Upload cmore_run_warpLabels2Ind.sh

OB_pipeline/cmore_run_warpLabels2Ind.sh

+#!/bin/bash
+
+# Author: Christoph Arthofer
+# Copyright: FMRIB 2021
+
+ID_PATH='cmore/data/IDs.csv'
+WARPS_DIR="cmore/data/nonlinear/"
+DATA_DIR="cmore/data/orig/"
+N_IMGS=$(cat ${ID_PATH} | wc -l)
+
+REF_PATH="${DATA_DIR}%s/T2_FLAIR/T2_FLAIR_unbiased.nii.gz"
+
+AFF_DIR='cmore/data/affine/'
+AFF_IN_PATH="${AFF_DIR}%s_to_T1_unbiased_affine_template_MNI_T1_brain_T2reg.mat"
+AFF_OUT_PATH="${AFF_DIR}%s_to_T1_unbiased_affine_template_MNI_T1_brain_T2reg_inverse.mat"
+qsub -o ukbb_invertAffines.log \
+  -N ukbb_invertAffines \
+  -q short.qc \
+  -t 1-${N_IMGS}:1 \
+  cmore_invertAffine.sh ${ID_PATH} ${AFF_IN_PATH} ${AFF_OUT_PATH}
+
+WARP_IN_PATH="${WARPS_DIR}%s_to_unbiased_nonlinear_template_it18_warp.nii.gz"
+WARP_OUT_PATH="${WARPS_DIR}%s_to_unbiased_nonlinear_template_it18_warp_inverse.nii.gz"
+qsub -o ukbb_invertWarps.log \
+  -N ukbb_invertWarps \
+  -q short.qc \
+  -t 1-${N_IMGS}:1 \
+  cmore_invertWarps.sh ${ID_PATH} ${REF_PATH} ${WARP_IN_PATH} ${WARP_OUT_PATH}
+
+LABEL_IN_PATH="template/ob_labels.nii.gz"
+LABEL_OUT_PATH="${WARPS_DIR}%s_ob_labels_trilinear.nii.gz"
+qsub -hold_jid ukbb_invertWarps,ukbb_invertAffines \
+  -o ukbb_warpLabels.log \
+  -N ukbb_warpLabels \
+  -q short.qc \
+  -t 1-${N_IMGS}:1 \
+  cmore_inverseWarpLabel.sh ${ID_PATH} ${REF_PATH} ${WARP_OUT_PATH} ${AFF_OUT_PATH} ${LABEL_IN_PATH} ${LABEL_OUT_PATH}