+Self-update: I figured out “.nii” works well. I thought “.mgz" should work
well, but "preproc-sess” tried to read “template.mgz.nii” while it creates
“template.nii”. So just the simple format “.nii” works well even in a harsh
virtual environment (e.g.,matlab>parallel-workers>bash>csh>matlab).
--
Seung-Goo KIM
> On 2017-02-03, at 15:51, Seung-Goo KIM <sol...@gmail.com> wrote:
>
> Hi all,
>
> So this is a question about running FAST through matlab parallel desktop: I
> know it is very funny (and inefficient) because I open up a bash in the
> matlab to run a csh script that generates and runs a matlab code, but just
> I’m familiar with matlab in doing many things including string manipulation,
> so that’s how I’m doing now. If there are matlab scripts that does a similar
> thing as csh scripts, it would be nice.
>
> Anyway, I realized that I cannot run all the fitting with different
> parameters and with the identical name of model (the GLM directory name) at
> the same time because the code appears to refer to the directory at
> $SUBJECTS_DIR.
>
> But I tried to run multiple subjects (with all different GLM names in their
> own native spaces) through MATLAB on a server, it returns (seems just one of
> random subject):
>
>> ERROR: could not read /tmp/tmp354512.nii
>> rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory
>> ERROR: loading ${filename}.nii.gz as analyze
>
> So I traced back to the functions that return those errors (i.e.,
> load_nifti.m run in MRIread.m) and it seems to be something with the
> temporary directory managed by matlab workers. The temporary file seems to be
> only necessary for nii.gz file.
>
> If so, I would rather just use .nii file format (or maybe .mgz?) format
> instead of dealing with the void complexity. Then can it be done by just
> putting:
>
>> setenv(‘FSF_OUTPUTFORMAT’,’.mgz’)
>
>
> before I run "preproc-sess" and "selxavg3-sess” in my scripts?
>
> Best regards,
> --
> Seung-Goo KIM
>
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