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 /Applications/freesurfer/subjects/fsgd/y.mgh
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 (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V).
I also attached the log file.
Thank you!
FYI, here is my previous discussion with Douglas about this issue:
Douglas N Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Wed, 09 Aug 2017 14:17:05 -0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170809
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
ETC
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
y.mgh is the input file, usually the output of mris_preproc (after smoothing). See the group analysis tutorial.
On 08/10/2017 11:48 AM, Nick Corriveau-Lecavalier wrote:
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 /Applications/freesurfer/subjects/fsgd/y.mgh
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 (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V).
I also attached the log file.
Thank you!
FYI, here is my previous discussion with Douglas about this issue:
Douglas N Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Wed, 09 Aug 2017 14:17:05 -0700 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170809
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
ETC
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Nick Corriveau-Lecavalier