Dear Donna,

Thanks for your fast response, I appreciate it!

My situation is as follows:

On the one hand, I have a group-averaged T1-weighted image, together with a
volumetric atlas (that is, an integer labeling of the
voxels) as well as a structural connectivity matrix (obtained via
fiber-tracking on the group-averaged diffusion-weighted image). On
the other hand, I have a T1-weighted image of an individual monkey. My aim
is to obtain a surface atlas (derived from volumetric atlas)
for the individual monkey.

Could I first to a volumetric-registration of the individual image to the
group-averaged image and subsequently project the induced
labeling of the voxels of the individual image to the individual surface?
Or do I have to extract the surface of the group-averaged
image, project the volumetric atlas to it, and subsequently perform a
spherical registration of the individual surface to the group-
averaged surface?

The first approach seems more straightforward, but I don't know if it is
correct. Also, a complication with the second approach is that
the extracted surface from the group-averaged image looks worse than that
extracted from the individual image (it is entirely ok, except
for that the primary visual cortex has a large part missing at the medial

And Donna, could you please tell me how to create a paint file from a
nifty-file? (the atlas I have is saved as a nifti-file)

The background is that we want to construct a computational model of
cortical dynamics using the structural connectivity information.
An alternative, I guess, would be to spherically register the individual
surface to the F99 template and subsequently, use the CoCoMAc
or other available connectivity data. The drawback of this, however, is
that the strength of connections is more or less qualitative, hence
not so well-suited for modeling. If you think, though, that this is the
best option for the creation of a surface-atlas, then I will go for it.

Thanks a lot Donna, and kind regards,

On Thu, Oct 30, 2014 at 3:13 PM, Donna Dierker <>

> On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT" <
>> wrote:
> >
> > 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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