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Merge branch 'hotfix-3.1.2' into main
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@SiemondeLange
SiemondeLange committed May 28, 2021
2 parents 0605d6e + 3db8471 commit 369a76e
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10 changes: 10 additions & 0 deletions bin/macos/3.1.2/LICENSE
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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.
4 changes: 4 additions & 0 deletions bin/macos/3.1.2/VERSION
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CATO 3.1.2
Operating system: macos (MACI64)
Compiled on: 17-May-2021 16:43:35
Compiled using: MATLAB Compiler 6.5 (R2017b)
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159 changes: 159 additions & 0 deletions bin/macos/3.1.2/functional_preprocessing/preprocess_default.sh
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#!/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
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197 changes: 197 additions & 0 deletions bin/macos/3.1.2/structural_preprocessing/preprocess_eddy.sh
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#!/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

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