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group_preprocess.sh
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group_preprocess.sh
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#!/bin/bash -v
################################################################################
#
# group_preprocess
# ----------------
#
# Extracts necessary dMRI and T1 files from HCP datasets and pre-process them
#
################################################################################
#
# Usage : group_preprocess.sh <path to the directory with the HCP minimally
# "pre-processed" diffusion and structural zip files>
#
# Output : Relevant HCP data files organized by subject (each subject has its own
# subdirectory ./<subject_number>)
# Log of each subjects pre-processing is in
# ./<subject_number>/pre_processing_log_<subject_number>.txt
#
# Author : Oren Civier
# Version: 1.01
# Date: 8/11/2017
#
################################################################################
HCP_data_dir=$1
# looping over subjects
for n in ${HCP_data_dir}/*Diffusion_preproc.zip; do
echo "================================="
echo pre-processing subject ${n}
echo "================================="
echo ${n}
subject=`basename -s _3T_Diffusion_preproc.zip ${n}`
echo ${subject}
mkdir ${subject}
cd ${subject}
mkdir hcp_preproc
cd hcp_preproc
unzip ${HCP_data_dir}/${subject}_3T_Diffusion_preproc.zip \
${subject}/T1w/Diffusion/bvals \
${subject}/T1w/Diffusion/bvecs \
${subject}/T1w/Diffusion/data.nii.gz; alert
ln -s hcp_preproc/${subject}/T1w/Diffusion/bvals ../bvals
ln -s hcp_preproc/${subject}/T1w/Diffusion/bvecs ../bvecs
ln -s hcp_preproc/${subject}/T1w/Diffusion/data.nii.gz ../data.nii.gz
unzip ${HCP_data_dir}/${subject}_3T_Structural_preproc.zip \
${subject}/T1w/T1w_acpc_dc_restore_brain.nii.gz; alert
ln -s hcp_preproc/${subject}/T1w/T1w_acpc_dc_restore_brain.nii.gz \
../T1w_acpc_dc_restore_brain.nii.gz
cd ..
../subject_preprocess.sh |& tee pre_processing_log_${subject}.txt
cd ..
done