Re: [Freesurfer] GLM error - cannot read fsgd file for reading

2017-08-10 Thread Douglas N Greve 
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 
> 
>  
> 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
> 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/

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Re: [Freesurfer] GLM error - cannot read fsgd file for reading

2017-08-10 Thread Nick Corriveau-Lecavalier 
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
 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

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


mri_glmfit.log
Description: mri_glmfit.log
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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
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Re: [Freesurfer] GLM error - cannot read fsgd file for reading

2017-08-09 Thread Douglas N Greve 
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


On 08/09/2017 05:12 PM, Nick Corriveau-Lecavalier wrote:
>
> 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
> Input 7308293 CTL
> Input 7424803 CTL
> Input 7459501 CTL
> Input 7543023 CTL
> Input 7661810 CTL
> Input 8069157 CTL
> Input 8330218 CTL
> Input 8656527 CTL
> Input 8875385 CTL
> Input 9296157 CTL
> Input 3025432 SCD
> Input 3494204 SCD
> Input 3702154 SCD
> Input 3708747 SCD
> Input 3865361 SCD
> Input 4316663 SCD
> Input 4509950 SCD
> Input 4548020 SCD
> Input 4893763 SCD
> Input 5381177 SCD
> Input 5477234 SCD
> Input 5522727 SCD
> Input 6121388 SCD
> Input 6168985 SCD
> Input 6258913 SCD
> Input 6274286 SCD
> Input 6334263 SCD
> Input 6417837 SCD
> Input 6427603 SCD
> Input 7435733 SCD
> Input 7485585 SCD
> Input 7712552 SCD
> Input 8827943 SCD
> Input 8980899 SCD
>
> Regards,
>
>
> 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/

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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
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dispose of the e-mail.

[Freesurfer] GLM error - cannot read fsgd file for reading

2017-08-09 Thread Nick Corriveau-Lecavalier 
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
Input 7308293 CTL
Input 7424803 CTL
Input 7459501 CTL
Input 7543023 CTL
Input 7661810 CTL
Input 8069157 CTL
Input 8330218 CTL
Input 8656527 CTL
Input 8875385 CTL
Input 9296157 CTL
Input 3025432 SCD
Input 3494204 SCD
Input 3702154 SCD
Input 3708747 SCD
Input 3865361 SCD
Input 4316663 SCD
Input 4509950 SCD
Input 4548020 SCD
Input 4893763 SCD
Input 5381177 SCD
Input 5477234 SCD
Input 5522727 SCD
Input 6121388 SCD
Input 6168985 SCD
Input 6258913 SCD
Input 6274286 SCD
Input 6334263 SCD
Input 6417837 SCD
Input 6427603 SCD
Input 7435733 SCD
Input 7485585 SCD
Input 7712552 SCD
Input 8827943 SCD
Input 8980899 SCD

Regards,


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
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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.