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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> >
> >
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