Try making a symbolic link to /usr/local/bin/python3 in your local directory.
Make sure your local directory in your PATH.
ln -s /usr/local/bin/python3 python
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Justin Oh
Sent: Monday, February 13, 2023 6:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FS FAST
External Email - Use Caution
Hi Avnish,
I added those two lines to my bash profile but i still get the same error
message. is there anything else i could try?
Best,
justin oh
On Fri, Feb 10, 2023 at 11:03 AM Kumar, Avnish
<avnish.ku...@mgh.harvard.edu<mailto:avnish.ku...@mgh.harvard.edu>> wrote:
It doesn't seem like your python --> /usr/bin/python3 linking is setup.
Can you add these two lines to your bash_profile:
alias python="python3"
alias pip="pip3"
Then either open a new terminal or source your bash_profile before testing that
a call to python is pointing to your python3 installation.
source ~/.bash_profile
python --version
Best,
Avnish
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Justin Oh <ohj...@gmail.com<mailto:ohj...@gmail.com>>
Sent: Thursday, February 9, 2023 12:16 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FS FAST
External Email - Use Caution
Hi Avnish,
Justins-MacBook-Air:~ justinoh$ whereis python3
python3: /usr/bin/python3
Justins-MacBook-Air:~ justinoh$ which python
Justins-MacBook-Air:~ justinoh$ which python3
/usr/local/bin/python3
Justins-MacBook-Air:~ justinoh$ brew info python
-bash: brew: command not found
Justins-MacBook-Air:~ justinoh$
I've posted the outputs. Thank you for your assistance!
Best,
Justin Oh
On Thu, Feb 9, 2023 at 9:53 AM Kumar, Avnish
<avnish.ku...@mgh.harvard.edu<mailto:avnish.ku...@mgh.harvard.edu>> wrote:
Can you post the outputs of these three commands:
which python
which python3
brew info python
Best,
Avnish
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Justin Oh <ohj...@gmail.com<mailto:ohj...@gmail.com>>
Sent: Tuesday, February 7, 2023 11:18 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FS FAST
External Email - Use Caution
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
<dgr...@mgh.harvard.edu<mailto:dgr...@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:
External Email - Use Caution
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
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
I have not idea, try it and see.
On 1/25/2023 9:25 AM, Justin Oh wrote:
External Email - Use Caution
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
<dgr...@mgh.harvard.edu<mailto:dgr...@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:
External Email - Use Caution
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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