[caret-users] Creating a surface-based atlas from a volumetric-atlas

HINDRIKS, RIKKERT rikkert.hindriks at upf.edu
Tue Nov 4 12:59:27 CST 2014


Hi Donna,

Thanks for the link.

Yes, I can imagine that it requires quit some effort (and experience)
to register a macaque surface using so many landmarks. I would
like to parcellate my macaque cortex using a (high-resolution)
atlas.

So what about if I do the following: I convert the freesurfer files for both
my individual caret-surface and for the F99 standard mesh, register
them in freesurfer (or Spherical Demons) and then convert the deformation
map to Caret-format (if that's possible).

Would this be a good way to go?

Kind regards,
Rikkert



On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker <donna at brainvis.wustl.edu>
wrote:

> Try this one:
>
>
> http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj
> login pub
> password download
>
> As I recall, though it's been a long time, the GUI Caret took either
> border or borderproj, but the command line caret_command wanted a
> borderproj.
>
> You indicated you know this is a human target, and you're just getting the
> feel for it.  With monkeys, we use more than the core 6 landmarks.  Some of
> the older tutorials have figures showing more of the sulci.
>
> There are many other tools for surface-based registration these days
> (e.g., ones that use sulc patterns to match without the need to draw
> landmarks).  The connectome project uses MSM:
>
> http://www.ncbi.nlm.nih.gov/pubmed/24939340
>
> You can still use Caret, but just making sure you know there are
> alternatives.
>
>
> On Nov 4, 2014, at 5:23 AM, "HINDRIKS, RIKKERT" <rikkert.hindriks at upf.edu>
> wrote:
>
> > Hi Donna,
> >
> > To get a feeling for the registration process in Caret, I start with
> performing a spherical registration of a human surface
> > to the PALS-atlas. I have extracted the surface and generated a border
> projection file containing the required cuts and
> > landmarks. However, when I want to perform the registration, I get a
> massage saying that Caret cannot find the target
> > border projection file. I used this file:
> >
> > http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499
> >
> > and indeed, it seems that there is no such file (nor coordinate files
> for the fiducial and inflated surfaces). Are some
> > files missing or do I do something wrong?
> >
> > Thanks and kind regards,
> > Rikkert
> >
> >
> >
> >
> > On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker <donna at brainvis.wustl.edu>
> wrote:
> > On Oct 30, 2014, at 11:29 AM, "HINDRIKS, RIKKERT" <
> rikkert.hindriks at 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 <
> donna at brainvis.wustl.edu> wrote:
> > > On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT" <
> rikkert.hindriks at 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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