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
> 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
> Wed, 09 Aug 2017 14:17:05 -0700
> 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
> Freesurfer mailing list
Douglas N. Greve, Ph.D.
Phone Number: 617-724-2358
Freesurfer mailing list
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.