On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu> 

> Dear all,
> I have an averaged T1-image and co-registered volumetric atlas of the macaque 
> brain (which has been digitized by a collaborator) and want to derive from it 
> a surface-based
> atlas. Subsequently, I would like to use this atlas to get a parcellation of 
> the cortical surface of an individual macaque brain). How should I approach 
> this problem?
> I have extracted the cortical surface from the averaged T1-weigthed scan.  
> Should I now
> just label each cortical vertex by determining to which ROI it belongs? And 
> what if some vertices fall outside all ROI's? Also, the result does not look 
> so smooth as existing atlases.

It sounds like you need to map the volume(s) onto the surface.  It also sounds 
like these are discrete parcellations (ROI/label/paint) as opposed to 
probabilistic atlases, since it sounds like it is an individual monkey's data, 
rather than group data.  It would be helpful to clarify this.

Assuming it is ROI/label (i.e., each intensity value -- e.g., 1, 2, 3, … -- 
corresponds to a region -- e.g., cingulate, arcuate, …), then I would map it as 
a paint volume.  I believe doing so constrains the mapping algorithms, but I am 
not certain.

If you load your anatomical T1 with your surfaces and toggle on the surface 
contours (Volume Surface Outline, on the D/C page selection), then you can 
overlay the volumetric atlas over these two anatomical underlays (T1+surface 
contours) to look for regions where the surface does not intersect the atlas.  
I see three choices:

* fix the volumetric atlas data
* fix the surfaces, so the intersection is improved
* accept the fact that there are real holes in your data

You will be better equipped to make that choice when you are looking at 
T1+surface contours+volumetric-atlas.

> And to parcellate an individual macaque brain, can I register both the 
> surfaces (that is, the template surface and the individual surface) 
> spherically?

Registering an individual monkey brain to a monkey atlas (e.g., F99) isn't 
really parcellating it, but there are parcellations already on the F99 atlas, 
so if you use spherical registration to register your monkey to F99, then you 
could look at the F99 parcellations overlaid on your monkey's surface.  But 
it's not a quick or easy process.  You need to draw registration borders.  
(Though there are other registration algorithms out there that use sulcal maps 
and/or other data to automatically derive the deformation.  I encourage others 
to chime in if they ones they have used and found not too hard.)  How would you 
be using the registered surface?

(Sorry for the delayed reply, but it wasn't a quick one. ;-)

> Thanks a lot,
> Rikkert
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