Yes, the tutorial was written when the 7.2 release was in the last stages of development. What happened between then and the final, released 7.2 was that it now just figures out that the input is 1D by checking the dimensions of the input, so you don't have to specify it on the command line.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Tarumi Takashi <takatr@gmail.com>
Sent: Thursday, January 20, 2022 7:59 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

 

        External Email - Use Caution        

Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the "--1d" flag. But, I thought that the flag is "required for any along-tract analysis" as stated in your TraculaStatistics instruction and highlighted in the release notes for v7.2 (added 1D capability for mri_glmfit-sim). I would greatly appreciate for your further clarifications. Thank you so much for your help.

Best regards,

Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

Hi Taka - Does it work when you remove the "--1d" from the command line? I think that must be an error in the documentation.

Anastasia.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Tarumi Takashi <takatr@gmail.com>
Sent: Wednesday, January 12, 2022 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

 

        External Email - Use Caution        

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics). But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac machine with macOS 12.1. Thank you so much for your help.

Sincerely,

Taka

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