Commit a2206424 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

Delete cmore_FLIRT_registration.sh

parent 01a80bde
#!/bin/bash
#$ -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
OUT_DIR=$3
IMG_REF_PATH=$4
IMG_REF_ID=$5
IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased_brain.nii.gz"
IMG_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1reg.nii.gz"
OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1reg.mat"
echo "flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -omat ${OMAT_OUT_PATH}"
flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -omat ${OMAT_OUT_PATH}
HEAD_IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T1/T1_unbiased.nii.gz"
echo "flirt -in ${HEAD_IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -applyxfm -init ${OMAT_OUT_PATH} -interp spline"
flirt -in ${HEAD_IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -applyxfm -init ${OMAT_OUT_PATH} -interp spline
rv=$?
echo `date`: task complete
exit $rv
\ No newline at end of file
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