Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



     Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 

===================

What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

    It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh?


    ===============
    Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

    Do you have permission to /scratch? Does it exist?

    ===============
    Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

    Hi all,

    We are trying to run recon-all with -localGI but running into an unknown
    permission denied error:

    $ recon-all -s sub-1001 -localGI

    ```

    make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
     exit
    =================


    < M A T L A B (R) >
    Copyright 1984-2017 The MathWorks, Inc.
    R2017a (9.2.0.556344) 64-bit (glnxa64)
    March 27, 2017


    >> reading filled volume...
    /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


    ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading

    ERROR: loading
    /path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
     as MGH
    Struct contents reference from a non-struct array object.


    Error in make_outer_surface (line 25)
    volume=vol.vol;

    >>
    ERROR: make_outer_surface did not create output file
    '/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


    recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

    ```

    Our MATLAB environment is properly setup and we regularly run other
    FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

    Best,
    Tashrif