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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!