Commit 75d2d607 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

Delete cmore_applyxfm2T2.sh

parent 73739900
#!/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}
IN_DIR=${2}
OUT_DIR=${IN_DIR}
DATA_DIR=${3}
IMG_REF_ID=${4}
IMG_REF_PATH=${5}
IMG_IN_ID=$(awk 'NR=='${SGE_TASK_ID} ${ID_PATH})
T2_2_T1_OMAT_PATH="${IN_DIR}${IMG_IN_ID}_T2_to_T1.mat"
T1_2_REF_PATH="${IN_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T1reg.mat"
T2_OMAT_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T2reg.mat"
convert_xfm -omat ${T2_OMAT_OUT_PATH} -concat ${T1_2_REF_PATH} ${T2_2_T1_OMAT_PATH}
IMG_IN_PATH="${DATA_DIR}${IMG_IN_ID}/T2_FLAIR/T2_FLAIR_unbiased.nii.gz"
IMG_OUT_PATH="${OUT_DIR}${IMG_IN_ID}_to_${IMG_REF_ID}_T2reg.nii.gz"
flirt -in ${IMG_IN_PATH} -ref ${IMG_REF_PATH} -out ${IMG_OUT_PATH} -applyxfm -init ${T2_OMAT_OUT_PATH} -interp spline
rv=$?
echo `date`: task complete
exit $rv
\ No newline at end of file
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