####################################### +# Error handling +####################################### +error() { + if [ -n "$1" ]; then + echo -e "error: $1\n" >&2 + else + read line file <<<$(caller) + echo "An error occurred in line $line of file $file:" >&2 + sed "${line}q;d" "$file" >&2 + fi + exit 1 + +} + +####################################### +# Parse input +####################################### +parse_input() +{ + + while [ -n "$1" ]; do + shopt -s nocasematch + case "$1" in + --freesurferDir=*) + freesurferDir=${1#*=} + shift + ;; + --referenceFile=*) + referenceFile=${1#*=} + shift + ;; + --registrationMatrixFile=*) + registrationMatrixFile=${1#*=} + shift + ;; + --parcellationFile=*) + parcellationFile=${1#*=} + shift + ;; + --forceFreesurferOverwrite=*) + forceFreesurferOverwrite=${1#*=} + shift + ;; + --*=*) + inputParam=${1:2}; + shift + ;; + *) + error Unkown input argument: $inputParam + shift + ;; + esac +done +} + +####################################### +# Main function +####################################### +trap error ERR +parse_input "$@" + +TEMPLATE=lausanne500 + +templateDir=$(dirname "$0") # describing the directory that includes the lh.colortable.txt, rh.colortable.txt, lh.economo.gcs, rh.economo.gcs datafiles +subjectDir=$(pwd) +freesurferDir=${subjectDir}/$freesurferDir +subjectFS=$(basename "${freesurferDir}") # FreeSurfer subject + +# Prepare Freesurfer +SUBJECTS_DIR=$(dirname "${freesurferDir}") +cd "${SUBJECTS_DIR}" + +if [ ! -f "$subjectFS/label/rh.${TEMPLATE}.annot" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create LH and RH annotation files + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" lh "${subjectFS}/surf/lh.sphere.reg" "${templateDir}/lh.${TEMPLATE}.gcs" "${subjectFS}/label/lh.${TEMPLATE}.annot" + mris_ca_label -t "${templateDir}/${TEMPLATE}.annot.ctab" "${subjectFS}" rh "${subjectFS}/surf/rh.sphere.reg" "${templateDir}/rh.${TEMPLATE}.gcs" "${subjectFS}/label/rh.${TEMPLATE}.annot" + + # Add cortical labels to the automatic segmentation volume (aseg) + mri_aparc2aseg --s "${subjectFS}" --annot "${TEMPLATE}" + +fi + +if [ ! -f "$subjectFS/stats/rh.${TEMPLATE}.stats" ] || [ "$forceFreesurferOverwrite" = true ] ; then + + # Create anatomical stat files + mris_anatomical_stats -a "${subjectFS}/label/lh.${TEMPLATE}.annot" -f "${subjectFS}/stats/lh.${TEMPLATE}.stats" "${subjectFS}" lh + mris_anatomical_stats -a "${subjectFS}/label/rh.${TEMPLATE}.annot" -f "${subjectFS}/stats/rh.${TEMPLATE}.stats" "${subjectFS}" rh + +fi + + +# Derive segmentation of dwi B0-reference volume +cd "${subjectDir}" +mri_label2vol --seg "${freesurferDir}/mri/${TEMPLATE}+aseg.mgz" \ + --temp "${referenceFile}" --reg "${registrationMatrixFile}" --o "${parcellationFile}" + +exit 0 diff --git a/bin/unix/3.1.2/templates/lausanne500/rh.lausanne500.gcs b/bin/unix/3.1.2/templates/lausanne500/rh.lausanne500.gcs new file mode 100755 index 0000000..968a488 Binary files /dev/null and b/bin/unix/3.1.2/templates/lausanne500/rh.lausanne500.gcs differ diff --git a/bin/unix/CATO-3.1.2-unix.zip b/bin/unix/CATO-3.1.2-unix.zip new file mode 100644 index 0000000..9adc578 Binary files /dev/null and b/bin/unix/CATO-3.1.2-unix.zip differ diff --git a/make_functional.m b/make_functional.m index d340504..012c6ed 100644 --- a/make_functional.m +++ b/make_functional.m @@ -81,8 +81,6 @@ function make_functional(catoVersion) if ismac cleanDir = fullfile(targetDir, cleanDir); rmdir(cleanDir, 's'); -elseif isunix - delete(fullfile(targetDir, 'functional_pipeline_bin')); end mkdir(fullfile(targetDir, 'templates')); diff --git a/make_structural.m b/make_structural.m index 584b181..c5de879 100644 --- a/make_structural.m +++ b/make_structural.m @@ -76,8 +76,6 @@ function make_structural(catoVersion) if ismac cleanDir = fullfile(targetDir, cleanDir); rmdir(cleanDir, 's'); -elseif isunix - delete(fullfile(targetDir, 'functional_pipeline_bin')); end mkdir(fullfile(targetDir, 'templates')); diff --git a/src/functional_pipeline/config_functional_default.json b/src/functional_pipeline/config_functional_default.json index 424752b..489a9a4 100644 --- a/src/functional_pipeline/config_functional_default.json +++ b/src/functional_pipeline/config_functional_default.json @@ -18,6 +18,7 @@ "logFile": "OUTPUTDIR/functional_pipeline.log", "statusFile": "OUTPUTDIR/functional_pipeline.STATUS", "computedConfigFile": "OUTPUTDIR/functional_configuration.json", + "maxNumberCompThreads": 1, "TEMPDIR": "", "fmriProcessedTMPFile": "TEMPDIR/SUBJECT_fmri.nii" }, diff --git a/src/functional_pipeline/functionalParameterProperties.xlsx b/src/functional_pipeline/functionalParameterProperties.xlsx index 4b7aae9..7ece5bf 100644 Binary files a/src/functional_pipeline/functionalParameterProperties.xlsx and b/src/functional_pipeline/functionalParameterProperties.xlsx differ diff --git a/src/functional_pipeline/functional_pipeline.m b/src/functional_pipeline/functional_pipeline.m index 5c41444..7ddf253 100644 --- a/src/functional_pipeline/functional_pipeline.m +++ b/src/functional_pipeline/functional_pipeline.m @@ -212,7 +212,7 @@ reconStepNames = reconStepNames(runSteps); reconStepNames = reconStepNames(:); -%% Start logging +%% Setup pipeline (outputDir, logfile, #threads and welcome message) [succes, message] = mkdir(configParams.general.outputDir); if ~succes @@ -228,6 +228,14 @@ try diary(configParams.general.logFile) end cleanupLog = onCleanup(@() diary('off')); +% Set maximum number of cores +if configParams.general.maxNumberCompThreads == 0 +maxNumCompThreads('automatic'); +else + maxNumCompThreads(configParams.general.maxNumberCompThreads); +end +nNumCompThreads = maxNumCompThreads; + status.general = 'running'; updateStatus(configParams.general.statusFile, status); @@ -236,6 +244,7 @@ try diary(configParams.general.logFile) fprintf('---CATO----\n'); fprintf('Version: %s\n', catoVersion); fprintf('Started at: %s\n', timeStart); +fprintf('Number of threads: %i\n', nNumCompThreads); fprintf('Subject name: %s\n', subjectName); fprintf('Subject directory: %s\n\n', subjectDir); diff --git a/src/structural_pipeline/config_structural_default.json b/src/structural_pipeline/config_structural_default.json index 95a2d1c..585b1df 100644 --- a/src/structural_pipeline/config_structural_default.json +++ b/src/structural_pipeline/config_structural_default.json @@ -29,6 +29,7 @@ "logFile": "OUTPUTDIR/structural_pipeline.log", "statusFile": "OUTPUTDIR/structural_pipeline.STATUS", "computedConfigFile": "OUTPUTDIR/structural_configuration.json", + "maxNumberCompThreads": 1, "maxMemoryGB": 2 }, "structural_preprocessing":{ diff --git a/src/structural_pipeline/structuralParameterProperties.xlsx b/src/structural_pipeline/structuralParameterProperties.xlsx index 75f91d9..1c025e1 100644 Binary files a/src/structural_pipeline/structuralParameterProperties.xlsx and b/src/structural_pipeline/structuralParameterProperties.xlsx differ diff --git a/src/structural_pipeline/structural_pipeline.m b/src/structural_pipeline/structural_pipeline.m index 4335f7e..741f673 100644 --- a/src/structural_pipeline/structural_pipeline.m +++ b/src/structural_pipeline/structural_pipeline.m @@ -196,7 +196,7 @@ reconStepNames = reconStepNames(runSteps); reconStepNames = reconStepNames(:); -%% Start logging +%% Setup pipeline (outputDir, logfile, #threads and welcome message) [succes, message] = mkdir(configParams.general.outputDir); if ~succes @@ -212,6 +212,14 @@ try diary(configParams.general.logFile) end cleanupLog = onCleanup(@() diary('off')); +% Set maximum number of cores +if configParams.general.maxNumberCompThreads == 0 +maxNumCompThreads('automatic'); +else + maxNumCompThreads(configParams.general.maxNumberCompThreads); +end +nNumCompThreads = maxNumCompThreads; + status.general = 'running'; updateStatus(configParams.general.statusFile, status); @@ -220,6 +228,7 @@ try diary(configParams.general.logFile) fprintf('---CATO----\n'); fprintf('Version: %s\n', catoVersion); fprintf('Started at: %s\n', timeStart); +fprintf('Number of threads: %i\n', nNumCompThreads); fprintf('Subject name: %s\n', subjectName); fprintf('Subject directory: %s\n\n', subjectDir);