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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