I am not entirely sure :(

I did see someone else have the same exact issue and it says it was solved here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62

But when I try to click the link and sign up I don't receive any verification to my email (checked spam too). Not sure if anyone else can open it and view the solution?

The recon -all finishes without error while using version 7.2.0, but when I run the following command:

addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab');
fsmri_pre_acpc = ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);

I get the next 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

And the scratch directory doesn't even exist.

Best,

Michael Ruvalcaba

Knight Lab

Helen Wills Neuroscience Institute

University of California, Berkeley

On Tue, Jan 9, 2024 at 8:25 PM fsbuild <fsbuild@contbay.com> wrote:

Is SUBJECTS_DIR for Freesurfer being set to live under a temporary scratch directory initially created by and then subsequently used by Matlab?

If so, maybe Freesurfer is deleting files and/or changing file permissions there - causing Matlab to subsequently complain. I would not expect multiple programs writing to the same directory tree to work together if they use different file permissions, privileges, and/or perform independent clean/delete functions in shared directories.

- R.

On Jan 9, 2024, at 14:47, Michael Ruvalcaba <michaelruvalcaba@berkeley.edu> wrote:

External Email - Use Caution

Hello,

I am trying to run the recon -all function in my MATLAB pipeline using Freesurfer 6.0.0 and I have no issues with it. However, when I run the recon -all step using Freesurfer 7.2.0 and run the following command (the recon -all step finishes without error by the way):

ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);

I get the following error:

/bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission denied

The issue is there is no scratch file and it looks like between version 6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory (which 6.0.0 doesn't)

Does anyone have any input on this? I hope this made sense!

Best,
Michael Ruvalcaba
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