Hi Donna,

I now have performed the spherical registration. What I would need is the
PHT atlas on the individual surface.

I am however, not sure how to interpret the generated surfaces. For
example, in the target directory there appear
coordinate files with the prefix "deformed" and refer to the individual
monkey. Although the shape of the fiducial
one is very similar to the shape of the (undeformed) individual surface,
there are some slight differences (for
example, the medial wall is smoothed). What is the exact interpretation of
these surfaces?

I noticed that I can view the different atlases defined on the template on
these deformed atlases. Does this
mean that I have mapped them to the individual surface (which is what I
want)?

One more question about exporting the results: When I export the deformed
surface with the atlas as a
.label.gii file and read it into Matlab, I get a nice list of ROI names and
corresponding RGB and alpha
values. However, the .cdata fields has 20 columns which I don't understand.
I hoped to get, for each
vertex, an index into the ROI list. I've also tried to export it as a
surf.gii file, the then the .cdata field has
4 columns whose meaning I don't understand as well. Could you please
clearify this for me and tell me
how to get a ROI-number for each vertex?

Much appreciated!
Kind regards,
Rikkert





On Wed, Nov 5, 2014 at 3:20 PM, Donna Dierker <do...@brainvis.wustl.edu>
wrote:

> On Nov 5, 2014, at 7:05 AM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu>
> wrote:
>
> >
> > 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).
>
> Use the right for both.  Caret with x-flip the left hems when it does its
> thing, provided the source spec file correctly identifies the hemisphere.
>
> In this way, the resulting left and right hem resampled surfaces are in
> register with one another.
>
> Just make sure there is a hemisphere tag that correctly identifies your
> left hem, and Caret will do the rest.
>
> > 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.
>
> Should be surface_shape, but depending on what spec file you are using,
> you might not have one.  Or if it is more recent, it might be shape.gii.
> The Sept 2006 tutorial has a surface_shape for the macaque F99 in the
> MACAQUE subdir, for example.
>
> If your individual was segmented in Caret, then it should have a sulcal
> depth map from the prepare for flattening step.  This should be in a
> surface shape file.  If you used something else, then are you sure you need
> the sulcal depth map?  If you just want something that looks like it for
> visualization, the Freesurfer .sulc is a good substitute.
>
> > 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?
>
> One hem, different specs.
>
> > 3. Why are there .topology files? (since the topology is determined by
> the triangulation, which is stored in .coord files)
>
> Coords contain only x,y,z coordinates.  Neighbor relationships are in the
> .topo files.
>
> > 4. After registering, how can I project any goodies defined on the
> template to the individual surface?
>
> Make sure the goodies are listed in the target atlas spec file, and make
> sure you check the box that indicates atlas to individual.  Then, whatever
> you specify in the target atlas gets resampled into your source directory
> onto source mesh.
>
> > 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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