Re: [Freesurfer] Permission denied error from -localGI

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

On 3/2/2022 9:50 AM, Billah, Tashrif wrote:

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer