/
pipeline_example
executable file
·42 lines (38 loc) · 1.53 KB
/
pipeline_example
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#!/bin/bash
echo "running pipeline"
homedir=$(pwd)
args="Js* TheraStride* Exert* METS* "
args+="-numthreads auto -memory 32 -maxthreads 24 -analysis Analyze -v"
nwpipe "dcm2nii -m N ../SPACE" \
$args -numthreads 1 \
-in ../SPACE -out ../SPACE/o*.nii.gz
nwpipe "unbias T2.nii.gz" \
$args -outdir unbiased \
-in ../SPACE/o*.nii.gz T2.nii.gz \
-out T2_unbiased.nii.gz
nwpipe "unbias T1.nii.gz" \
$args -outdir unbiased \
-in ../MPRAGE/o*.nii.gz T1.nii.gz \
-out T1_unbiased.nii.gz
nwpipe "bet_nw ../unbiased/T2 t2_brain -R -png -d -s -m -f 0.4 -g -0.2" \
$args -outdir bet_notunbiased \
-in unbiased/T2.nii.gz \
-out t2_brain.nii.gz
nwpipe "${NWTOOLS}/lesion_mapper -in ../bet_notunbiased/t2_brain.nii.gz -v -png -no2fast" \
$args -outdir lesions_no2fast \
-in bet_notunbiased/t2_brain.nii.gz \
-out lesionmapT2.nii.gz \
-out lesionstats.csv \
-out lesions45.png
nwpipe "bet_nw ../unbiased/T1_unbiased.nii.gz I_brain -IN2 ../unbiased/T2_unbiased.nii.gz -png -d -s -m -f 0.4 -g -0.2" \
$args -outdir bet_multispectral \
-in unbiased/T1_unbiased.nii.gz \
-in unbiased/T2_unbiased.nii.gz \
-out bet9.png
nwpipe "sienax_nw ../unbiased/T1_unbiased.nii.gz -o . -in2 ../unbiased/T2_unbiased.nii.gz -d -betdir ../bet_multispectral -lmt2 ../lesions_no2fast/lesionmapT2.nii.gz -nossm -S \"-N\"" \
$args -outdir sienax_no2fast \
-in unbiased/T1_unbiased.nii.gz \
-in unbiased/T2_unbiased.nii.gz \
-in lesions_no2fast/lesionmapT2.nii.gz \
-out report.html \
-out volumes.txt