Hi Donna,

I've constructed a .borderproj file (and a .bordercolor file) containing
the 23 LANDMARKS that correspond to the 23 LANDMARKS
in the file
Macaque.F99UA1.LR.AVERAGE.LANDMARKS_for_FULL-HEMISPHERE_RegWithPHT00.73730.borderproj
with
corresponding .bordercolor filee Macaque.LANDMARKS_for_FULL-HEM.bordercolor
and I think there is a good correspondence
between the individual and template LANDMARKS.

To perform the spherical registration however, I need the template sphere
of the left hemisphere, while I can only find the one of the
right hemisphere (Macaque.ATLAS.sphere.6.73730.coord). Do you know where I
can find it? (Maybe I can obtain it by mirroring, but
I have no idea how this could be done).

And I have a couple of general questions:

1. In which file-types are the sulcal-depths stored? (this applies both to
individual as well as template data)?  I quess this should be a
.surface_shape file, but I cannot find it. I ask this because I want to
make a new directory which only contains those files that I need.

2. In connection with this: What is the best way to organize the data
files? I now make different folders (one  for flattening, one for
landmarks, and one for the registration, each containing a different set of
data files and a single .spec file). Should I put everything
in one folder and make different .spec files for the different procedures?

3. Why are there .topology files? (since the topology is determined by the
triangulation, which is stored in .coord files)


4. After registering, how can I project any goodies defined on the template
to the individual surface? For example, I would like to
view the PHT parcellation on the individual surface (or at least have a
label for each vertex so that I can view it in matlab).

I would appreciate it if you find the time to provide some comments.

Kind regards,
Rikkert







On Tue, Nov 4, 2014 at 11:09 PM, Donna Dierker <do...@brainvis.wustl.edu>
wrote:

> I doubt you'll be able to convert the deformation map to Caret, but it
> won't be necessary, if Spherical Demons can resample what you need onto the
> source or target mesh, after it computes the registration.
>
> If it's not too hard, give it a shot and let us know how it goes.
>
>
> On Nov 4, 2014, at 12:59 PM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu>
> wrote:
>
> > 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 <do...@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.hindr...@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 <
> do...@brainvis.wustl.edu> wrote:
> > > 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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