hcp_organize.sh

#!/bin/bash

# Stolen ahem I mean borrowed from @gkiar

rawdir='HCP900/raw'

cd ${rawdir}

for i in `ls `;
do
        cd ${i}
        mkdir ${i}"_95LR" ${i}"_95RL" ${i}"_96LR" ${i}"_96RL" ${i}"_97LR" ${i}"_97RL"
        rm -rf *BIAS*
        rm -rf *SBRef*
  mv *dir95_LR* ${i}"_95LR"
  mv *dir95_RL* ${i}"_95RL"
  mv *dir96_LR* ${i}"_96LR"
  mv *dir96_RL* ${i}"_96RL"
  mv *dir97_LR* ${i}"_97LR"
  mv *dir97_RL* ${i}"_97RL"

        for j in `ls -d */`;
        do
                echo $j
                cp ./*T1w_MPR1.nii.gz ${j}
                cd ${j}
                        for m in `ls | grep MPR1`;
                        do
                                echo ${m} 'HCP500_'`echo ${j} | cut -c -11`'_MPRAGE'`echo ${m} | cut -c 19-`;
                                mv ${m} 'HCP500_'`echo ${j} | cut -c -11`'_MPRAGE'`echo ${m} | cut -c 19-`;
                        done
                        for m in `ls | grep DWI`;
                        do
                                echo ${m} 'HCP500_'`echo ${j} | cut -c -11`'_DTI'`echo ${m} | cut -c 23-`;
                                mv ${m} 'HCP500_'`echo ${j} | cut -c -11`'_DTI'`echo ${m} | cut -c 23-`;
                        done
                cd ..
        done
        rm -rf *T1w_MPR1.nii.gz
        cd ..
done