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.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tarumi Takashi
<tak...@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
<ayend...@mgh.harvard.edu<mailto:ayend...@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.
________________________________
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 Tarumi Takashi <tak...@gmail.com<mailto:tak...@gmail.com>>
Sent: Wednesday, January 12, 2022 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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<https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
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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