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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
