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) >

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