What is your command line? It should be something like "--subject fsaverage lh", assuming that you are using fsaverage as your standard space and the left hemisphere. doug
bbruijn@bidmc.harvard.edu wrote:
Ok, good, thanks!
And for my error-message, I was wondering whether you tell me where I need to include my subject and hemi information. I've already tried the words 'subject1pair' and the actual subject code+'pair' but I keep getting the same message.
From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 10, 2011 11:09 AM To: Bruijn,Bente (BIDMC - Neurology); freesurfer Subject: Re: [Freesurfer] error mri_glmfit
Yes, the --osgm is the right thing to use there. If you run mri_glmfit with --help, it will tell you how to use the --surf option. There are also examples on the wiki. doug
bbruijn@bidmc.harvard.edu wrote:
Hi Doug,
Thanks for the fast response! Sorry, I should have included the command line, it's:
mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --osgm
So, my first question would be; is it correct to use the flag --osgm because I just want to to a paired T-test without regressors? And second; I need to include these (subject names and hemi) in my fsgd file or in my command?
Thanks again,
Bente
From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 10, 2011 10:39 AM To: Bruijn,Bente (BIDMC - Neurology) Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error mri_glmfit
Hi Bente, it's hard to say without seeing the command line (always a good thing to include when posting a question), but it looks like you need to include '--surface subject hemi' where subject is the name of the subject whose surface the analysis is being performed on and hemi is the name of the hemisphere (lh or rh). This information is needed to compute the spatial smoothness.
doug
bbruijn@bidmc.harvard.edu wrote:
Dear FS experts,
I came across an error-message that I can't figure out, hopefully you can help me. I want to do a paired T-test (first without regressors) and I am following the steps on the Freesurfer website. Preprocessing and smoothing all went OK and I've just created the second fsgd file;
GroupDescriptorFile 1 Class Main Input subject1pair Main Input subject2pair Main Input subject3pair Main Input subject4pair Main Input subject5pair Main Input subject6pair Main Input subject7pair Main Input subject8pair Main
Because I don't want to include any regressors I put in the flag --osgm (is this right?) and didn't include the contrasts.
This is the error message I receive after putting in the mri_glmfit command:
ERROR: you must use '--surface subject hemi' with surface data
Did I do everything correct or did I forget a step?
Thank you so much in advance,
Bente _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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