Hi Freesurfer team,

First, sorry making a new post, I'm having trouble with my email and I'm not 
able to reply directly on my yesterday's post.

Here's my issue: I'm trying to make a group analysis with 3 groups using the 
mri_glmfit command.

This it what the terminal says: Loading y from 

mghRead(/Applications/freesurfer/subjects/fsgd/y.mgh, -1): could not open file

ERROR: loading y /Applications/freesurfer/subjects/fsgd/y.mgh

The terminal says that it cannot load the y.mgh file, which seems logic to me, 
since there is no such file in my folder. What is that file supposed to be? It 
isn't mentionned in the tutorial I've been following 

I also attached the log file.

Thank you!

FYI, here is my previous discussion with Douglas about this issue:

Douglas N 
 Wed, 09 Aug 2017 14:17:05 

make sure you pass the full path to the fsgd, otherwise it looks in the
current folder. Also make sure it is readable by you

> Hi Freesurfer team,
> I'm trying to run a GLM analysis with three groups (Controls, MCI, AD)
> with 0 covariables at the moment, but I would like to add two
> eventually. I've been following the tutorial on this link:
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write
> the command it says ''cannot open g3v0.fsgd for reading''.
> In my /subjects/fsgd file, there is my fsgd file, and my contrast
> file. Am I missing an additionnal file or something? Is the format of
> my files correct?
> If it can help, here's what my fsgd file looks likes:
> GroupDescriptorFile 1
> Title OSGM
> Class Control
> Class SCD
> Class MCI
> Variables
> Input 3431566 CTL
> Input 3514091 CTL
> Input 4051959 CTL
> Input 4344061 CTL
> Input 4557550 CTL
> Input 7060373 CTL
> Input 7274924 CTL


Nick Corriveau-Lecavalier, B.Sc. (Hons)
Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur à la recherche, Association étudiante des cycles supérieurs en 
psychologie de l'Université de Montréal (AÉCSPUM)
Université de Montréal
Centre de recherche de l'Institut universitaire de gériatrie de Montréal, 
bureau M7819

Attachment: mri_glmfit.log
Description: mri_glmfit.log

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