On Thu, Feb 9, 2023 at 9:53 AM Kumar, Avnish <Avnish.Kumar@mgh.harvard.edu> wrote:

Can you post the outputs of these three commands:

which python

which python3

brew info python

Best,
Avnish

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justin Oh <ohjp89@gmail.com>
Sent: Tuesday, February 7, 2023 11:18 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FS FAST
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Hi all,

I'm trying to run preproc-sess on a resting state MRI and I've tried to define python to python3 path. I assume it's trying to call python into the environment but I'm not sure how to do this. I'm running a macOS m1 apple chip.

I've tried including each of these in my bash profile but still comes up with the same error.

python=/usr/bin/python3

set python=/usr/bin/python3

export python=/usr/bin/python3

This is the what appears in my terminal when i run preproc-sess

/Users/justinoh/Desktop/subject/11

stc.fsl --i /Users/justinoh/Desktop/subject/11/session_11/rest/901/fmcpr.nii.gz --o /Users/justinoh/Desktop/subject/11/session_11/rest/901/fmcpr.up.nii.gz --ngroups 1 --up

Tue Feb 7 11:10:54 EST 2023

/Users/justinoh/Desktop/subject/11

/Applications/freesurfer/7.3.2/fsfast/bin/stc.fsl

--i /Users/justinoh/Desktop/subject/11/session_11/rest/901/fmcpr.nii.gz --o /Users/justinoh/Desktop/subject/11/session_11/rest/901/fmcpr.up.nii.gz --ngroups 1 --up

FreeSurferEnv.csh 7.3.2

Justins-MacBook-Air.local

/Users/justinoh/Desktop/subject/11

mri_info --nslices --o /Users/justinoh/Desktop/subject/11/session_11/rest/901/tmp.3413/nslices.dat /Users/justinoh/Desktop/subject/11/session_11/rest/901/fmcpr.nii.gz

nslices = 46

slicedelay --nslices 46 --up --o /Users/justinoh/Desktop/subject/11/session_11/rest/901/tmp.3413/sdf.txt --ngroups 1

env: python: No such file or directory

Thank you!
On Thu, Jan 26, 2023 at 10:11 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Something like
set MATLAB=/usr/pubsw/common/matlab/8.4
Now that I think about it, you may be able to use the compiled version of fsfast. There are only two programs that use matlab, mkcontrast-sess and selxavg3-sess. You can try adding -bin on to both of those to use the compiled version (which does not require a license but you still have the runtime libraries installed).

On 1/25/2023 12:19 PM, Justin Oh wrote:
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My bash profile currently sets up my freesurfer environment with each terminal. Should I also be exporting matlab into my environment and define a path to the application? If so what should i include in my bash profile.
On Wed, Jan 25, 2023 at 11:00 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
I have not idea, try it and see.

On 1/25/2023 9:25 AM, Justin Oh wrote:
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Is the student version of MATLAB enough to run in the background? Our institution does not provide a license unfortunately. I tried using octave but i can't seem to get octave to work.

Best,
Justin Oh
On Thu, Jan 12, 2023 at 9:38 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Just the basic is ok. Although I have not done it in a while, you should also be able to use octave (which is free). Once you get octave install and in your path, set the env variable FS_USE_OCTAVE to 1. Like I said, I have not used it in a while, but it I think it should still work.

On 1/11/2023 9:31 AM, Justin Oh wrote:
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Dear Freesurfer team,

I am new to freesurfer and I'm working on learning how to pre process and analyze resting state fMRI. It's my understanding that MATLAB and FSL have to run in the background from what I took away from online tutorials. Is there a specific program within MATLAB that is necessary or will purchasing the basic student package from MATLAB be sufficient?

Thank you for your time!

-Justin Oh
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