Hi Xuelin,
Just seen your new post, but I think the error message is clearer in
this one, and almost certainly from the same problem:
> system(['sh -c "FSLOUTPUTTYPE=NIFTI_PAIR; export FSLOUTPUTTYPE; $FSLDIR/bin/avwmaths ', fname, ' ', tmpname,'"']);
[...]
> "sh; line 1: /bin/avwmaths: No such file or directory"
The error shows that $FSLDIR/bin/avwmaths expanded to just
/bin/avwmaths, or in other words that $FSLDIR is not set.
You probably need to run something like this first:
system(['sh -c "source /path/to/your/fsldir/etc/fslconf/fsl.sh"']);
Or maybe just start Matlab after you have set-up FSL in the terminal
window.
Hopefully after that, something like
system('echo $FSLDIR');
should show the right location for FSL.
For example, if I run the following lines:
fslsh = '/my/path/to/fsl/etc/fslconf/fsl.sh';
cmd = 'avwstats++ $FSLDIR/etc/standard/avg152T1 -x';
system(['sh -c "source ' fslsh '"']);
[stat out] = system(['sh -c "' cmd '"'])
I get the result:
status = 0
output = 77 76 14
Hope that helps,
Ged
