Commit 582227e7 authored by Christoph Arthofer's avatar Christoph Arthofer
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parent f3dfbd43
#!/bin/bash
# Author: Christoph Arthofer
# Copyright: FMRIB 2021
#$ -cwd -j y
#$ -r y
echo `date`: Executing task ${SGE_TASK_ID} of job ${JOB_ID} on `hostname` as user ${USER}
echo SGE_TASK_FIRST=${SGE_TASK_FIRST}, SGE_TASK_LAST=${SGE_TASK_LAST}, SGE_TASK_STEPSIZE=${SGE_TASK_STEPSIZE}
. ~/.bash_profile
. $MODULESHOME/init/bash
module load fsl/6.0.3
ID_PATH=$1
DATA_DIR=$2
TEMP_DIR=$3
OUT_DIR=$4
IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
IMG_REF_PATH="${TEMP_DIR}T1_template_brain.nii.gz"
T1_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_template_T1reg.mat"
echo "flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T1_OMAT_OUT_PATH} -dof 12"
flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T1_OMAT_OUT_PATH} -dof 12
IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T2_FLAIR/T2_FLAIR_unbiased_brain.nii.gz"
IMG_REF_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
T2_to_T1_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_T2_to_T1.mat"
echo "flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T2_to_T1_OMAT_OUT_PATH} -dof 6"
flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${T2_to_T1_OMAT_OUT_PATH} -dof 6
T2_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_template_T2reg.mat"
echo "convert_xfm -omat ${T2_OMAT_OUT_PATH} -concat ${T1_OMAT_OUT_PATH} ${T2_to_T1_OMAT_OUT_PATH}"
convert_xfm -omat ${T2_OMAT_OUT_PATH} -concat ${T1_OMAT_OUT_PATH} ${T2_to_T1_OMAT_OUT_PATH}
rv=$?
echo `date`: task complete
exit $rv
\ No newline at end of file
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