Hello,
I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu)https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system:
My issue is with step 3.2: Correcting for Multiple Comparisons. [cid:8a8a9d8a-afaf-420d-8092-2525282e7e16]
When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized.
[cid:e82f076f-dc27-4767-90c9-8c4fc2603831]
Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information.
Do you have any recommendations for what to do? Is it an issue with my version of freesurfer?
Thank you,
Sophia
Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University
My guess is that something is wrong with the version. Can you send your version of mri_glmfit-sim ? You can get it by typing which mri_glmfit-sim
On 7/5/2022 9:27 AM, Tchir, Sophia Mae wrote:
Hello,
I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu) https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system:
My issue is with step 3.2: Correcting for Multiple Comparisons.
When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized.
Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information.
Do you have any recommendations for what to do? Is it an issue with my version of freesurfer?
Thank you,
Sophia
Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
When I run that I get: albus[0]:tutorial_subjs$ which mri_glmfit-sim /cluster/nrg/tools/current/apps/arch/linux_x86_64/freesurfer/5.3.0/bin/mri_glmfit-sim
Thank you!
Sophia ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Sunday, July 10, 2022 6:01 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with FreeSurfer Tutorial FsFast Group Level
My guess is that something is wrong with the version. Can you send your version of mri_glmfit-sim ? You can get it by typing which mri_glmfit-sim
On 7/5/2022 9:27 AM, Tchir, Sophia Mae wrote: Hello,
I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu)https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system:
My issue is with step 3.2: Correcting for Multiple Comparisons. [cid:part1.2CJOVU2H.zKUyO0o1@mgh.harvard.edu]
When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized.
[cid:part2.Cr0GMsvU.AWTIE0B4@mgh.harvard.edu]
Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information.
Do you have any recommendations for what to do? Is it an issue with my version of freesurfer?
Thank you,
Sophia
Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You are using the 5.3 version, not the 6.0 version. Make sure to source the proper version of FS
On 7/11/2022 12:00 PM, Tchir, Sophia Mae wrote:
Hello,
When I run that I get: albus[0]:tutorial_subjs$ which mri_glmfit-sim /cluster/nrg/tools/current/apps/arch/linux_x86_64/freesurfer/5.3.0/bin/mri_glmfit-sim
Thank you!
Sophia
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Sunday, July 10, 2022 6:01 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help with FreeSurfer Tutorial FsFast Group Level My guess is that something is wrong with the version. Can you send your version of mri_glmfit-sim ? You can get it by typing which mri_glmfit-sim
On 7/5/2022 9:27 AM, Tchir, Sophia Mae wrote:
Hello,
I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu) https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system:
My issue is with step 3.2: Correcting for Multiple Comparisons.
When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized.
Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information.
Do you have any recommendations for what to do? Is it an issue with my version of freesurfer?
Thank you,
Sophia
Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Tchir, Sophia Mae