On Jan 8, 2015, at 11:12 AM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu> wrote:
> Hi Donna, > > Thank you very much for your response. > > You're right about the smoothing: the deformed individual surface in the > target directory is indeed the same as the > original one (after the flattening). Clear. > > Would the deformed individual surface in the target directory be considered > native space? The only difference with > the unregistered surface is that it is resampled onto standard mesh (but the > shape is the same). The deformed surface is in the same *stereotaxic space* as the source surface. The surfaces in the atlas directory are on the same mesh as the atlas surface. > All goodies also > project nicely to it. I also plotted them over one another and they perfectly > overlap. FYI: I am calculating an EcoG > leadfield on the surface so the exact shape needs to stay the same. I would think you'd want to work on native mesh, then (individual/source directory). > And am I correct that the deformed template surfaces in the source directory > are resampled onto the individual > mesh? In this directory, however, I only see the deformed spherical. I that > all the boxes "Deform coordinate files to > atlas" so these I assume, are the deformed surfaces in the target directory. > I see however, no box "atlas to individual". Whatever files were in the atlas/target spec file when you ran registration will get resampled onto the source subject's mesh and saved in the source directory. You can also apply the deform_map in the source dir to your atlas goodies, or just re-run registration using a spec file that points to the goodies you want resampled onto native mesh. > I figured out how to export a paint file and input it in Matlab: I save it as > a labeled GIFTI file and open it in Matlab > with gifti.m (from the GIFTI toolbox). I then have all 19 columns at once! Now you have to ponder which are useful to you. > Kind regards, > Rikkert > > P.S. I noticed that in the Paxinos atlas, V5 is merged with the medial wall. > > > On Thu, Jan 8, 2015 at 3:51 PM, Donna Dierker <do...@brainvis.wustl.edu> > wrote: > On Jan 7, 2015, at 10:16 AM, "HINDRIKS, RIKKERT" <rikkert.hindr...@upf.edu> > wrote: > > > > > Hi Donna, > > > > I now have performed the spherical registration. What I would need is the > > PHT atlas on the individual surface. > > If you checked the box requesting atlas to individual, then you should have > that in your individual/source directory. > > > 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? > > Yes, the medial wall gets smoothed at the beginning of flattening, if I > recall correctly (it's been a long time!), and a version of the sphere is > generated from the fiducial with the smoothed medial wall. This is what goes > into registration. > > What you are seeing in the atlas directory is the source/individual > midthickness (with smoothed medial wall) resampled onto the target mesh. It > will be slighter smoother than the source, and thus have slightly smaller > surface area. But it will look a lot like the source. > > > 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)? > > It sounds like things went reasonably well. Now you're at a point where you > need to decide: > > * do I work with atlas goodies on my native individual surface > (assuming you checked that box)? or > * do I work with individual goodies on atlas surfaces > > The answer depends on what you're doing with the data. If it's more > important that the surface stays native (e.g., for folding/areal > measurements), then the former option is better. If it's handy to have > things on the atlas standard mesh for other reasons, then atlas-land is the > way to go. With just one subject, native-land may be fine. I did skim the > history below, but don't have the time to fully digest it at the moment. But > maybe this will get you further along in your own thinking about next steps. > > > 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? > > The atlas label/paint file may have multiple columns for multiple > parcellations (e.g., LVE00 vs OrbitalFrontal). You might need to extract > just one of these and work with a single parcellation at a time. This is my > best guess as to what is going on there. > > > > > 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 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > caret-users mailing list > > > > > > > caret-users@brainvis.wustl.edu > > > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > caret-users mailing list > > > > > > caret-users@brainvis.wustl.edu > > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > _______________________________________________ > > > > > > caret-users mailing list > > > > > > caret-users@brainvis.wustl.edu > > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > > > _______________________________________________ > > > > > caret-users mailing list > > > > > caret-users@brainvis.wustl.edu > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > _______________________________________________ > > > > > caret-users mailing list > > > > > caret-users@brainvis.wustl.edu > > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > _______________________________________________ > > > > caret-users mailing list > > > > caret-users@brainvis.wustl.edu > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > _______________________________________________ > > > > caret-users mailing list > > > > caret-users@brainvis.wustl.edu > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > _______________________________________________ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
