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init_hcp3.sh
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#!/bin/bash
SUB=$1
OUT=$2
ID_0005=105115
ID_0006=110411
ID_0007=111312
ID_0008=113619
ID=$(eval echo "\$ID_$SUB")
SRC=/N/dc2/projects/lifebid/2t1/HCP
### PREPROCESS ANAT
mkdir -p ${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/anat
cp ${SRC}/${ID}/anatomy/T1w_acpc_dc_restore_1p25.nii.gz \
${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/anat/sub-${SUB}_T1w.nii.gz
### PREPROCESS DWI
DWI=dwi_data_b2000
mkdir -p ${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/dwi
cp ${SRC}/${ID}/diffusion_data/${DWI}_aligned_trilin.nii.gz \
${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi.nii.gz
cp ${SRC}/${ID}/diffusion_data/${DWI}.bvals \
${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi.bvals
cp ${SRC}/${ID}/diffusion_data/${DWI}.bvecs \
${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi.bvecs
cp ${SRC}/${ID}/dt6_b2000trilin/bin/brainMask.nii.gz \
${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/dwi/sub-${SUB}_dwi_brainmask.nii.gz
### RECON MODELS
mkdir -p ${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/anat
cp ${SRC}/${ID}/dt6_b2000trilin/bin/wmMask.nii.gz \
${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/anat/sub-${SUB}_T1_wmmask.nii.gz
mkdir -p ${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/dwi
DWI=dwi_data_b2000_aligned_trilin
mrconvert ${SRC}/${ID}/fibers_new/${DWI}_dt.mif \
${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi_DTI.nii.gz
mrconvert ${SRC}/${ID}/fibers_new/${DWI}_ev.mif \
${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi_EV.nii.gz
mrconvert ${SRC}/${ID}/fibers_new/${DWI}_fa.mif \
${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi_FA.nii.gz
mrconvert ${SRC}/${ID}/fibers_new/${DWI}_lmax8.mif \
${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi_ODF.nii.gz
cp ${SRC}/${ID}/fibers_new/${DWI}_response.txt \
${OUT}/O3D_HCP3T/derivatives/recon_models/sub-${SUB}/dwi/sub-${SUB}_b-2000_dwi_dwiresponse.txt
### TRACTOGRAPHY
TCK=dwi_data_b2000_aligned_trilin
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_dtidet_tck/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
cp ${SRC}/${ID}/fibers_new/${TCK}_wm_tensor-NUM${N}-500000.tck \
${OUT}/O3D_HCP3T/derivatives/tracking_dtidet_tck/sub-${SUB}/dwi/sub-${SUB}_dwi_var-dtidet_run-${N}_tract.tck
done
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_csddet_tck/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
cp ${SRC}/${ID}/fibers_new/${TCK}_csd_lmax8_wm_SD_STREAM-NUM${N}-500000.tck \
${OUT}/O3D_HCP3T/derivatives/tracking_csddet_tck/sub-${SUB}/dwi/sub-${SUB}_dwi_var-csddet_run-${N}_tract.tck
done
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_csdprob_tck/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
cp ${SRC}/${ID}/fibers_new/${TCK}_csd_lmax8_wm_SD_PROB-NUM${N}-500000.tck \
${OUT}/O3D_HCP3T/derivatives/tracking_csdprob_tck/sub-${SUB}/dwi/sub-${SUB}_dwi_var-csdprob_run-${N}_tract.tck
done
REF=${OUT}/O3D_HCP3T/derivatives/preprocess/sub-${SUB}/dwi/sub-${SUB}_dwi_brainmask.nii.gz
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_dtidet_trk/sub-${SUB}/dwi
TCK=${OUT}/O3D_HCP3T/derivatives/tracking_dtidet_tck/sub-${SUB}/dwi
TRK=${OUT}/O3D_HCP3T/derivatives/tracking_dtidet_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TCK}/sub-${SUB}_dwi_var-dtidet_run-${N}_tract.tck \
-o ${TRK}/sub-${SUB}_dwi_var-dtidet_run-${N}_tract.trk \
-a ${REF} -f
done
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_csddet_trk/sub-${SUB}/dwi
TCK=${OUT}/O3D_HCP3T/derivatives/tracking_csddet_tck/sub-${SUB}/dwi
TRK=${OUT}/O3D_HCP3T/derivatives/tracking_csddet_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TCK}/sub-${SUB}_dwi_var-csddet_run-${N}_tract.tck \
-o ${TRK}/sub-${SUB}_dwi_var-csddet_run-${N}_tract.trk \
-a ${REF} -f
done
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_csdprob_trk/sub-${SUB}/dwi
TCK=${OUT}/O3D_HCP3T/derivatives/tracking_csdprob_tck/sub-${SUB}/dwi
TRK=${OUT}/O3D_HCP3T/derivatives/tracking_csdprob_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TCK}/sub-${SUB}_dwi_var-csdprob_run-${N}_tract.tck \
-o ${TRK}/sub-${SUB}_dwi_var-csdprob_run-${N}_tract.trk \
-a ${REF} -f
done
### LIFE STRUCT
FE=/N/dc2/projects/lifebid/code/ccaiafa/Caiafa_Pestilli_paper2015/Revision_Feb2017/Results/Single_TC/fe_structures
mkdir -p ${OUT}/O3D_HCP3T/derivatives/life_struct/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
cp ${FE}/${ID}/fe_structure_${ID}_STC_run01_tensor__connNUM${N}.mat \
${OUT}/O3D_HCP3T/derivatives/life_struct/sub-${SUB}/dwi/sub-${SUB}_dwi_var-dtidetlife_run-${N}_life.mat
done
for N in 01 02 03 04 05 06 07 08 09 10; do
cp ${FE}/${ID}/fe_structure_${ID}_STC_run01_SD_STREAM_lmax8_connNUM${N}.mat \
${OUT}/O3D_HCP3T/derivatives/life_struct/sub-${SUB}/dwi/sub-${SUB}_dwi_var-csddetlife_run-${N}_life.mat
done
for N in 01 02 03 04 05 06 07 08 09 10; do
cp ${FE}/${ID}/fe_structure_${ID}_STC_run01_SD_PROB_lmax8_connNUM${N}.mat \
${OUT}/O3D_HCP3T/derivatives/life_struct/sub-${SUB}/dwi/sub-${SUB}_dwi_var-csdproblife_run-${N}_life.mat
done
### LIFE TRACTOGRAPHY
FE=${OUT}/O3D_HCP3T/derivatives/life_struct/sub-${SUB}/dwi
ADD1="addpath(genpath('/N/dc2/projects/lifebid/Paolo/local/matlab'))"
ADD2="addpath(genpath('/N/dc2/projects/o3d/code/utils'))"
VAR=dtidet
PRE=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
MAT=${FE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_life.mat
TRK=${PRE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.trk
RAS=${PRE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract_RAS.trk
CMD="fe2trk $MAT $REF $RAS"
matlab -nojvm -nodesktop -nosplash -r "${ADD1};${ADD2};${CMD};exit"
TractConverter.py -i $RAS -o $TRK -a $REF -f
rm $RAS
done
VAR=csddet
PRE=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
MAT=${FE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_life.mat
TRK=${PRE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.trk
RAS=${PRE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract_RAS.trk
CMD="fe2trk $MAT $REF $RAS"
matlab -nojvm -nodesktop -nosplash -r "${ADD1};${ADD2};${CMD};exit"
TractConverter.py -i $RAS -o $TRK -a $REF -f
rm $RAS
done
VAR=csdprob
PRE=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
MAT=${FE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_life.mat
TRK=${PRE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.trk
RAS=${PRE}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract_RAS.trk
CMD="fe2trk $MAT $REF $RAS"
matlab -nojvm -nodesktop -nosplash -r "${ADD1};${ADD2};${CMD};exit"
TractConverter.py -i $RAS -o $TRK -a $REF -f
rm $RAS
done
VAR=dtidet
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_tck
TCK=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_tck/sub-${SUB}/dwi
TRK=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TRK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.trk \
-o ${TCK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.tck \
-a ${REF} -f
done
VAR=csddet
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_tck
TCK=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_tck/sub-${SUB}/dwi
TRK=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TRK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.trk \
-o ${TCK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.tck \
-a ${REF} -f
done
VAR=csdprob
mkdir -p ${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_tck
TCK=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_tck/sub-${SUB}/dwi
TRK=${OUT}/O3D_HCP3T/derivatives/tracking_${VAR}_trk/sub-${SUB}/dwi
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TRK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.trk \
-o ${TCK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_tract.tck \
-a ${REF} -f
done
### AFQ DISSECTION
/N/dc2/projects/o3d/code/init_dissection_fe2trk.sh HCP3T ${SUB} test3 dtidet
/N/dc2/projects/o3d/code/init_dissection_fe2trk.sh HCP3T ${SUB} test3 csddet
/N/dc2/projects/o3d/code/init_dissection_fe2trk.sh HCP3T ${SUB} test3 csdprob
SET='ATRl ATRr CSTl CSTr CCgl CCgr CHyl CHyr FMJ FMI IFOFl IFOFr ILFl ILFr SLFl SLFr UFl UFr ARCl ARCr'
VAR=dtidet
TCK=${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_tck/sub-${SUB}/dwi/
TRK=${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_trk/sub-${SUB}/dwi/
mkdir -p ${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_tck/sub-${SUB}/dwi
for S in $SET; do
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TRK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_var-afq_set-${S}_tract.trk \
-o ${TCK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_var-afq_set-${S}_tract.tck \
-a ${REF} -f
done
done
VAR=csddet
TCK=${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_tck/sub-${SUB}/dwi/
TRK=${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_trk/sub-${SUB}/dwi/
mkdir -p ${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_tck/sub-${SUB}/dwi
for S in $SET; do
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TRK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_var-afq_set-${S}_tract.trk \
-o ${TCK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_var-afq_set-${S}_tract.tck \
-a ${REF} -f
done
done
VAR=csdprob
TCK=${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_tck/sub-${SUB}/dwi/
TRK=${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_trk/sub-${SUB}/dwi/
mkdir -p ${OUT}/O3D_HCP3T/derivatives/dissection_${VAR}_tck/sub-${SUB}/dwi
for S in $SET; do
for N in 01 02 03 04 05 06 07 08 09 10; do
TractConverter.py \
-i ${TRK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_var-afq_set-${S}_tract.trk \
-o ${TCK}/sub-${SUB}_dwi_var-${VAR}life_run-${N}_var-afq_set-${S}_tract.tck \
-a ${REF} -f
done
done
### CONNECTOME