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.nfs000000022671204f000608a8
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.nfs000000022671204f000608a8
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function copy()
{
subject=$1
input=/space/erebus/1/users/HCPD/HCPDUnprocessed/
output=/space/erebus/1/users/HCPD/preprocessed_viv/
mkdir -p ${output}/${subject}
#copy diffusion
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir98_AP.nii.gz ${output}/${subject}/dMRI_AP1.nii.gz
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir98_AP.bval ${output}/${subject}/dMRI_AP1.bvals
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir98_AP.bvec ${output}/${subject}/dMRI_AP1.bvecs
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir99_AP.nii.gz ${output}/${subject}/dMRI_AP2.nii.gz
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir99_AP.bval ${output}/${subject}/dMRI_AP2.bvals
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir99_AP.bvec ${output}/${subject}/dMRI_AP2.bvecs
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir98_PA.nii.gz ${output}/${subject}/dMRI_PA1.nii.gz
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir98_PA.bval ${output}/${subject}/dMRI_PA1.bvals
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir98_PA.bvec ${output}/${subject}/dMRI_PA1.bvecs
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir99_PA.nii.gz ${output}/${subject}/dMRI_PA2.nii.gz
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir99_PA.bval ${output}/${subject}/dMRI_PA2.bvals
cp ${input}/${subject}/unprocessed/Diffusion/${subject}_dMRI_dir99_PA.bvec ${output}/${subject}/dMRI_PA2.bvecs
#resting state
cp ${input}/${subject}/unprocessed/rfMRI_REST1_AP/${subject}_rfMRI_REST1_AP.nii.gz ${output}/${subject}/fMRI_rest1_AP.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST1_AP/${subject}_SpinEchoFieldMap1_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_1.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST1_AP/${subject}_SpinEchoFieldMap1_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_1.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST1_PA/${subject}_rfMRI_REST1_PA.nii.gz ${output}/${subject}/fMRI_rest2_PA.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST2_AP/${subject}_rfMRI_REST2_AP.nii.gz ${output}/${subject}/fMRI_rest3_AP.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST2_AP/${subject}_SpinEchoFieldMap3_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_2.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST2_AP/${subject}_SpinEchoFieldMap3_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_2.nii.gz
cp ${input}/${subject}/unprocessed/rfMRI_REST2_PA/${subject}_rfMRI_REST2_PA.nii.gz ${output}/${subject}/fMRI_rest4_PA.nii.gz
#structural
cp ${input}/${subject}/unprocessed/T1w_MPR_vNav_4e_RMS/${subject}_T1w_MPR_vNav_4e_RMS.nii.gz ${output}/${subject}/T1.nii.gz
cp ${input}/${subject}/unprocessed/T2w_SPC_vNav/${subject}_T2w_SPC_vNav.nii.gz ${output}/${subject}/T2.nii.gz
#gambling
cp ${input}/${subject}/unprocessed/tfMRI_GUESSING_AP/${subject}_tfMRI_GUESSING_AP.nii.gz ${output}/${subject}/tfMRI_gambling1_AP.nii.gz
cp ${input}/${subject}/unprocessed/tfMRI_GUESSING_PA/${subject}_tfMRI_GUESSING_PA.nii.gz ${output}/${subject}/tfMRI_gambling2_PA.nii.gz
#facematching
cp ${input}/${subject}/unprocessed/tfMRI_EMOTION_PA/${subject}_tfMRI_EMOTION_PA.nii.gz ${output}/${subject}/tfMRI_faceMatching1_PA.nii.gz
cp ${input}/${subject}/unprocessed/tfMRI_GUESSING_PA/${subject}_SpinEchoFieldMap2_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_3.nii.gz
cp ${input}/${subject}/unprocessed/tfMRI_GUESSING_PA/${subject}_SpinEchoFieldMap2_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_3.nii.gz
}
function copyDownloaded()
{
cd /autofs/space/erebus_001/users/HCPD/HCPDUnprocessed/downloaded
output=/space/erebus/1/users/HCPD/preprocessed_viv/
for f in vsiless*/;
do
cd ${f}
for s in HCD*/;
do
cd ${s}
subject=${s/_A/_MR}
subject=${subject/_B/_MR}
echo ${subject}
mkdir -p ${output}/${subject}
cp 20/NIFTI/*_T1w_MPR_vNav_4e_RMS.nii.gz ${output}/${subject}/T1.nii.gz
cp 14/NIFTI/*_T1w_MPR_vNav_4e_RMS.nii.gz ${output}/${subject}/T1.nii.gz
cp 24/NIFTI/*_T1w_MPR_vNav_4e_RMS.nii.gz ${output}/${subject}/T1.nii.gz
cp 24/NIFTI/*_T2w_SPC_vNav.nii.gz ${output}/${subject}/T2.nii.gz
cp 28/NIFTI/*_T2w_SPC_vNav.nii.gz ${output}/${subject}/T2.nii.gz
cp */NIFTI/*_dMRI_dir98_AP.nii.gz ${output}/${subject}/dMRI_AP1.nii.gz
cp */NIFTI/*_dMRI_dir98_AP.bval ${output}/${subject}/dMRI_AP1.bvals
cp */NIFTI/*_dMRI_dir98_AP.bvec ${output}/${subject}/dMRI_AP1.bvecs
cp */NIFTI/*_dMRI_dir99_AP.nii.gz ${output}/${subject}/dMRI_AP2.nii.gz
cp */NIFTI/*_dMRI_dir99_AP.bval ${output}/${subject}/dMRI_AP2.bvals
cp */NIFTI/*_dMRI_dir99_AP.bvec ${output}/${subject}/dMRI_AP2.bvecs
cp */NIFTI/*_dMRI_dir98_PA.nii.gz ${output}/${subject}/dMRI_PA1.nii.gz
cp */NIFTI/*_dMRI_dir98_PA.bval ${output}/${subject}/dMRI_PA1.bvals
cp */NIFTI/*_dMRI_dir98_PA.bvec ${output}/${subject}/dMRI_PA1.bvecs
cp */NIFTI/*_dMRI_dir99_PA.nii.gz ${output}/${subject}/dMRI_PA2.nii.gz
cp */NIFTI/*_dMRI_dir99_PA.bval ${output}/${subject}/dMRI_PA2.bvals
cp */NIFTI/*_dMRI_dir99_PA.bvec ${output}/${subject}/dMRI_PA2.bvecs
cp */NIFTI/*_V1_A_rfMRI_REST_AP.nii.gz ${output}/${subject}/fMRI_rest1_AP.nii.gz
cp */NIFTI/*_V1_A_rfMRI_REST_PA.nii.gz ${output}/${subject}/fMRI_rest2_PA.nii.gz
cp */NIFTI/*_V1_B_rfMRI_REST_AP.nii.gz ${output}/${subject}/fMRI_rest3_AP.nii.gz
cp */NIFTI/*_V1_B_rfMRI_REST_PA.nii.gz ${output}/${subject}/fMRI_rest4_PA.nii.gz
cp */NIFTI/*_tfMRI_GUESSING_AP.nii.gz ${output}/${subject}/tfMRI_gambling1_AP.nii.gz
cp */NIFTI/*_tfMRI_GUESSING_PA.nii.gz ${output}/${subject}/tfMRI_gambling2_PA.nii.gz
cp */NIFTI/*_tfMRI_EMOTION_PA.nii.gz ${output}/${subject}/tfMRI_faceMatching1_PA.nii.gz
cp 7/NIFTI/*_A_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_1.nii.gz
cp 8/NIFTI/*_A_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_1.nii.gz
cp 7/NIFTI/*_V1_B_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_2.nii.gz
cp 13/NIFTI/*_V1_B_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_2.nii.gz
cp 12/NIFTI/*_V1_B_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_2.nii.gz
cp 8/NIFTI/*_V1_B_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_2.nii.gz
cp 14/NIFTI/*_V1_B_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_2.nii.gz
cp 13/NIFTI/*_V1_B_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_2.nii.gz
cp 25/NIFTI/*_A_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_3.nii.gz
cp 27/NIFTI/*_A_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_3.nii.gz
cp 29/NIFTI/*_A_SpinEchoFieldMap_AP.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_AP_3.nii.gz
cp 26/NIFTI/*_A_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_3.nii.gz
cp 28/NIFTI/*_A_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_3.nii.gz
cp 30/NIFTI/*_A_SpinEchoFieldMap_PA.nii.gz ${output}/${subject}/fMRI_SpinEchoFieldMap_PA_3.nii.gz
cd ..
done
cd ..
done
}
function copyDownloadedBs()
{
cd /autofs/space/erebus_001/users/HCPD/HCPDUnprocessed/downloaded
output=/space/erebus/1/users/HCPD/preprocessed_viv/
for f in vsiless*/;
do
cd ${f}
for s in HCD*/;
do
cd ${s}
subject=${s/_A/_MR}
subject=${subject/_B/_MR}
echo ${subject}
cp */NIFTI/*_dMRI_dir98_AP.bval ${output}/${subject}/dMRI_AP1.bvals
cp */NIFTI/*_dMRI_dir98_AP.bvec ${output}/${subject}/dMRI_AP1.bvecs
cp */NIFTI/*_dMRI_dir99_AP.bval ${output}/${subject}/dMRI_AP2.bvals
cp */NIFTI/*_dMRI_dir99_AP.bvec ${output}/${subject}/dMRI_AP2.bvecs
cp */NIFTI/*_dMRI_dir98_PA.bval ${output}/${subject}/dMRI_PA1.bvals
cp */NIFTI/*_dMRI_dir98_PA.bvec ${output}/${subject}/dMRI_PA1.bvecs
cp */NIFTI/*_dMRI_dir99_PA.bval ${output}/${subject}/dMRI_PA2.bvals
cp */NIFTI/*_dMRI_dir99_PA.bvec ${output}/${subject}/dMRI_PA2.bvecs
cd ..
done
cd ..
done
}
function movepreprocessed()
{
file=$1
input=/space/erebus/1/users/HCPD/preprocessed_viv
output=/space/erebus/1/users/HCPD/preprocessed_viv2
inputFS=/autofs/space/erebus_001/users/HCPD/preprocessed_viv/FS_STRUCTURE
outputFS=/autofs/space/erebus_001/users/HCPD/preprocessed_viv/FS_STRUCTURE2
mkdir ${output}
mkdir ${outputFS}
for s in `cat ${file}`;
do
subject=${s/^M/}_V1_MR
mv ${input}/${subject} ${output}/${subject}
mv ${inputFS}/${subject} ${outputFS}/${subject}
done
}
function moveUnpreprocessed()
{
file=$1
input=/space/erebus/1/users/HCPD/HCPDUnprocessed
output=/space/erebus/1/users/HCPD/unpreprocessed
for s in `cat ${file}`;
do
subject=${s/^M/}_V1_MR
mv ${input}/${subject} ${output}/${subject}
done
}
function copyFunctional()
{
file=$1
output=/space/erebus/1/users/HCPD/preprocessed_viv/
for s in `cat ${file}`;
do
subject=${s/^M/}_V1_MR
echo ${subject} > ${output}/FS_STRUCTURE/${subject}/subjectname
#mkdir -p ${output}/FS_STRUCTURE/${subject}/rest/001/
#mkdir -p ${output}/FS_STRUCTURE/${subject}/rest/002/
#cp ${output}/${subject}/fMRI_rest1_AP_topup.nii.gz ${output}/FS_STRUCTURE/${subject}/rest/001/f.nii.gz
#cp ${output}/${subject}/fMRI_rest2_PA_topup.nii.gz ${output}/FS_STRUCTURE/${subject}/rest/002/f.nii.gz
done
}
function prepareBedpostx()
{
file=$1
output=/space/erebus/1/users/HCPD/preprocessed_viv/
for s in `cat ${file}`;
do
subject=${s/^M/}_V1_MR
echo ${s} ${subject}
mkdir -p ${output}/${subject}/bedpostxr/
fdt_rotate_bvecs ${output}/${subject}/bvecs ${output}/${subject}/bvecs_rotated ${output}/${subject}/dMRI_topup_eddy.nii.gz.eddy_parameters
cp ${output}/${subject}/bvecs_rotated ${output}/${subject}/bedpostxr/bvecs
#cp ${output}/${subject}/dMRI_topup_eddy.nii.gz ${output}/${subject}/bedpostxr/data.nii.gz
#cp ${output}/${subject}/bvals ${output}/${subject}/bedpostxr/
#cp ${output}/${subject}/dMRI_brain_mask.nii.gz ${output}/${subject}/bedpostxr/nodif_brain_mask.nii.gz
done
}
function copyFunctionalBANDA()
{
file=$1
output=/space/erebus/1/users/data/preprocess/
for s in `cat ${file}`;
do
subject=${s/^M/}
echo ${s}
echo ${subject} > ${output}/FS/MGH_HCP/${subject}/subjectname
#mkdir -p ${output}/FS/MGH_HCP/${subject}/rest/001/
#mkdir -p ${output}/FS/MGH_HCP/${subject}/rest/002/
#cp ${output}/${subject}/fMRI_rest1_AP_topup.nii.gz ${output}/FS/MGH_HCP/${subject}/rest/001/f.nii.gz
#cp ${output}/${subject}/fMRI_rest2_PA_topup.nii.gz ${output}/FS/MGH_HCP/${subject}/rest/002/f.nii.gz
done
}
function prepareBedpostxBANDA()
{
file=$1
output=/space/erebus/1/users/data/preprocess/
for s in `cat ${file}`;
do
subject=${s/^M/}
echo ${s} ${subject}
mkdir -p ${output}/${subject}/bedpostx/
cp ${output}/${subject}/dMRI_topup_eddy.nii.gz ${output}/${subject}/bedpostx/data.nii.gz
cp ${output}/${subject}/bv* ${output}/${subject}/bedpostx/
cp ${output}/${subject}/dMRI_brain_mask.nii.gz ${output}/${subject}/bedpostx/nodif_brain_mask.nii.gz
done
}
function all()
{
cd /space/erebus/1/users/HCPD/HCPDUnprocessed/
for s in */;
do
$0 $1 ${s///}
done
}
$@