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, 2022Warning: Function iscolumn has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function ismatrix has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isrow has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function narginchk has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isequaln has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function istable has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfile has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfolder has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict..Warning: Function isstring has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/1A7cHJG7OTQToCpTNsg3ycqt5UEObzYbnyuy3_pfg1wlC1F... product information, visit http://secure-web.cisco.com/1PkNE_zNSBM0yzYMjwH_cGeVC4O7UdJdfnliIOnqoaBcy5GH...; 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 1I 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_64-7.4.1-20230614-7eb84602)Platform: Ubuntu 20.04.6 LTS3)recon-all.log: see attachedThanks for any help you can provide!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer