External Email - Use Caution
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 deniedThe 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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I am not entirely sure :(
I did see someone else have the same exact issue and it says it was solved here: https://secure-web.cisco.com/1CITrHzRp2iUgFdotZPCjYwChbUZqcT7oSVSJaU_8J6xwEI...
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 CautionHello,
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ChO_NcNoY9m6kgyc6Eqjwkz8Be1xpyj3-4TMeWFqLBMcQ1...
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Michael Ruvalcaba