[caret-users] Mapping Data to a Surface

[Donna Dierker]

Hi Rishi,

See inline replies below.

Donna

On 08/01/2007 10:23 AM, Rishi Kalwani wrote:
> Hi,
>
> I have a registered surface and am trying to map Volume Data to the 
> surface but the data doesn't show up on the surface.
>
> I have been trying to do this using Volume data saved in Analyze 
> format (.hdr) and using the Map Volume to Surface option under 
> Attributes.
True Analyze format .hdr files don't specify the origin, so this might 
be your problem.

Use File: Open Data file: volume anatomy file to open the anatomical 
volume used to generate the surface.
Use File: Open Data file: volume functiona file to open the volume you 
want to map to the surface.

Switch to VOLUME configuration in Caret, and select Overlay/Underlay 
Volume from the D/C menu.

On the Setting tab, make sure Anatomy is underlay, functional is overlay.

Toggle on Show surface contour, and make sure the fiducial used as the 
map target is selected as the contour substrate.

The contour should align with the anatomical volume, and the functional 
volume should align with the anatomical volume.  If it doesn't, then use 
Volume: Edit Volume Attributes to adjust the functional volume's origin, 
so that it aligns with the anatomical.  Then, after you get it aligned, 
save the functional volume as AFNI or NIfTI, which more reliably 
communicates origin information.

>
> How do you specify the orientation of the Volume being mapped to the 
> surface?
With Analyze, your only option is to select or deselect the volume is 
right on left checkbox when loading the volume into Caret.

My advice:  Don't use Analyze format.  Switch to NIfTI or AFNI.

If you're stuck with Analyze, you might try using caret_command 
-volume-set-origin, if you have a bunch of volumes whose origins need 
specification.

> What orientation does the surface expect?
Usually, the surface is left-to-right, posterior-to-anterior, 
inferior-to-superior (LPI), so the volume should be the same way, if 
you're using Analyze.  If you're using AFNI or NIfTI, it might flip the 
volume to LPI if the orientation is something else.

I doubt this will work with Analyze, simply because the hdr format 
doesn't support it, the way AFNI and NIfTI do:

caret_command -volume-set-orientation

It is possible to transform the surface, so that its orientation matches 
your functional volume's orientation.  Use Window: Transformation Matrix 
Editor or AFNI/SUMA's Vecwarp to do so.  I recommend keeping separate 
versions of the coord files, e.g.:

my_monkey.FIDUCIAL_LPI.coord
my_monkey.FIDUCIAL_ASR.coord
>
> Any help would be great.
>
> rishi kalwani
>
>
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