Dear FSL experts, I'm sorry it's me again.
I have started the fsl course and so far all the programs have been working properly thanks to your help, and I've been able to follow the video lectures. However when I moved onto the brain extraction part, I could not progress.
The Bet_gui interface opens appropriately, and I'm selecting the structural.nii.gz file. I'm also keeping the output name with _brain as suggested, but when I hit 'Go', the terminal spits an error that states:
Jessicas-MBP:intro jessicaquezada$ Bet_gui
/usr/local/fsl/bin/bet /Users/jessicaquezada/fsl_course_data/intro/structural /Users/jessicaquezada/fsl_course_data/intro/structural_brain -f 0.5 -g 0
/usr/local/fsl/bin/bet failed during operation
libc++abi.dylib: terminating with uncaught exception of type NiftiIO::NiftiException: Error: cant open file /Users/jessicaquezada/fsl_course_data/intro/structural_brain.nii.gz
/usr/local/fsl/bin/bet: line 401: 2599 Abort trap: 6 ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
Finished
I checked that I have permission to write and modify the folder and files, so there shouldn't be a problem, but when I try to perform the next exercise with the command line (without the gui)
bet structural structural_brain2 -f 0.5 -m
it returns the following:
libc++abi.dylib: terminating with uncaught exception of type NiftiIO::NiftiException: Error: cant open file structural_brain2.nii.gz
/usr/local/fsl/bin/bet: line 401: 2674 Abort trap: 6 ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
/usr/local/fsl/bin/bet failed during operation
I thought there was a problem with the permissions, so I tried the same command but with sudo, but then again returns another error, this time displaying:
/usr/local/fsl/bin/bet: line 159: /bin/remove_ext: No such file or directory
/usr/local/fsl/bin/bet failed during operation
So I'm quite lost now as to where the problem is.
As usual, your help is greatly appreciated.
Hoping you're safe during these difficult times,
Seb.
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