External Email - Use Caution        


If you have not already done so, I would try installing and using the newest version of the 
Matlab runtime environment that the 7.4.1 release was tested with, i.e. R2019b.  Once you have set $FREESURFER_HOME, then run the fs_install_mcr script included with the freesurfer distribution ...

$ export FREESURFER_HOME=<your install path>

$ cd $FREESURFER_HOME/bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b

… answer y to any installer questions ...

Then I think it should work to find the Matlab libraries by at least start off with setting,

$ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64

Please make sure you have otherwise removed from your environment and references to the previous Matlab R2022b setup.

- R.

Begin forwarded message:

From: Benjamin Cole Sherman <bsherma@stanford.edu>
Subject: [Freesurfer] recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
Date: August 30, 2023 at 12:02:09 EDT
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

        External Email - Use Caution        

Hi FreeSurfer Team,

I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output:

MATLAB is selecting SOFTWARE OPENGL rendering.

                            < M A T L A B (R) >
                  Copyright 1984-2022 The MathWorks, Inc.
                  R2022b (9.13.0.2049777) 64-bit (glnxa64)
                              August 24, 2022

Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest
you rename the function to avoid a potential name conflict.
Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest
you rename the function to avoid a potential name conflict.
Warning: Function isrow has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.
Warning: Function narginchk has the same name as a MATLAB builtin. We suggest
you rename the function to avoid a potential name conflict.
Warning: Function isequaln has the same name as a MATLAB builtin. We suggest
you rename the function to avoid a potential name conflict.
Warning: Function istable has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.
Warning: Function isfile has the same name as a MATLAB builtin. We suggest you
rename the function to avoid a potential name conflict.
Warning: Function isfolder has the same name as a MATLAB builtin. We suggest
you rename the function to avoid a potential name conflict.
Warning: Function isstring has the same name as a MATLAB builtin. We suggest
you rename the function to avoid a potential name conflict.
 
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>> Unrecognized function or variable 'make_outer_surface'.
 
>> 
ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Command exited with non-zero status 1

I haven't been able to find anything in the support archives so I was hoping you could help us out.

1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4..1-20230614-7eb8460
2)Platform: Ubuntu 20.04.6 LTS
3)recon-all.log: see attached

Thanks for any help you can provide!
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