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Suggested edit to Freesurfer wiki

CT conversion from DICOM to MGZ

Justin Oh

11 Jan 2023 11 Jan '23

9:31 a.m.

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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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Douglas N. Greve

12 Jan 12 Jan

9:37 a.m.

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Justin Oh

25 Jan 25 Jan

9:25 a.m.

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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:
    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

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/12_iTb-HdC1PaTnlohzMR7QEJwpWsiLik6aq8xjTMFXePXh... 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 https://secure-web.cisco.com/13baPsIRwAe6NBx7SpUvfwmNbyoI8-wXcJSCQgRxAIDfJ1g... < https://secure-web.cisco.com/13baPsIRwAe6NBx7SpUvfwmNbyoI8-wXcJSCQgRxAIDfJ1g... .

Douglas N. Greve

10:59 a.m.

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.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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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Justin Oh

12:19 p.m.

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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:
    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.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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Zhao, Don

1:16 p.m.

New subject: Password FS_7_2_0_ubuntu_18_04_06.ova.

External Email - Use Caution

Hi,

I am new to this mailing list. I was wondering how I could get the password for FS_7_2_0_ubuntu_18_04_06.ova.

Thank you,

Don

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Justin Oh Sent: Wednesday, January 25, 2023 12:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS FAST

[[***CAUTION*** This email originated from outside of Messiah University]]

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,

Thank you for your time! -Justin Oh

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Douglas N. Greve

26 Jan 26 Jan

10:10 a.m.

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

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:

...

        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.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

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
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Justin Oh

7 Feb 7 Feb

11:18 a.m.

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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:
    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.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.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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Kumar, Avnish

9 Feb 9 Feb

9:52 a.m.

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

External Email - Use Caution

Hi all,

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:

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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 1/11/2023 9:31 AM, Justin Oh wrote:

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Dear Freesurfer team,

Thank you for your time! -Justin Oh

Justin Oh

12:16 p.m.

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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.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
    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.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.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.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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Kumar, Avnish

10 Feb 10 Feb

11:02 a.m.

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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Justin Oh ohjp89@gmail.com Sent: Thursday, February 9, 2023 12:16 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS FAST

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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'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 1/25/2023 12:19 PM, Justin Oh wrote:

External Email - Use Caution

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 1/11/2023 9:31 AM, Justin Oh wrote:

External Email - Use Caution

Dear Freesurfer team,

Thank you for your time! -Justin Oh

Justin Oh

13 Feb 13 Feb

6:34 p.m.

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.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.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justin Oh < ohjp89@gmail.com> *Sent:* Thursday, February 9, 2023 12:16 PM *To:* Freesurfer support list 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.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:
    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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Huang, Yujing

7:17 p.m.

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

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Hi all,

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 1/25/2023 12:19 PM, Justin Oh wrote:

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:

Best, Justin Oh

External Email - Use Caution Dear Freesurfer team,

Thank you for your time! -Justin Oh

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