Dear Dr Rorden,

thank you very much for your response. Hope you do not mind if I come 
back to you again.

Yes, the steps below, this is what we did. Everything works fine with 
uploading the background image and adding the different VOIs in 
different colours. Our problem is that window-render works for the 
addition of one, sometimes two VOIs, but not for three or more. We do 
not get an error message, but there is no 3D picture build - the 
program does not seem to start working.

Thank you for your time.

Dagmar


Am 19:22 27.10.2008 schrieben Sie:
>With MRIcron, use File/Open to open your background image (e.g. a T1 scan).
>Then use Overlay/Add to add each of your Volumes of Interest. You can now
>adjust the color-scheme used for each layer and you can adjust the
>translucency using the Overlay/TransparencyOnBackground and Overlay/
>TransparencyOnOtherOverlays. This is illustrated in the 'Layers' 
>section of this
>web page:
>   http://www.sph.sc.edu/comd/rorden/mricron/main.html
>When you choose Window/Render you can then tune how the overlays appear
>on the 3D image. You will want to adjust the Overlay/SearchDepth menu to
>adjust how deep below the cortical surface you want to hunt for an overlay -
>'infinite' creates a glass brain (seeing overlays at any depth), while '1mm'
>shows only objects near the cortical surface.  You will also want to 
>adjust the
>Overlay/Search option to your taste.
>
>If you are using Windows, you can click on the .bat' files that are 
>in MRIcron's
>folder - these load different overlays and renderings, so you can look for a
>setting that works with your data.
>
>On Thu, 23 Oct 2008 20:05:17 +0100, Dagmar Timmann-Braun
><[log in to unmask]> wrote:
>
> >Dear Dr. Rorden,
> >
> >I hope you do not mind the following question:
> >
> >We used 7T MRI to get structural images of the cerebellar nuclei. We used
>MRICro to create
> >ROIs of the dentate, emboliform, globose and fastigial nuclei.
> >
> >We would like to view the ROIs of the cerebellar nuclei together 
> in a 3D view.
> >
> >We managed to see 2 VOIs in two colors using MRICroN using the render
>option (one as the
> >background the other as an added VOI).  Although you can add more VOIs in
>different colors
> >in MRICroN it did not work for us for the 3D visualization. Furthermore
>"shading" appeared
> >to work for the background image only.
> >
> > Can you help? Is there a way to visualize more than two ROIs in different
>colors in 3D in
> >MRICro or MRICroN?
> >
> >Thank you very much for your kind help and time,
> >
> >Dagmar

Dagmar Timmann, MD
Department of Neurology
University of Essen
Hufelandstrasse 55
45122 Essen, FRG
Phone: +49 201 723 3816
Fax: +49 201 723 5901
Email: [log in to unmask]