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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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.Kumar@mgh.harvard.edumailto:Avnish.Kumar@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justin Oh <ohjp89@gmail.commailto:ohjp89@gmail.com> Sent: Thursday, February 9, 2023 12:16 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.Kumar@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justin Oh <ohjp89@gmail.commailto:ohjp89@gmail.com> Sent: Tuesday, February 7, 2023 11:18 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 <dgreve@mgh.harvard.edumailto: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:
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 <dgreve@mgh.harvard.edumailto:dgreve@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 <dgreve@mgh.harvard.edumailto: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:
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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If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1vrUiL-3RQWprxWpGhsrEAEG9CNz6Kfeqjtkl5_hzKjo5h11dzw2GqGLDXdmYGrkuGUmZ5vHryNi8vpbaQbWrSVRH33cnA7BKMaEAcNJAnNC52z4hhpJWqIcKook5jt2mLS5GVwRpyZ0td4mP1rCvP3S-xbWj4-mVU4D8Fqwb5XkENb8r8dyOAMBBOnIliOYaZf8sJKzI6-N1Met4fhAM6yzEqd-kgJTHTYcdo18OLKwx2-ytuKd1HG-F4ktvqMVn_3U8IS_VINl8yTMFHo7Pnb9tI1J-Duk6NKzqY4Xn32rQ7-2ZyUu2DvjrbPT4XYbPpIkJYfYILKOuYcjLPmoH5w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1vrUiL-3RQWprxWpGhsrEAEG9CNz6Kfeqjtkl5_hzKjo5h11dzw2GqGLDXdmYGrkuGUmZ5vHryNi8vpbaQbWrSVRH33cnA7BKMaEAcNJAnNC52z4hhpJWqIcKook5jt2mLS5GVwRpyZ0td4mP1rCvP3S-xbWj4-mVU4D8Fqwb5XkENb8r8dyOAMBBOnIliOYaZf8sJKzI6-N1Met4fhAM6yzEqd-kgJTHTYcdo18OLKwx2-ytuKd1HG-F4ktvqMVn_3U8IS_VINl8yTMFHo7Pnb9tI1J-Duk6NKzqY4Xn32rQ7-2ZyUu2DvjrbPT4XYbPpIkJYfYILKOuYcjLPmoH5w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/13aI1YSYjNHikrRqyEMfF2X0yOZXgcuffSInY1cPzcdcHGYO4GP62tjY6LVQ3nBn_A90p-DK8EGT78SnGZm20e3OniX6rgjFEViOw8uR7bauDMhq1KqF7uaIhwk5_fL-9AtGco2BW0X5RxGF5qXehoNToi1ehzFjDzjhx4UzFKhakHVog6vskWFTlmoJlM_um1yvT3_MtiKrK40AhuerX0RsZGiM1O3OYb_PBHmg1hc0FkBg1lLQPLKbkbfUE5jDNLS4Ww6wUKfEbqNMKWc7XOd6Uw9cL30ujiWRwoddq6NAuVLY5nlaXZjX5vIUlsaIJVSIpUz8o-9bkxsG0EN0sgA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1iaAo3S6zwLktoX8flfvWpotsa7kpBjEF_7D14ln-ceKMO-TJJ44Q_TSe-qoPq5GmAu1Ize90cxPvDUsfeFmnTLbFy5cUwjxlJGorCq6dqZOvJYvlAyFYG44xR7d3MsC4O-QPcrvVjAcswJreTk9SE8B71RvRDqFmI9CBjEkO39D8Qf_jN6OCZ4GdJhmvWdBpiUmINXfJOqgxvHrBuFh5IBr7crvuulYJx9jdoeb-ukXt03EQcBmpwRcapcNLwcfa95NYDyuG47aVjSD_EPoh9rgjAbyKVgDl2_fxtR_iNbrma56RPf3fkvHcXIiM6G0b5M5NeeL5x4D2PZqsQt_Qjw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1iaAo3S6zwLktoX8flfvWpotsa7kpBjEF_7D14ln-ceKMO-TJJ44Q_TSe-qoPq5GmAu1Ize90cxPvDUsfeFmnTLbFy5cUwjxlJGorCq6dqZOvJYvlAyFYG44xR7d3MsC4O-QPcrvVjAcswJreTk9SE8B71RvRDqFmI9CBjEkO39D8Qf_jN6OCZ4GdJhmvWdBpiUmINXfJOqgxvHrBuFh5IBr7crvuulYJx9jdoeb-ukXt03EQcBmpwRcapcNLwcfa95NYDyuG47aVjSD_EPoh9rgjAbyKVgDl2_fxtR_iNbrma56RPf3fkvHcXIiM6G0b5M5NeeL5x4D2PZqsQt_Qjw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .