Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
On Jan 8, 2015, at 11:12 AM, "HINDRIKS, RIKKERT" 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 > 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
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 > > > > > > > > > > > > On Wed, Nov 5, 2014 at 3:20 PM, Donna Dierker > 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_
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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 > > > > > > 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
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 > 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 >
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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 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 tu
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, 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
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 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'
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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" > 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" > > 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 o
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 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 > so
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
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" > 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 newe
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 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, th
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, 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, an
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
On Oct 30, 2014, at 11:29 AM, "HINDRIKS, RIKKERT" 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 > wrote: > On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT" > 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
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 > 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 > > > > > > __
Re: [caret-users] Creating a surface-based atlas from a volumetric-atlas
On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT" 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
