Hi Mark,
Thanks for your reply. I found that under fsl_course_data/intro/, there is no structural_brain.nii.gz
Please note that I am the administrator of this MacBook Pro. For strange reason, quiet often I need to add the keyword sudo before doing anything to the files in /usr/local/fsi
I also issued "sudo chmod 777 fsl_course_data"
fsl_course_data:
total 0
drwxrwxr-x@ 6 7887 2616 204 Jun 21 20:35 fdt
drwxr-xr-x 10 root wheel 340 Oct 1 00:16 fmri
drwxrwxr-x@ 19 7887 2616 646 Oct 1 00:15 intro
drwxrwxr-x@ 8 7887 2616 272 Jun 21 20:36 melodic
drwxrwxr-x@ 19 7887 2616 646 Oct 1 00:15 reg
drwxrwxr-x@ 25 7887 2616 850 Oct 1 00:16 scripting
drwxrwxr-x@ 9 7887 2616 306 Oct 1 00:15 seg_struc
drwxrwxr-x@ 11 7887 2616 374 Jun 21 20:44 tbss
Tried to run bet_gui again but still go the error message:
bash-3.2$ bet_gui
/usr/local/fsl/bin/bet /usr/local/fsl/Course/fsl_course_data/intro/structural /usr/local/fsl/Course/fsl_course_data/intro/structural_brain -f 0.5 -g 0 -m -s
Error: failed to open file /usr/local/fsl/Course/fsl_course_data/intro/structural_brain.nii.gz
Image Exception : #22 :: ERROR: Could not open image /usr/local/fsl/Course/fsl_course_data/intro/structural_brain
libc++abi.dylib: terminate called throwing an exception
/usr/local/fsl/bin/bet: line 392: 3524 Abort trap: 6 ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
Finished
Is there something wrong?
> Date: Mon, 30 Sep 2013 07:19:54 +0000
> From: [log in to unmask]
> Subject: Re: [FSL] Error while running BET
> To: [log in to unmask]
>
> Hi,
>
> This indicates that the file /usr/local/fsl/Course/fsl_course_data/intro/structural_brain.nii.gz cannot be opened, probably because you do not have the correct permissions set in that directory. Try copying the structural.nii.gz image to another directory (where you know you have the correct permissions) and see if it works in that directory.
>
> All the best,
> Mark
>
>
> On 30 Sep 2013, at 07:03, humanbrain <[log in to unmask]> wrote:
>
> > Hello, I am going through the "Intro Practical". Under "Running BET", I used the bet_gui to load the file "structural". Then, I turned on various optional outputs and pressed Go to create the structural_brain. However, the file was not created. On the terminal, I got the following error:
> >
> > bash-3.2$ bet_gui
> > /usr/local/fsl/bin/bet /usr/local/fsl/Course/fsl_course_data/intro/structural /usr/local/fsl/Course/fsl_course_data/intro/structural_brain -f 0.5 -g 0 -m -s
> > Error: failed to open file /usr/local/fsl/Course/fsl_course_data/intro/structural_brain.nii.gz
> > Image Exception : #22 :: ERROR: Could not open image /usr/local/fsl/Course/fsl_course_data/intro/structural_brain
> > libc++abi.dylib: terminate called throwing an exception
> > /usr/local/fsl/bin/bet: line 392: 12045 Abort trap: 6 ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
> > Finished
> >
> > Anybody knows how to resolve the issue? Thanks.
