Does that file exist? If so what are its perms?
On 4/29/2022 3:53 PM, Billah, Tashrif wrote:
Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error:
reading filled volume...
/bin/bash: /scratch/tp44447785365264536.load_mgh.m.mgh: Permission denied
ERROR: could not open /scratch/tp44447785365264536.load_mgh.m.mgh for reading ERROR: loading /data/pnl/FS_SUBJECTS_DIR/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
What can we do now?
-Tashrif
=================== Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700 Can you just try it with 7.2? We had some problems at one point with temporary files in lGI that were fixed with 7.2
=================== On 4/27/2022 9:36 AM, Billah, Tashrif wrote: 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
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