[caret-users] Talairach group data to individual surface

[Sarah Hillenbrand]

Hi,

Thanks for the advice Donna.  That is, in fact, what we are trying to do.
However, I am realizing the source of my problems is at a much more basic
level, so I have abandoned the talairached data and am working with
individual data.

Right now, I'm attempting to map some individual data onto the individual
surface and am running into some problems.

I wrote the functional data into the original anatomical's grid as per
http://brainmap.wustl.edu/help/mapper.html#afniwriteanat.

I then proceeded to mimic the directions at
http://brainmap.wustl.edu/help/map_individual.html
Using my functional data in anatomical grid, the original anatomical to
which it was mapped, and a surface I generated for this same subject using 4
anatomicals (including the aforementioned "original" one),
registered/averaged/uniformized/resampled/converted to MINC in  AFNI.

The functional data maps fine onto the original anatomical, but not onto the
surface.  I think there may be some alignment issues between the original
anatomical and the processed one used for the segmentation/surface.  Can you
recommend something to fix this?

Thanks so much,
Sarah





On 12/6/07 10:32 AM, "Donna Dierker" <donna at brainvis.wustl.edu> wrote:

> Hi Sarah,
> 
> This is not something we do every day -- map group results to an
> individual's surface.  Maybe some context might clarify.
> 
> But let me illustrate an example where something like this might make
> sense.  Suppose I have functional group differences, and I want to
> investigate whether anatomical difference might underly the functional
> differences.  I can imagine doing something like this:
> 
> * Use some sort of volume-based registration (VBR) to warp the
> individual's anatomical volume into the same stereotaxic space as my
> functional group results.  Spend a fair amount of time fussing about
> what VBR method to use (e.g., linear vs nonlinear).  It might be
> reasonable to use the same VBR method used to generate the functional
> group results, but give this step some thought before charging ahead.
> 
> * Use caret_command or AFNI's Vecwarp to apply the resulting affine
> transform, if a linear VBR method was used, to your individual's
> surface, so the surface is now in atlas space.  (If a nonlinear method
> is used, then you'll need to apply the deformation map using alternate
> methods.  The SPM links here give you a feel for how that works:
> 
>     http://brainvis.wustl.edu/help/pals_volume_normalization
> 
> * Map the functional results onto the atlas-space surface.
> 
> * Perhaps smooth/threshold the results, using Caret's Attributes:
> Metric: Clustering and Smoothing and/or Surface: ROI features.
> 
> * Perhaps even use Surface: ROI to threshold the map and convert it to
> Paint, so that now I have a ROI on the individual's surface; then,
> Attributes: Paint: convert paint column to paint volume to project the
> ROI on the individual's surface to the atlas-warped individual's
> anatomy.  I might use this as a starter segmentation, perhaps clean it
> up, perhaps not, for the purpose of applying some sort of volumetric
> morphometric method.
> 
> This may be nothing like what you want to do, but it's the kind of
> context under which it might make sense to map group fMRI onto
> individual surfaces.
> 
> Donna
> 
> On 12/06/2007 09:11 AM, Sarah Hillenbrand wrote:
>> I have functional group data in Talairach space that I need mapped to an
>> individual surface.  I'm having trouble with this and am not sure at which
>> step in the process I may have gone astray.
>> 
>> What are the correct steps to follow here?
>> 
>> Much obliged,
>> Sarah
>> 
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