It should use whatever matlab is in your path. It looks like it is expecting to find it in /usr/local/freesurfer/stable5_1_0/matlab/
which is kind of strange since you are using FS6. Look in your cshrc or bashrc file to see if that is being added to your path and if so remove it. What happens if you type
which matlab
?

On 12/25/2021 10:53 PM, Yadav, Shrikanth Muralidhar wrote:

Hello Freesurfer Developers,

I am having trouble with my first level analysis using selxavg3-sess. I passed the -debug flag in my command and noticed that MATLAB 2021a was being used. However, the command worked as expected before MATLAB was updated from 2020b. Is there a way I can specify freesurfer (v6.0.0) to use a specific version of MATLAB?

I tried passing the -octave flag but got the following error

ERROR: cannot find /usr/local/freesurfer/stable5_1_0/matlab/

The full command:

selxavg3-sess -s 002_S_0413_V1_fMRI -overwrite -a lh-FastADNI12state1 -no-preproc -force -debug

Thank you

Shrikanth
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