ATPP_CLI V2.0

0_gen_WD.sh

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+#! /bin/bash
+# generate working directory for ATPP
+#
+# Directory structure:
+#	  Working_dir
+#     |-- sub1
+#     |   |-- T1_sub1.nii
+#     |   `-- b0_sub1.nii
+#     |-- ...
+#     |-- subN
+#     |   |-- T1_subN.nii
+#     |   `-- b0_subN.nii
+#     |-- ROI
+#     |   |-- ROI_L.nii
+#     |   `-- ROI_R.nii
+#     `-- log 
+#
+# !! Please modify the following codes to organzie these files according to the above structure
+
+
+WD=$1
+shift
+DATA_DIR=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+ROI_DIR=$1
+
+# generate ROI directory
+mkdir -p ${WD}/ROI
+mkdir -p ${WD}/log
+
+# unzip ROIs if they are in gz format 
+gunzip ${ROI_DIR}/${ROI}_L.nii.gz
+gunzip ${ROI_DIR}/${ROI}_R.nii.gz
+
+# copy ROIs from ROI_DIR to ROI directory in working directory
+cp -vrt ${WD}/ROI ${ROI_DIR}/${ROI}_L.nii ${ROI_DIR}/${ROI}_R.nii
+
+# copy T1 and b0 files from DATA_DIR for each subject
+for sub in `cat ${SUB_LIST}`
+do
+    mkdir -p ${WD}/${sub} 
+	cp -vrt ${WD}/${sub} ${DATA_DIR}/${sub}/T1_brain.nii.gz ${DATA_DIR}/${sub}/DTI/nodif_brain.nii.gz
+	gunzip ${WD}/${sub}/nodif_brain.nii.gz
+	gunzip ${WD}/${sub}/T1_brain.nii.gz
+	mv -v ${WD}/${sub}/T1_brain.nii ${WD}/${sub}/T1_${sub}.nii	
+	mv -v ${WD}/${sub}/nodif_brain.nii ${WD}/${sub}/b0_${sub}.nii	
+done

10_postprocess_mpm.sh

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+#! /bin/bash
+# smooth the mpm image
+
+PIPELINE=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+MAX_CL_NUM=$1
+shift
+NIFTI=$1
+shift
+MPM_THRES=$1
+shift
+VOX_SIZE=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${PIPELINE}');addpath('${NIFTI}');postprocess_mpm_group_xmm('${WD}','${ROI}','${SUB_LIST}',${MAX_CL_NUM},${MPM_THRES},${VOX_SIZE},${LEFT},${RIGHT});exit"

11_validation.sh

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+#! /bin/bash
+# produce various validity indices
+
+pipeline=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB=$1
+shift
+METHOD=$1
+shift
+VOX_SIZE=$1
+shift
+MAX_CL_NUM=$1
+shift
+N_ITER=$1
+shift
+POOLSIZE=$1
+shift
+GROUP_THRES=$1
+shift
+MPM_THRES=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+shift
+split_half=$1
+shift
+pairwise=$1
+shift
+leave_one_out=$1
+shift
+cont=$1
+shift
+hi_vi=$1
+shift
+silhouette=$1
+shift
+tpd=$1
+
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${pipeline}');validation('${WD}','${ROI}','${SUB}','${METHOD}',${VOX_SIZE},${MAX_CL_NUM},${N_ITER},${POOLSIZE},${GROUP_THRES},${MPM_THRES},${LEFT},${RIGHT},${split_half},${pairwise},${leave_one_out},${cont},${hi_vi},${silhouette},${tpd});exit" 
+

12_indices_plot.sh

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+#! /bin/bash
+# plot indices
+
+pipeline=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+VOX_SIZE=$1
+shift
+MAX_CL_NUM=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+shift
+split_half=$1
+shift
+pairwise=$1
+shift
+leave_one_out=$1
+shift
+cont=$1
+shift
+hi_vi=$1
+shift
+silhouette=$1
+shift
+tpd=$1
+
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${pipeline}');addpath('${pipeline}/export_fig');indices_plot('${WD}','${ROI}','${SUB_LIST}',${VOX_SIZE},${MAX_CL_NUM},${LEFT},${RIGHT},${split_half},${pairwise},${leave_one_out},${cont},${hi_vi},${silhouette},${tpd});exit"

1_ROI_registration_spm.sh

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+#! /bin/bash
+# ROI registration, from MNI space to DTI space, using spm batch
+
+PIPELINE=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+POOLSIZE=$1
+shift
+SPM=$1
+shift
+NIFTI=$1
+shift
+TEMPLATE=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+
+source ${PIPELINE}/config.sh
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${PIPELINE}');addpath('${SPM}');addpath('${NIFTI}');ROI_registration_spm('${WD}','${ROI}','${SUB_LIST}',${POOLSIZE},'${TEMPLATE}',${LEFT},${RIGHT});exit"
+
+
+for sub in `cat ${SUB_LIST}`
+do
+	if [ "${LEFT}" == "1" ]; then
+		mv ${WD}/${sub}/w${ROI}_L.nii ${WD}/${sub}/${sub}_${ROI}_L_DTI.nii
+		gzip ${WD}/${sub}/${sub}_${ROI}_L_DTI.nii
+	fi
+	if [ "${RIGHT}" == "1" ]; then
+		mv ${WD}/${sub}/w${ROI}_R.nii ${WD}/${sub}/${sub}_${ROI}_R_DTI.nii
+        gzip ${WD}/${sub}/${sub}_${ROI}_R_DTI.nii
+	fi
+done
+
+

2_ROI_calc_coord.sh

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+#! /bin/bash
+# calculate ROI coordinates in DTI space
+
+PIPELINE=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+POOLSIZE=$1
+shift
+NIFTI=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${PIPELINE}');addpath('${NIFTI}');ROI_calc_coord('${WD}','${ROI}','${SUB_LIST}','${POOLSIZE}',${LEFT},${RIGHT});exit"

3_ROI_probtrackx.sh

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+#! /bin/bash
+# generate probabilistic tractography for each voxel in ROI
+
+WD=$1
+shift
+DATA_DIR=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+N_SAMPLES=$1
+shift
+DIS_COR=$1
+shift
+LEN_STEP=$1
+shift
+N_STEPS=$1
+shift
+CUR_THRES=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+
+# create a directory to check the status
+if [ -d ${WD}/qsub_jobdone ]
+then
+	rm -rf ${WD}/qsub_jobdone
+	mkdir -p ${WD}/qsub_jobdone
+else
+	mkdir -p ${WD}/qsub_jobdone
+fi
+
+
+for sub in $(cat ${SUB_LIST})
+do
+# single voxel probtrackx
+if [ "${LEFT}" == "1" ]; then
+	job_id=$(${COMMAND_FSLSUB} -l ${WD}/log ${COMMAND_PROBTRACKX} --mode=simple --seedref=${DATA_DIR}/${sub}/DTI.bedpostX/nodif_brain_mask -o ${ROI}_L -x ${WD}/${sub}/${sub}_${ROI}_L_coord.txt -l ${DIS_COR} -c ${CUR_THRES} -S ${N_STEPS} --steplength=${LEN_STEP} -P ${N_SAMPLES} --forcedir --opd -s ${DATA_DIR}/${sub}/DTI.bedpostX/merged -m ${DATA_DIR}/${sub}/DTI.bedpostX/nodif_brain_mask --dir=${WD}/${sub}/${sub}_${ROI}_L_probtrackx &)
+	echo "${sub}_L probtrackx is running...! job_ID is ${job_id}"
+	mute=$(${COMMAND_FSLSUB} -j ${job_id} -N running... -l ${WD}/log touch ${WD}/qsub_jobdone/${sub}_L.jobdone)
+fi
+
+if [ "${RIGHT}" == "1" ]; then
+	job_id=$(${COMMAND_FSLSUB} -l ${WD}/log ${COMMAND_PROBTRACKX} --mode=simple --seedref=${DATA_DIR}/${sub}/DTI.bedpostX/nodif_brain_mask -o ${ROI}_R -x ${WD}/${sub}/${sub}_${ROI}_R_coord.txt -l ${DIS_COR} -c ${CUR_THRES} -S ${N_STEPS} --steplength=${LEN_STEP} -P ${N_SAMPLES} --forcedir --opd -s ${DATA_DIR}/${sub}/DTI.bedpostX/merged -m ${DATA_DIR}/${sub}/DTI.bedpostX/nodif_brain_mask --dir=${WD}/${sub}/${sub}_${ROI}_R_probtrackx &)
+	echo "${sub}_R probtrackx is running...! job_ID is ${job_id}"
+	mute=$(${COMMAND_FSLSUB} -j ${job_id} -N running... -l ${WD}/log touch ${WD}/qsub_jobdone/${sub}_R.jobdone)
+fi
+
+done
+
+
+# check whether the tasks are finished or not
+N=$(cat ${SUB_LIST}|wc -l)
+if [ "${LEFT}" == "1" -a "${RIGHT}" == "0" ]
+then
+	while [ "$(ls ${WD}/qsub_jobdone|wc -l)" != "${N}"  ]
+	do
+		sleep 30s
+	done	
+fi
+
+if [ "${LEFT}" == "0" -a "${RIGHT}" == "1" ]
+then
+	while [ "$(ls ${WD}/qsub_jobdone|wc -l)" != "${N}"  ]
+	do
+		sleep 30s
+	done	
+fi
+
+if [ "${LEFT}" == "1" -a "${RIGHT}" == "1" ]
+then
+	while [ "$(ls ${WD}/qsub_jobdone|wc -l)" != "$((${N}*2))"  ]
+	do
+		sleep 30s
+	done	
+fi
+
+echo "=========== Finally Probtrackx All Done!! ==========="

4_ROI_calc_matrix.sh

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+#! /bin/bash
+# calculate connectivity matrix between each voxel in ROI and the remain voxels of whole brain 
+# and correlation matrix among voxels in ROI
+
+PIPELINE=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+POOLSIZE=$1
+shift
+NIFTI=$1
+shift
+VAL_THRES=$1
+shift
+DOWN_SIZE=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${PIPELINE}');addpath('${NIFTI}');ROI_calc_matrix('${WD}','${ROI}','${SUB_LIST}',${POOLSIZE},${VAL_THRES},${DOWN_SIZE},${LEFT},${RIGHT});exit"

5_ROI_parcellation.sh

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+#! /bin/bash
+# ROI parcellation using spectral clustering, to generate 2 to max cluster number subregion
+
+PIPELINE=$1
+shift
+WD=$1
+shift
+ROI=$1
+shift
+SUB_LIST=$1
+shift
+MAX_CL_NUM=$1
+shift
+POOLSIZE=$1
+shift
+METHOD=$1
+shift
+LEFT=$1
+shift
+RIGHT=$1
+
+${COMMAND_MATLAB} -nodisplay -nosplash -r "addpath('${PIPELINE}');ROI_parcellation('${WD}','${ROI}','${SUB_LIST}',${MAX_CL_NUM},${POOLSIZE},'${METHOD}',${LEFT},${RIGHT});exit"