[caret-users] Issue with displaying voxel intensities
Dear all, When I load a T1-weighted scan into Caret, the image looks like a mask, that is, all white voxels covering the brain. The voxel intensities themselves are, however, nicely distributed and the grey and white matter peaks are clearly visible. Also, the intensities are normalized between 0 and 255. This problem does not occur when I view the scan with MRIcron or SPM. Does anyone know what is going on here? Thanks alot, Rikkert ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Issue with displaying voxel intensities
Hi Donna, I tried to upload the file but am not sure if it worked though. Please let me know... Kind regards, Rikkert On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker wrote: > Hi Rickert, > > Assuming you used File: Open Data File: type = Volume Anatomy File, you > should see a normal T1w image. > > If you see solid white, then please upload the volume here, so we can try > to replicate the problem: > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > Donna > > > On Jun 18, 2014, at 12:32 PM, "HINDRIKS, RIKKERT" < > rikkert.hindr...@upf.edu> wrote: > > > > > Dear all, > > > > When I load a T1-weighted scan into Caret, the image looks like a mask, > that is, all white voxels covering the brain. The voxel intensities > themselves are, however, nicely distributed and the grey and white matter > peaks are clearly visible. Also, the intensities are normalized between 0 > and 255. This problem does not occur when I view the scan with MRIcron or > SPM. Does anyone know what is going on here? > > > > Thanks alot, > > 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
Re: [caret-users] Issue with displaying voxel intensities
Hi Donna, I'm sorry but I am unable to upload the file... Kind regards, Rikkert On Thu, Jun 19, 2014 at 5:27 PM, Donna Dierker wrote: > Hi Rikkert, > > Please try again. There was a problem with permissions when I tried just > now, but I fixed it. > > Donnba > > > On Jun 19, 2014, at 1:12 AM, "HINDRIKS, RIKKERT" > wrote: > > > Hi Donna, > > > > I tried to upload the file but am not sure if it worked though. > > Please let me know... > > > > Kind regards, > > Rikkert > > > > > > On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker > wrote: > > Hi Rickert, > > > > Assuming you used File: Open Data File: type = Volume Anatomy File, you > should see a normal T1w image. > > > > If you see solid white, then please upload the volume here, so we can > try to replicate the problem: > > > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > > > Donna > > > > > > On Jun 18, 2014, at 12:32 PM, "HINDRIKS, RIKKERT" < > rikkert.hindr...@upf.edu> wrote: > > > > > > > > Dear all, > > > > > > When I load a T1-weighted scan into Caret, the image looks like a > mask, that is, all white voxels covering the brain. The voxel intensities > themselves are, however, nicely distributed and the grey and white matter > peaks are clearly visible. Also, the intensities are normalized between 0 > and 255. This problem does not occur when I view the scan with MRIcron or > SPM. Does anyone know what is going on here? > > > > > > Thanks alot, > > > 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
Re: [caret-users] Issue with displaying voxel intensities
Hi Tim, Thank a lot for your fast response! Ok, clear. Ok, so I decrease the FOV before loading it in Caret. About the NaNs, I noticed that and replaced them with zeros now. MRI is new for me so most likely I will post some more trivial issues. Kind regards, Rikkert P.S. Please delete the scan; it came from collaborator's lab. On Thu, Jun 19, 2014 at 11:45 PM, Timothy Coalson wrote: > It is doing that because the FOV is so large compared to the brain - the > total number of positive voxels is only 2.1% of the total number of voxels. > Thus, the default display of clipping the top and bottom 2% of values > results in a very low "max" for palette scaling. Changing the Draw Type in > Volume Settings in display control to Min to Max shows the variation in the > data, though a bit darker than what 2% to 98% does on more > approriately-sized volumes. > > It should also be noted that ~50% of your voxels are NaN, which are > generally quite unfriendly to computation such as smoothing. > > Tim > > > > On Thu, Jun 19, 2014 at 2:41 PM, HINDRIKS, RIKKERT < > rikkert.hindr...@upf.edu> wrote: > >> Hi Donna, >> >> I'm sorry but I am unable to upload the file... >> >> Kind regards, >> Rikkert >> >> >> >> On Thu, Jun 19, 2014 at 5:27 PM, Donna Dierker >> wrote: >> >>> Hi Rikkert, >>> >>> Please try again. There was a problem with permissions when I tried >>> just now, but I fixed it. >>> >>> Donnba >>> >>> >>> On Jun 19, 2014, at 1:12 AM, "HINDRIKS, RIKKERT" < >>> rikkert.hindr...@upf.edu> wrote: >>> >>> > Hi Donna, >>> > >>> > I tried to upload the file but am not sure if it worked though. >>> > Please let me know... >>> > >>> > Kind regards, >>> > Rikkert >>> > >>> > >>> > On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker < >>> do...@brainvis.wustl.edu> wrote: >>> > Hi Rickert, >>> > >>> > Assuming you used File: Open Data File: type = Volume Anatomy File, >>> you should see a normal T1w image. >>> > >>> > If you see solid white, then please upload the volume here, so we can >>> try to replicate the problem: >>> > >>> > http://pulvinar.wustl.edu/cgi-bin/upload.cgi >>> > >>> > Donna >>> > >>> > >>> > On Jun 18, 2014, at 12:32 PM, "HINDRIKS, RIKKERT" < >>> rikkert.hindr...@upf.edu> wrote: >>> > >>> > > >>> > > Dear all, >>> > > >>> > > When I load a T1-weighted scan into Caret, the image looks like a >>> mask, that is, all white voxels covering the brain. The voxel intensities >>> themselves are, however, nicely distributed and the grey and white matter >>> peaks are clearly visible. Also, the intensities are normalized between 0 >>> and 255. This problem does not occur when I view the scan with MRIcron or >>> SPM. Does anyone know what is going on here? >>> > > >>> > > Thanks alot, >>> > > 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] Creating a surface-based atlas from a volumetric-atlas
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. And to parcellate an individual macaque brain, can I register both the surfaces (that is, the template surface and the individual surface) spherically? Thanks a lot, Rikkert ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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. 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? 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? 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). 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) 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. Thanks a lot Donna, and kind regards, Rikkert On Thu, Oct 30, 2014 at 3:13 PM, Donna Dierker 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 > deformati
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
Hi Donna, Thanks for you extended reply. The plan is to do the following: Surface-register the individual image to the F99 surface, select one of the existing atlasses on this surface, extend the atlas to a volume-atlas, volume-register to the T2-weighted image, and re-do the fiber-tracking (I do not necessarily need the atlas I have now; I just need white-matter tracts in register with an atlas) Thank again, Rikkert On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker 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
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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 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
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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 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" > 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 > 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
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
I will try to perform the registration in Caret (since I use Windows, I cannot access the required compiler to run Spherical Demons in Matlab). I found the needed files for registering a macaque cortex and will draw the landmarks by hand. Probably I will have to call for your help again during the process... Kind regards, Rikkert On Tue, Nov 4, 2014 at 11:09 PM, Donna Dierker 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" > 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 > 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 subseque
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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 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" > 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 > 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,
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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 wrote: > On Nov 5, 2014, at 7:05 AM, "HINDRIKS, RIKKERT" > 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 >
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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). 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. 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". 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! 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 wrote: > On Jan 7, 2015, at 10:16 AM, "HINDRIKS, RIKKERT" > 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 > > > > > >
[caret-users] read border file into Matlab
Hi all, Is it possible to load a .border file into Matlab? I am conducting my analysis in Matlab and would like to use the border file of different cortical parcellations for visualization. And generally, what kind of structure does a border file have? Thanks and kind regards, Rikkert Hindrik ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] read border file into Matlab
Dear Rouhi, Thanks for your fast reply. I already have the atlas file itself loaded into Matlab (at the moment, I use the multi-model atlas from [Glasser, 2013] but this could be any atlas) and I just want to be able to visualize the ROI borders, that's all. Kind regards, Rikkert On Mon, Nov 14, 2016 at 2:57 PM, Rouhollah Abdollahi wrote: > Dear Rikkert, > > What kind of analysis do you want to carry out? Do you want to check the > overlapping surfaces? > As far as I know, it is much easier to work with paint or metric, files, > because you are dealing with surface nodes and it is only one column of > data. Also it is easily readable in Matlab if you are using Gifti format > using Gifti Library. (https://www.nitrc.org/projects/gifti/). > > Hope it helps. > > best regards > Rouhi > > > *Institut für Neurowissenschaften und Medizin (INM-3)* > Forschungszentrum Jülich > Leo-Brandt-Straße > 52425 Jülich, GermanyTel: +49 2461 61-9324 > > > > On Mon, Nov 14, 2016 at 11:28 AM, HINDRIKS, RIKKERT < > rikkert.hindr...@upf.edu> wrote: > >> Hi all, >> >> Is it possible to load a .border file into Matlab? I am conducting my >> analysis in Matlab and would like to use the border file of different >> cortical parcellations >> for visualization. And generally, what kind of structure does a border >> file have? >> >> Thanks and kind regards, >> Rikkert Hindrik >> >> ___ >> 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
Re: [caret-users] read border file into Matlab
I will. thanks again Rikkert On Mon, Nov 14, 2016 at 5:17 PM, Rouhollah Abdollahi wrote: > > Then you may check this link to find out the file structure: > > http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/ > file_formats/file_formats.html > > > Best Regards > Rouhi > > Best Regards > Rouhollah Abdollahi > > *Institut für Neurowissenschaften und Medizin (INM-3)* > Forschungszentrum Jülich > Leo-Brandt-Straße > 52425 Jülich, GermanyTel: +49 2461 61-9324 > > > > On Mon, Nov 14, 2016 at 4:33 PM, HINDRIKS, RIKKERT < > rikkert.hindr...@upf.edu> wrote: > >> Dear Rouhi, >> >> Thanks for your fast reply. I already have the atlas file itself loaded >> into Matlab (at the moment, I use the >> multi-model atlas from [Glasser, 2013] but this could be any atlas) and I >> just want to be able to visualize >> the ROI borders, that's all. >> >> Kind regards, >> Rikkert >> >> On Mon, Nov 14, 2016 at 2:57 PM, Rouhollah Abdollahi >> wrote: >> >>> Dear Rikkert, >>> >>> What kind of analysis do you want to carry out? Do you want to check >>> the overlapping surfaces? >>> As far as I know, it is much easier to work with paint or metric, files, >>> because you are dealing with surface nodes and it is only one column of >>> data. Also it is easily readable in Matlab if you are using Gifti format >>> using Gifti Library. (https://www.nitrc.org/projects/gifti/). >>> >>> Hope it helps. >>> >>> best regards >>> Rouhi >>> >>> >>> *Institut für Neurowissenschaften und Medizin (INM-3)* >>> Forschungszentrum Jülich >>> Leo-Brandt-Straße >>> 52425 Jülich, GermanyTel: +49 2461 61-9324 >>> >>> >>> >>> On Mon, Nov 14, 2016 at 11:28 AM, HINDRIKS, RIKKERT < >>> rikkert.hindr...@upf.edu> wrote: >>> >>>> Hi all, >>>> >>>> Is it possible to load a .border file into Matlab? I am conducting my >>>> analysis in Matlab and would like to use the border file of different >>>> cortical parcellations >>>> for visualization. And generally, what kind of structure does a border >>>> file have? >>>> >>>> Thanks and kind regards, >>>> Rikkert Hindrik >>>> >>>> ___ >>>> 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
