43 lines
1.9 KiB
(Stored with Git Annex)
Shell
43 lines
1.9 KiB
(Stored with Git Annex)
Shell
#! bin/bash
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# you must module load fsl(most up_to_date version) using fsl_load.sh in $BDL
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root=/dors/gpc/JamesBooth/JBooth-Lab/BDL/ELP/bids_dwi_preproc/
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cd $root
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#subjects=$(ls | grep "sub-5*")
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subjects="sub-5002 sub-5003" #your subject list
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ses=ses-5
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param=/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/ELP/Jin_code/dwi_preprocessing/acqparam.txt
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index1=/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/ELP/Jin_code/dwi_preprocessing/index1.txt
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index2=/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/ELP/Jin_code/dwi_preprocessing/index2.txt
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index3=/gpfs51/dors2/gpc/JamesBooth/JBooth-Lab/BDL/ELP/Jin_code/dwi_preprocessing/index3.txt
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# loop through subjects and folders
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for sub in $subjects
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do
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echo $sub
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cd $root/${sub}/${ses}
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folder=$(ls | grep "dwi")
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cd $root/${sub}/${ses}/$folder
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files=$(ls | grep "dwi.nii")
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for f in $files
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do
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shortnm=$(basename $f .nii)
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# run fslroi to extract the b0 image
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$FSLDIR/bin/fslroi $f ${shortnm}_bet.nii 0 1
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# run bet
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$FSLDIR/bin/bet ${shortnm}_bet.nii ${shortnm}_bet_brain.nii -m
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# count number of volumes based on bvecs
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bvals=$(cat ${shortnm}.bval)
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volnum=$(( $(grep -o ' ' <<< "$bvals" | wc -l) + 1 ))
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echo $volnum
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# run eddy
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if [[ "$volnum" -eq 69 ]]; then
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$FSLDIR/bin/eddy --imain=$f --mask=${shortnm}_bet_brain_mask.nii --acqp=${param} --index=${index1} --bvecs=${shortnm}.bvec --bvals=${shortnm}.bval --out=eddy_corrected_${shortnm} --cnr_maps=true;
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elif [[ "$volnum" -eq 70 ]]; then
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$FSLDIR/bin/eddy --imain=$f --mask=${shortnm}_bet_brain_mask.nii --acqp=${param} --index=${index2} --bvecs=${shortnm}.bvec --bvals=${shortnm}.bval --out=eddy_corrected_${shortnm} --cnr_maps=true;
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else
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$FSLDIR/bin/eddy --imain=$f --mask=${shortnm}_bet_brain_mask.nii --acqp=${param} --index=${index3} --bvecs=${shortnm}.bvec --bvals=${shortnm}.bval --out=eddy_corrected_${shortnm} --cnr_maps=true;
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fi
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done # for files
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done #for subjects
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