Dear FSL users,
I am having trouble defining ROIs in MNI space. I tried to write a script based on several tutorials and reading the fslmaths manual, but I am not sure why this script will not run. I have also tried line by line - it runs without error, but does not give an ROI with any value when I check it in FSLEYES.
Script:
echo "Input image: MNI152_T1_2mm_brain.nii.gz"
echo "ROI coordinates: ${1} ${2} ${3} "
echo "ROI size: ${4} "
echo "Output name: ${5}"
fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -roi ${1} 1 ${2} 1 ${3} 1 0 1 tmp_point -odt float
fslmaths tmp_point -kernel sphere ${4} -fmean tmp_sphere
fslmaths tmp_sphere -bin ${5}_sphere_${1}_${2}_${3}.nii.gz
rm tmp_point*
echo "Done! The output file is called '${5}_sphere_${1}-${2}-${3}_${4}mm' "
echo " "
Error:
Error in command line: unknown option "tmp_point"
Image Exception : #63 :: No image files match: tmp_point
libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: No image files match: tmp_point
make_sphere_roi.sh: line 8: 52736 Abort trap: 6 fslmaths tmp_point -kernel sphere ${4} -fmean tmp_sphere
Image Exception : #63 :: No image files match: tmp_sphere
libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: No image files match: tmp_sphere
make_sphere_roi.sh: line 9: 52737 Abort trap: 6 fslmaths tmp_sphere -bin ${5}_sphere_${1}_${2}_${3}.nii.gz
rm: tmp_point*\r: No such file or directory
Best wishes, Andreas
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