Sorry, I mean the gamma.mgh maps for the cross-sectional differences appear to be blank as no overlay is overlaid on the fsaverage when I do the same command as with the longitudinal gamma.mgh. The commands I am running for the cross-sectional group comparison are:
mri_glmfit --glmdir lh_groupdiff.dir --fsgd fsgd.fsgd doss --y lh.thickness10.mgh --C groupdiff.mtx --surf fsaverage lh --cortex
tksurfer fsaverage lh inflated -overlay /lh_groupdiff.dir/groupdiff/gamma.mgh
Thanks
Message: 8 Date: Wed, 16 Oct 2013 11:47:59 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] gamma.mgh To: freesurfer@nmr.mgh.harvard.edu Message-ID: 525EB52F.5000006@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
what do you mean they are "coming up blank"
On 10/16/2013 05:15 AM, Rees, Elin wrote:
Dear FreeSurfers,
I've been looking at between-group (controls and disease) differences in cortical thickness cross-sectionally and longitudinally (PC1). I've outputted sig.mgh maps and effect size maps (gamma.mgh) but the cross-sectional gamma.mgh maps are coming up blank. Could you explain why this is (and why it works for the longitudinal data) and how I can create a cross-sectional effect size map?
As the scans I am an analysing are from four different scanners I am also looking at scanner differences in the controls only. No significant differences are coming up but the effect size maps are showing both positive and negative differences across the whole brain and the gammavar.mgh maps are completely yellow (5 on the colour bar). How do I interpret this?
Any help would be much appreciated. Thanks, Elin
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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Message: 9 Date: Wed, 16 Oct 2013 11:51:41 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DOSS FS 5.3 To: amirhossein manzouri a.h.manzouri@gmail.com Cc: free surfer freesurfer@nmr.mgh.harvard.edu Message-ID: 525EB60D.1010808@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
From the command line you will need to run mri_glmfit. The mri_glmfit.log file in the QDEC output folder will have a sample mri_glmfit command line. You will need to modify this by adding "doss" after the FSGD file. You will also need to create new contrast matrices to match the DOSS model. Search for fsgd on our wiki to get examples
doug
On 10/16/2013 03:19 AM, amirhossein manzouri wrote:
Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again.
-- Best regards, Amirhossein Manzouri
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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End of Freesurfer Digest, Vol 116, Issue 29 *******************************************