On Oct 30, 2014, at 11:29 AM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu> 
wrote:

> 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.

This is an interesting scenario, and I've not encountered it before.

> 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?

This seems reasonable and not too hard.  The lower variability in macaque 
folding may make it less problematic than for humans.

> 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?

People do extract surfaces from group averaged anatomical volumes for some 
purposes, but I doubt it will be worth it in this case.  I hope others will 
voice their opinions if they feel otherwise.

> 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 
> side).  

This is to be expected.  A more reasonable thing to do if you want an average 
surface is generate surfaces for the individuals and compute an average from 
them.  You probably don't have those surfaces, so honestly I'd try the first 
option and vet the resulting mapping using the T1+contour+volumetric-overlay 
view.

Still another option would be to use surface based registration to get your 
individual monkey in register with the F6 atlas (part 3, 
http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_Tutorial_Sep22.pdf)
 or Donald McLaren's population average macaque atlas 
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659879).  You could do something 
like this:

* volumetrically warp your atlas goodies to match the mean anatomical McLaren 
image.
* surface-based register your individual macaque atlas to the McLaren standard 
mesh surface.
* map your warped atlas goodies to the McLaren population surface.
* view your mapped results on your individual's standard mesh surface.

But that second step isn't trivial, and your easier route might suffice.  So 
I'd give that a go first.

> 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)

In caret5, Attributes: Map Volume to Surface and choose paint.  But getting the 
color lookup is a bit messy.  The newer CIFTI format contains a label lookup 
table, and we also have a nifti extension for that, but it's not understood by 
other viewers.

Caret5 has two volume formats that store that color lookup info:  AFNI, using a 
caret-specific header extension, and wustl's IFH/4dfp.  The ifh header lists 
the lookup, with an offset of 2.  (Like I said:  Messy.)  I can point you to 
some helpful threads on caret-users if needed.

> 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.

See how far you get with the easy option.  If not far enough, then it's 
possible the McLaren atlas mesh is in register with F99.  I can't recall 
clearly, but read that link above for more info.

> Thanks a lot Donna, and kind regards,
> Rikkert
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Thu, Oct 30, 2014 at 3:13 PM, Donna Dierker <do...@brainvis.wustl.edu> 
> wrote:
> On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu> 
> 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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> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> 
> 
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