Re: [Freesurfer] Displaying clusters from different QDEC analyses, overlapped

yea, you can do it on the fsaverage/305, but if you want to see it as a volume, you'll have to run mri_surf2vol doug

On 10/03/2014 02:48 PM, Tudor Popescu wrote:

Thanks Doug. Is it not easier to use the /mc-z.abs.th13.sig.cluster.mgh /images to display the clusters as surfaces instead of volumes, superimposed on the standard FreeSurfer brain (MNI305) as opposed to on the MNI152? T

On 3 October 2014 18:23, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

That mgh file will have surface data in it. You need to convert it to
volume data to show it on a volume. If you want to show it on the
mni152, then use mri_surf2vol with --reg
$FREESURFER_HOME/average/mni152.register.dat and specify the 2mm
MNI152
brain as the target. Also tell it to fill the ribbon
doug

On 10/02/2014 08:48 AM, Tudor Popescu wrote:
> Dear FS list,
>
> I have significant clusters from several QDEC analyses (each one
for a
> different DV< i.e. thickness, area, etc). I would like to generate a
> picture of a standard brain (talairach or MNI) with several of these
> clusters superimposed on the same brain, to show where there are
e.g.
> regions of increased thickness and of decreased volume.
>
> I thought I could just load a standard brain in FreeView and
then add
> the MGH files corresponding to all my contrasts of interest (after
> they've been MonteCarlo-corrected), in order to view all my clusters
> on the same brain. However, when I load any
> /mc-z.abs.th13.sig.cluster.mgh /in FreeView, the image seems to be
> blank, although in QDEC it shows a large blue cluster. I played around
> with the Min/Max/Level values in FreeView, but that didn't help.
>
> Can anyone suggest how to accomplish this?
>
> Thanks!
>
> Tudor
>
>
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