Hi Sarah,
Problems like these are relatively common -- especially if the surface
is old (i.e., generated by SureFit, which used to place the origin at
the lower left corner of the cropped bounding box -- not the anterior
commissure or atlas space origin, as Caret commonly does).
I would make a FAQ, but the problems tend to be so case-specific, that
common threads are few. Uploading the dataset and letting me have a look
is usually the shortest path to solution:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
I need the following files:
* fiducial surface coord
* topo file
* anatomy volume to which functional aligns
* functional volume (optional -- almost always, if I can get surf and
anat aligned, the rest follows)
If your surface is in VTK form, that can substitute for coord/topo.
Donna
On 12/10/2007 02:04 PM, Sarah Hillenbrand wrote:
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" <[EMAIL PROTECTED]> 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
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
