Commit f3dfbd43 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

Delete cmore_run_warpLabels2Ind.sh

parent 3d26d1cc
#!/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}
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