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run_autotrack_PNC.sh
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run_autotrack_PNC.sh
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#!/bin/bash
participant_file=/cbica/projects/thalamocortical_development/sample_info/PNC/PNC_NonVariantDWI_participantlist.txt
QSIRECON_DIR=/cbica/projects/thalamocortical_development/qsirecon_0.16.0RC3/PNC
BUNDLES_DIR=/cbica/projects/thalamocortical_development/thalamocortical_structuralconnectivity/individual/PNC
for id in $(cat $participant_file); do
FIB_FILE=${QSIRECON_DIR}/${id}/ses-PNC1/dwi/${id}_ses-PNC1_space-T1w_desc-preproc_gqi.fib.gz
GFA_FILE=${QSIRECON_DIR}/${id}/ses-PNC1/dwi/${id}_ses-PNC1_space-T1w_desc-preproc_desc-gfa_gqiscalar.nii.gz
OUTPUT_DIR=${BUNDLES_DIR}/${id}
if ! [ -d ${BUNDLES_DIR}/${id}/thalamus-R_VIP-autotrack ]
then
qsub -pe threaded 9 -o /cbica/projects/thalamocortical_development/code/thalamocortical_development/thalamocortical_structuralconnectivity/individual/PNC/autotrack_logs/${id}-PNC-autotrack-bundles.o -e /cbica/projects/thalamocortical_development/code/thalamocortical_development/thalamocortical_structuralconnectivity/individual/PNC/autotrack_logs/${id}-PNC-autotrack-bundles.e /cbica/projects/thalamocortical_development/code/thalamocortical_development/thalamocortical_structuralconnectivity/individual/thalamocortical_autotrack.sh ${FIB_FILE} ${OUTPUT_DIR} ${GFA_FILE} 0
sleep 1
fi
done