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#! /bin/bash
in=$1
if [[ ! -s $in ]] || [[ ${#in} -lt 3 ]] ; then
echo open this example file and take a look to see what is done
exit
fi
out=motcorr
# average the time series
antsMotionCorr -d 3 -a $in -o ${out}_avg.nii.gz
# do affine motion correction
antsMotionCorr -d 3 -o [${out},${out}.nii.gz,${out}_avg.nii.gz] -m gc[ ${out}_avg.nii.gz , $in , 1 , 1 , Random, 0.05 ] -t Affine[ 0.005 ] -i 20 -u 1 -e 1 -s 0 -f 1 -n 10
# do affine and deformable correction
antsMotionCorr -d 3 -o [${out},${out}.nii.gz,${out}_avg.nii.gz] -m gc[ ${out}_avg.nii.gz , $in , 1 , 1 , Random, 0.05 ] -t Affine[ 0.005 ] -i 20 -u 1 -e 1 -s 0 -f 1 -m CC[ ${out}_avg.nii.gz , $in , 1 , 2 ] -t GaussianDisplacementField[0.15,3,0.5] -i 20 -u 1 -e 1 -s 0 -f 1 -n 10
# check a result by taking a 3d slice from 4d
ExtractSliceFromImage 4 ${out}.nii.gz temp.nii.gz 0 32
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