You can just use the norm.mgz file. Lilla

On Mon, 30 Jan 2012, Antonella Kis wrote:

Dear Doug,

I don't have an orig.mgz file for the cvs_avg35 and I suppose I need when I will replace the fsaverage.In the mri file I have olny the norm.mgz Can you please help me to get the orig.mgz for the cvs_avg35?

Many thanks, Antonella

---

From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, January 26, 2012 3:17 PM Subject: Re: How to visualize the group results after corrections by multiple comparison

Use cvs_avg35 instead of fsaverage doug

Antonella Kis wrote:

...

Hi Doug,

Sorry I forgot to ask one more question: after I am getting my clusters for my FA group study should I use the fsaverage (which is not on the CVS

space) or the concatenated file GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz (registered over the CVS space) or I should use the CVS space to visualize my results, I mean should I use:

...

tkmedit fsaverage orig.mgz \   -ov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh \   -seg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.anat.mgh  \         /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.lut \   -fminmax 1.3 5

or

freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz \             /media/1Tra/Antonella_2011/DTI_FS/dtrecon/Group_Analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh:colormap=heat

Also do I need to use the average value GroupAnalysis.Average-fa-masked.ANAT+CVS-to-avg35.mgz when I run the mri_glmfit or just the concatenated file

GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz?

...

THANKS SO MUCH! Antonella

-- 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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