Delete cmore_run_reg2template.sh

OB_pipeline/cmore_run_reg2template.sh

-#!/bin/bash
-
-# Author: Christoph Arthofer
-# Copyright: FMRIB 2021
-
-TAG='cmore'
-BASE_DIR="cmore/data/"
-DATA_DIR="cmore/data/orig/"
-ID_PATH="cmore/data/IDs.csv"
-
-N_IMGS=$(cat ${ID_PATH} | wc -l)
-AFF_IMG_REF_ID="T1_unbiased_affine_template_MNI_T1_brain"
-NLN_IMG_REF_ID="unbiased_nonlinear_template_it18"
-AFF_REF_DIR="template/affine/"
-AFF_REF_PATH="${AFF_REF_DIR}${AFF_IMG_REF_ID}.nii.gz"
-NLN_REF_DIR="template/nonlinear/"
-NLN_REF_PATH="${NLN_REF_DIR}${NLN_IMG_REF_ID}.nii.gz"
-PARAM_IT_PATH="${NLN_REF_DIR}mmorf_config.ini"
-i_outp=0
-
-# Create output directory for affine registrations
-AFFINE_DIR="${BASE_DIR}affine/"
-mkdir -p ${AFFINE_DIR}
-
-# Register all individual images to the affine reference template
-i_outp=$((i_outp+1))
-printf -v i "%04d" $i_outp
-qsub -o ${BASE_DIR}${i}_output_affine_FLIRT.log \
-  -N ${TAG}_registrations_affine_it1 \
-  -q short.qc \
-  -t 1-${N_IMGS}:1 \
-  cmore_FLIRT_registration.sh ${ID_PATH} ${DATA_DIR} ${AFFINE_DIR} ${AFF_REF_PATH} ${AFF_IMG_REF_ID}
-
-# Register indivdiual T2 images to corresponding T1 images
-i_outp=$((i_outp+1))
-printf -v i "%04d" $i_outp
-qsub -o ${BASE_DIR}${i}_output_affine_FLIRT_T2_2_T1_it1.log \
-  -N ${TAG}_registrations_affine_t2_2_t1_it1 \
-  -q short.qc \
-  -t 1-${N_IMGS}:1 \
-  cmore_FLIRT_registrations_T1_2_T2.sh ${ID_PATH} ${DATA_DIR} ${AFFINE_DIR}
-
-i_outp=$((i_outp+1))
-printf -v i "%04d" $i_outp
-qsub -hold_jid ${TAG}_registrations_affine_t2_2_t1_it1,${TAG}_registrations_affine_testing_it1 \
-  -o ${BASE_DIR}${i}_output_affine_transform_T2_2_MNI.log \
-  -N ${TAG}_transform_T2_2_MNI \
-  -q short.qc \
-  -t 1-${N_IMGS}:1 \
-  cmore_applyxfm2T2.sh ${ID_PATH} ${AFFINE_DIR} ${DATA_DIR} ${AFF_IMG_REF_ID} ${AFF_REF_PATH}
-
-# ----------------------------------------------------------------------------------------------------------------------
-# Nonlinear registrations with MMORF
-NLN_DIR="${BASE_DIR}nonlinear/"
-mkdir -p ${NLN_DIR}
-
-i_outp=$((i_outp+1))
-printf -v i "%04d" $i_outp
-REF_DIR=${NLN_REF_DIR}
-REF_ID=${NLN_IMG_REF_ID}
-qsub -hold_jid ${TAG}_transform_T2_2_MNI \
-  -o ${BASE_DIR}${i}_output_nln_registrations_it1.log \
-  -N ${TAG}_registrations_mmorf \
-  -q gpu8.q \
-  -l gpu=1 \
-  -l gputype=p100 \
-  -t 1-${N_IMGS}:1 \
-  cmore_mmorf.sh ${ID_PATH} ${REF_DIR} ${REF_ID} ${AFFINE_DIR} ${DATA_DIR} ${NLN_DIR} ${PARAM_IT_PATH}
-
-# Applying unbiased warps to CMORE T1 whole-head images
-IMG_PATH="${DATA_DIR}%03d/T1/T1_unbiased.nii.gz"
-WARP_PATH="${NLN_DIR}%03d_to_unbiased_nonlinear_template_it18_warp.nii.gz"
-WARPED_IMG_PATH="${NLN_DIR}%03d_to_unbiased_nonlinear_template_it18_T1_head.nii.gz"
-WARPED_IMG_NORM_PATH="${NLN_DIR}%03d_to_unbiased_nonlinear_template_it18_T1_head_norm.nii.gz"
-AFFMAT_PATH="${AFFINE_DIR}%03d_to_T1_unbiased_affine_template_MNI_T1_brain_T1reg.mat"
-REF_PATH="${NLN_REF_DIR}unbiased_nonlinear_template_it18_T1_head.nii.gz"
-i_outp=$((i_outp+1))
-printf -v i "%04d" $i_outp
-qsub -hold_jid ${TAG}_registrations_mmorf \
-  -o ${BASE_DIR}${i}_output_nln_applyUnbiased2T1Head_it1.log \
-  -N ${TAG}_nln_applyUnbiased2T1Head_it1 \
-  -q short.qc \
-  -t 1-${N_IMGS}:1 \
-  cmore_applyWarp.sh ${ID_PATH} ${IMG_PATH} ${WARP_PATH} ${WARPED_IMG_PATH} ${WARPED_IMG_NORM_PATH} ${AFFMAT_PATH} ${REF_PATH}
-
-# Applying unbiased warps to CMORE T2 whole-head images
-IMG_PATH="${DATA_DIR}%03d/T2_FLAIR/T2_FLAIR_unbiased.nii.gz"
-WARP_PATH="${NLN_DIR}%03d_to_unbiased_nonlinear_template_it18_warp.nii.gz"
-WARPED_IMG_PATH="${NLN_DIR}%03d_to_unbiased_nonlinear_template_it18_T2_head.nii.gz"
-WARPED_IMG_NORM_PATH="${NLN_DIR}%03d_to_unbiased_nonlinear_template_it18_T2_head_norm.nii.gz"
-AFFMAT_PATH="${AFFINE_DIR}%03d_to_T1_unbiased_affine_template_MNI_T1_brain_T2reg.mat"
-REF_PATH="${NLN_REF_DIR}unbiased_nonlinear_template_it18_T2_head.nii.gz"
-i_outp=$((i_outp+1))
-printf -v i "%04d" $i_outp
-qsub -hold_jid ${TAG}_registrations_mmorf \
-  -o ${BASE_DIR}${i}_output_nln_applyUnbiased2T1Head_it1.log \
-  -N ${TAG}_nln_applyUnbiased2T1Head_it1 \
-  -q short.qc \
-  -t 1-${N_IMGS}:1 \
-  cmore_applyWarp.sh ${ID_PATH} ${IMG_PATH} ${WARP_PATH} ${WARPED_IMG_PATH} ${WARPED_IMG_NORM_PATH} ${AFFMAT_PATH} ${REF_PATH}