[caret-users] Reconstruct into surface command line
Hi, Does the caret have a command line function to reconstruct a surface from contours, equivalent to the GUI: Layers-Reconstruct into Surface? I can't seem to find it. Cheers, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Volume segmentation error: RadialPositionMap
Hi Donna, Thanks, but that -volume-segment command is what I tried in the first email and it produces the error I mentioned. It appears there is no command equivalent for the GUI Volume - Segmentation - Reconstruct into surface, I'll just have to work around it for now. Cheers, Tristan On Mon, Jul 29, 2013 at 11:58 PM, Donna Dierker do...@brainvis.wustl.eduwrote: Yes, I think it does require a surface as input. You can generate it in the GUI, like you cite below, or you can see if you can get this to work, toggling off 1-6 and toggling on what you need in 7-17. I never used this much, and I'm not sure it will work in your case, but the fact that it takes an input segmentation volume is encouraging. caret_command -volume-segment input-anatomy-volume-file-name input-segmentation-volume-file-name spec-file-name operation-code gray-peak white-peak padding-code structure error-correction-method write-volume-type Perform segmentation operations. Operation_Code characters Specify each with either a Y or N. All characters must be specified. Character Operation Description - - 1 Disconnect Eye and Skull 2 Disconnect Hindbrain 3 Use High Threshold for Hindbrain disconnection 4 Cut Corpus Callossum 5 Generate Segmentation 6 Fill Ventricles 7 Generate Raw and Fiducial Surfaces 8 Reduce polygons in surfaces 9 Correct topological errors in surfaces 10 Generate Inflated Surface 11 Generate Very Inflated Surface 12 Generate Ellipsoid Surface (For Flattening) 13 Generate Spherical Surface 14 Generate Comp Med Wall Surface 15 Generate Hull Surface 16 Generate Curvature, Depth, and Paint Attributes 17 Generate Registration and Flattening Landmark Borders gray-peak specifies the intensity of the gray matter peak in the anatomy volume. white-peak specifies the intensity of the white matter peak in the anatomy volume. padding-code Specify padding for any cut faces when segmenting a partial hemisphere. Specify each with either a Y for padding or N for no padding. All characters must be specified. Character Padding Description - --- 1 Pad Negative X 2 Pad Positive X 3 Pad Posterior Y 4 Pad Anterior Y 5 Pad Inferior Z 6 Pad Superior Z structure Specifies the brain structure. Acceptable values are RIGHT or LEFT spec-file-name Name of specification file. input-anatomy-volume-file-name If there is not an anatomy volume file, leave this item blank (two consecutive double quotes). input-segmentation-volume-file-name If there is not a segmentation volume file, leave this item blank (two consecutive double quotes). error-correction-method NONE GRAPH SUREFIT SUREFIT_THEN_GRAPH GRAPH_THEN_SUREFIT write-volume-type Type of volume files to write. Specifies the type of the volume files that will be written during the segmentation process. Valid values are AFNI NIFTI NIFTI_GZIP (RECOMMENDED) SPM WUNIL All input volumes must be in a Left-Posterior-Inferior orientation and their stereotaxic coordinates must be set so that the origin is at the anterior commissure. On Jul 28, 2013, at 10:31 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: But doesn't this require you already have a surface? I'm trying to create a surface from a segmentation volume. In the same way the GUI operation of Volume - Segmentation - Reconstruct into surface. On Fri, Jul 26, 2013 at 2:00 AM, Donna Dierker donna.dier
Re: [caret-users] Volume segmentation error: RadialPositionMap
But doesn't this require you already have a surface? I'm trying to create a surface from a segmentation volume. In the same way the GUI operation of Volume - Segmentation - Reconstruct into surface. On Fri, Jul 26, 2013 at 2:00 AM, Donna Dierker donna.dier...@sbcglobal.netwrote: Sounds like you have a segmentation already, so don't use -volume-segment. Try something like this instead: caret_command -surface-identify-sulci $SPECFNAME $HEM $SEGVOL $TOPO $FIDUCIAL $FIDUCIAL --- caret_command -surface-identify-sulci spec-file-name structure segmentation-volume-file-name closed-topology-file-name raw-coordinate-file-name fiducial-coordinate-file-name volume-write-type Identify Sulci with shape and paint. Create a surface shape file containing depth and curvature measurements, a paint file identifying the sulci, and an area color file. If there is no raw coordinate file, specify fiducial coordinate file instead. NOTE: This command MUST be run in the directory containing the files. structure Specifies the brain structure. Acceptable values are RIGHT or LEFT write-volume-type Type of volume files to write. Specifies the type of the volume files that will be written during the segmentation process. Valid values are: AFNI NIFTI NIFTI_GZIP (RECOMMENDED) SPM WUNIL On Jul 24, 2013, at 9:14 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: Hi, I am trying to create a surface from a segmentation volume using the command line. The anatomy volume was not segmented with Caret. When I do this: caret_command -volume-segment seg.nii Other.Case.L.spec NNYYN 1 0 NN LEFT SUREFIT_THEN_GRAPH NIFTI_GZIP I get: VOLUME SEGMENTATION ERROR: Unable to find volume file RadialPositionMap+orig.* I also get the same error when using the GUI, Volume - Segmentation Operations (Surefit) ... But if I use the GUI and use Volume - Segmentation - Reconstruct into surface, it works. I'm using Caret 5.65 on OSX 10.8.4. Any ideas why this is happening? Cheers, Tristan ___ 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] Volume segmentation error: RadialPositionMap
Hi, I am trying to create a surface from a segmentation volume using the command line. The anatomy volume was not segmented with Caret. When I do this: caret_command -volume-segment seg.nii Other.Case.L.spec NNYYN 1 0 NN LEFT SUREFIT_THEN_GRAPH NIFTI_GZIP I get: VOLUME SEGMENTATION ERROR: Unable to find volume file RadialPositionMap+orig.* I also get the same error when using the GUI, Volume - Segmentation Operations (Surefit) ... But if I use the GUI and use Volume - Segmentation - Reconstruct into surface, it works. I'm using Caret 5.65 on OSX 10.8.4. Any ideas why this is happening? Cheers, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Body weight of the F99UA1 case
Thanks David and Colin, I'll look into the references you provided. Regards, Tristan On Sun, Jun 23, 2013 at 2:41 PM, David Van Essen vanes...@wustl.edu wrote: Tristan, I was unable to find the weight from Nikos Logothetis, from whose lab it was scanned. However, you can get information on F99 brain size relative to the brain sizes of the McLaren et al. 112RM-SL atlas in Table 1 from: Cortical parcellations of the macaque monkey analyzed on surface-based atlases. http://www.ncbi.nlm.nih.gov/pubmed/22052704 *Van Essen DC*, Glasser MF, Dierker DL, Harwell J. Cereb Cortex. 2012 Oct;22(10):2227-40. doi: 10.1093/cercor/bhr290. Epub 2011 Nov 2. PMID: 22052704 David On Jun 17, 2013, at 7:34 PM, Tristan Chaplin wrote: Hi, Does anyone know the weight of the F99UA1 macaque? I can't seem to find it anywhere. Thanks, Tristan ___ 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] Mirroring hemispheres and Landmark Vector Difference registration
Hi David, Thanks, I didn't realise the spherical mesh also had to be in LPI orientation as well, I've fixed that. The borders are now roughly in the correct regions after registration but they are nowhere near as good as LPR. It almost looks as the borders haven't actually been morphed - as if they've just been projected from sphere to another (which would explain my original problem). Is there a chance I've done something that has stopped the LVD morphing from working? Something that only gives me straight sphere to sphere registration? I've tried changing the parameters but it doesn't seem to affect anything (number of morphing cycles, forces, vector displacement). I've just re-downloaded the current version of Caret (64 bit version) and it's the same. I'm using OS X 10.6. Any help or suggestions about what is going on here would be greatly appreciated. Cheers, Tristan On Sat, Mar 24, 2012 at 02:04, David Van Essen vanes...@wustl.edu wrote: Tristan, Registering from a left hem source to a right hem target (or vice versa) should work for the LVD as well as the LPR algorithm. I've done it myself on multiple occasions. Importantly, your source and target spec files must have the correct hemisphere assignment. Check that 'Structure' is correct when you open each spec file, and change it if necessary. If the hemispheres differ, this leads to the requisite mirror-flipping, as is now explained in: http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/SurfaceBasedRegistration#Algorithm_for_All_Registration_Operations * If the structure (left or right) differs in the source and target spec files, mirror-flip the source landmarks. Another item is to verify that the left and right spheres are correctly oriented in a dorsal view (medial wall is on the correct side, that is, if viewing the right sphere, the medial wall should be on the left in a dorsal view. For a left hem, it should be on the right.). It's puzzling that you had a problem only for LVD and not LPR, but I'm guessing that one of the above will take care of the problem. If not, let me know offline, as we might need to take a look at your dataset. David On Mar 23, 2012, at 1:15 AM, Tristan Chaplin wrote: Hi, I've been registering left hemispheres to a right hemispheres using the landmark pinned relaxation algorithm and getting reasonable results, so I presume process automatically mirrors hemispheres so they match. I wanted to try the new landmark vector difference algorithm. Using similar settings the registration completes but all the borders are not matched and are in completely the wrong spot - e.g. medial wall is on the lateral side and appear to be upside down. Is there a chance it's not mirroring? Or have I just not got the settings right? Thanks, Tristan ___ 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] Mirroring hemispheres and Landmark Vector Difference registration
Hi, I've been registering left hemispheres to a right hemispheres using the landmark pinned relaxation algorithm and getting reasonable results, so I presume process automatically mirrors hemispheres so they match. I wanted to try the new landmark vector difference algorithm. Using similar settings the registration completes but all the borders are not matched and are in completely the wrong spot - e.g. medial wall is on the lateral side and appear to be upside down. Is there a chance it's not mirroring? Or have I just not got the settings right? Thanks, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] Open vs closed borders for registration
Hi, I just wondering, is there advantage/disadvantage to using open or closed borders in registration? e.g. why is the medial wall two borders and not a single closed border? I had heard a while back that originally borders could only be drawn on flat surfaces so this must have been necessary then, but now you can draw borders on the 3d surface. Is there something simpler and thus better about using open borders for registration? I was wondering, if you were placing a border on a cortical area with that has a topographic organization, e.g. V1, is it better to use two borders, one for the upper field boundary, one for the lower field boundary, to give it some indication of the topology? I figure the closed border has a specific start point, end point and order, so if you do it the same in both source and target then it should match up in the same way. I have been reading Van Essen et al. (2011) Cortical Parcellations of the Macaque Monkey Analyzed on Surface-Based Atlases, but I can't seem to work it out from based on the description of the algorithm there. It seems like it would make no difference if closed or open borders are used. Any insight or practical experience would be greatly appreciated. Cheers, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] marmoset
Colin, the person working on the marmoset atlas was me. My boss, Marcello Rosa, and his colleagues Paxinos, Watson, Petrides and Tokuna recently published an atlas in book form: http://www.amazon.com/The-Marmoset-Brain-Stereotaxic-Coordinates/dp/0124158188/ref=sr_1_4?s=booksie=UTF8qid=1332126409sr=1-4 I've made surface models from this data, I'll send you a private email with more info, if anyone else is interested let me know. Cheers, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Interspecies comparisons - creating a new atlas for a different primate species
Ah I think that change resolution command is what I want. It made a nice fiducial mesh for me. I must admit I hadn't payed much attention to the command line caret features, I see now there is a lot of cool things in there. If run into any problems later with the actual registration I'll post a new topic. One quick question though - does flat morphing work better if the fiducial mesh is first standardised? On Wed, Feb 22, 2012 at 05:47, Timothy Coalson tsc...@mst.edu wrote: The way I understand it, if you already have an atlas sphere, you can (and probably should) register the native mesh to the spherical atlas directly, and the result is that (among other things) you get a new surface that aligns with your native surface, but has topology and node spacing similar to the atlas sphere. However, if you do not yet have an atlas sphere, the way I understand it, we made our atlas sphere without any dependence on the native mesh, by taking the borders on the subject sphere and unprojecting them to not rely on a mesh (then averaging them across subjects, but since you have only one subject, this doesn't apply), and then projecting them onto the sphere we wanted to use, giving us our atlas sphere with landmarks. Again though, I haven't done this, it is just my understanding of how it was described to me. If what you want is a surface with more regular spacing than what you have in the subject native surface, you can do that and then register to the new atlas sphere, or maybe just use the subject sphere and a new sphere to generate a deformation map, and deform the subject native surfaces to the new mesh (this is approximately what spec file change resolution does). Tim On Mon, Feb 20, 2012 at 6:55 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: Sorry I should have specified this before, for our atlas we have only a single indvidual with cytoarchitecture. We have a native mesh for this and the associated morphed spherical and flat meshes, as well as the cytoarchitecture as a paint file. I thought that to register this atlas to another individual, or for interespecies registration (which is want we really want to do) it was necessary to make standard fiducial mesh which has evenly spaced nodes, rather than the native mesh created after reconstruction from contours. I think I understand how to make a standard spherical mesh but do I need to make a standard fiducial mesh to allow intra and interspecies registration? Cheers, Tristan On Sat, Feb 18, 2012 at 05:31, Timothy Coalson tsc...@mst.edu wrote: The new atlases we are making (I think they may be included in the 5.65 release, but I am not sure, the fs_LR atlases are the ones I mean) use this new kind of sphere. If you want to take a look at node spacing regularity, there is an option in caret to generate the node areas of a surface under Surface-Region Of Interest Operations... Select all the nodes (clicking select with the default settings should do this), click next, select Assign metric with node areas, click the Assign Metric Node Areas button, and there you have it. Of course, the node regularity on the sphere doesn't translate directly to node regularity on subject surfaces, there is distortion inherent to registering on a sphere, since the brain isn't a sphere, but it should help. The new sphere code is only used in a few commands, so I would have to know more about what commands generate the surfaces in your current methods to hazard a guess at whether you would need to do something different to get a new sphere. Tim On Fri, Feb 17, 2012 at 11:02 AM, Colin Reveley cm...@sussex.ac.ukwrote: Tim - what you say is interesting. I have actually wondered about node spacing in fiducial surfaces registered to F99 via macaque.sphere6. It's not always 100% super straight forward to register (without lots of crossovers and issues). I'm fairly pleased with what I have. the matches are quite good. however, for my purposes, a node spacing that is a regular as possible in the context just of registering my surface to F99 has real advantages, because I use nodes as tractography seeds and I'd like their spacing to be roughly even. Might I benefit from trying your new approach? How hard would it be? f99 is still 73730, as are all the atlas files. DVE's most recent free surfer macaque to F99 tutorial still very much uses 73730. My surfaces are from FS and look pretty evenly spaced. So maybe register F99 on to my mesh, and make a deform_map for the F99 data? essentially following the menu driven landmark pinned reg. Other than fiducials (WM,GM, mean) the topos and other surfaces are made with caret operations. I'm guessing if I repeat those operations with caret5.65, it will follow the new scheme of things in terms of how node spacing is decided? Colin Reveley, sussex. On 17 February 2012 05:17, caret-users-requ...@brainvis.wustl.eduwrote: Send caret-users
Re: [caret-users] Interspecies comparisons - creating a new atlas for a different primate species
Thanks for information, but I must confess I don't understand why you create the sphere first. I thought the procedure for atlases was to make a surface, then resample it as a standard mesh, then do spherical morphing etc. Is the idea instead to create the fiducial surface, do spherical morphing, then align the sphere to one of these standard spheres? FYI we've already made a fiducial surface with cytoarchitecure as paint. On Fri, Feb 17, 2012 at 16:08, Timothy Coalson tsc...@mst.edu wrote: We have moved away from the 73730 mesh, we are now using a new method to generate meshes which results in much more regular node spacing. Making a sphere is actually relatively easy, especially with the new release of caret. The hard part is making it into an atlas, which I defer to someone else. The command: caret_command -surface-create-spheres Will generate a pair of matched left/right spheres (mirror node correspondence, topologies with normals oriented out). I think that command made it into the 5.65 release, if not you can use spec file change resolution, and grab just the new sphere, and ditch the rest. The odd bit about spec file change resolution, though, is if you give it an old node count, like 73730, it will give you the old sphere (this is in case someone is relying on its old behavior). However, ask it for 73731 nodes, and you will get a new highly regular sphere instead (though it won't have 73730 nodes, because the 73730 node mesh wasn't a regularly divided geodesic sphere, but it will give you something close). If all else fails, there are a few spheres in the caret data directory. Tim On Thu, Feb 16, 2012 at 6:56 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: Hi, A while back I asked about creating standard mesh of 73,730 nodes, similar to what is used for PALS atlas. I never got a chance to follow it up then but I'd like to give it a go now. It seemed at the time that the knowledge for creating such meshes was limited to a select few so if anyone has any experience with this or has the contact details of someone I would greatly appreciate hearing from them. The reason for creating this mesh is for making atlas for the marmoset monkey. We are very interested registering this atlas to the macaque monkey and doing analyses similar to Hill et al. (2010). Thanks, Tristan Chaplin On Mon, Feb 7, 2011 at 16:04, Tristan Chaplin tristan.chap...@gmail.comwrote: Ok thanks for the information. On Fri, Feb 4, 2011 at 03:25, Donna Dierker do...@brainvis.wustl.eduwrote: On 02/01/2011 07:31 PM, Tristan Chaplin wrote: Hi, I've been reading about the creation of your atlases, and I see that PALS and the macaque atlases have standard size mesh of 73,730 nodes. I was wondering, is this the same across species to allow interspecies registration? i.e. is it still possible to do interspecies comparisons of other species with different size meshes? Possible, but more difficult. Not to say that achieving vertex correspondence across species is trivial. Interspecies comparisons are really hard. I think David Van Essen is the only one in our lab that is doing them, although Matt Glasser might also be doing some. I was also wondering how the standard mesh was was actually made. The PALS paper refers to the Saad 2004 paper, which I think uses SUMA. SUMA has a program called MapIcosahedron to create standard meshes. Is this still how you would recommend making a standard mesh? Tim Coalson (a student who works summers here) also developed a utility that creates meshes of specified resolution. Making a standard mesh is not something I ever do. You do it with a specific motivation -- typically some other important data is already available on that mesh. And the way you usually get your data on that mesh is to register it to an atlas target already on that mesh. If you are talking about creating, say, a sparser mesh for mice/rats, then you're out of my orbit. Thanks, Tristan ___ 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] Problems after flattening - clear temp files?
Hi, I've been using caret for a while but just started having some trouble with flattening, I'm hoping someone has a quick technical fix. I'm using OSX 10.6.7. After running the morphing, it displays the crossover and errors screen, but you can't click close, you have to force quit the process. At this time caret is using 100% cpu. The popup also claims there are thousands of crossovers, when there actually isn't any. Sometimes a restart fixes this, but not always. I think I've managed to get caret into a bad state and I need to clear some cache or temp files. I tried install a fresh copy of the current version but it has the same problems (it still remembers all my recent spec files, I was hoping it would be completely fresh). Thanks, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Standard mesh of 73,730 nodes.
Ok thanks for the information. On Fri, Feb 4, 2011 at 03:25, Donna Dierker do...@brainvis.wustl.eduwrote: On 02/01/2011 07:31 PM, Tristan Chaplin wrote: Hi, I've been reading about the creation of your atlases, and I see that PALS and the macaque atlases have standard size mesh of 73,730 nodes. I was wondering, is this the same across species to allow interspecies registration? i.e. is it still possible to do interspecies comparisons of other species with different size meshes? Possible, but more difficult. Not to say that achieving vertex correspondence across species is trivial. Interspecies comparisons are really hard. I think David Van Essen is the only one in our lab that is doing them, although Matt Glasser might also be doing some. I was also wondering how the standard mesh was was actually made. The PALS paper refers to the Saad 2004 paper, which I think uses SUMA. SUMA has a program called MapIcosahedron to create standard meshes. Is this still how you would recommend making a standard mesh? Tim Coalson (a student who works summers here) also developed a utility that creates meshes of specified resolution. Making a standard mesh is not something I ever do. You do it with a specific motivation -- typically some other important data is already available on that mesh. And the way you usually get your data on that mesh is to register it to an atlas target already on that mesh. If you are talking about creating, say, a sparser mesh for mice/rats, then you're out of my orbit. Thanks, Tristan ___ 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] Sulcal depth from histological slices without an MRI/atlas
Hi everyone, I've made a few models from histological slices and I was wondering if there is any way of calculating sulcal depth without an MRI volume or atlas. There aren't any MRIs for my animals and there aren't any atlases for this species. I understand the I need a cerebral hull, which is usually generated by dilating and eroding the mid thickness of the MRI volume. I tried to simulate this by slightly inflating the fiducial surface and saving it as a vtk file and using it as a cerebral hull. It works ok, but I was wondering if anyone knows a better way. Thanks, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Calculating mid-thickness and accurately drawing borders
Hi David, Thanks for the information. We had actually been using layer 4 as the surface but I thought that since atlases are based on MRI mid-thickness it would better to use mid-thickness. But I take your point about histology quality and alignment accuracy being a much bigger source of error. Thanks for giving me Erin's contact details, I may need to ask her a few things. If you have C++ code that can do it, let us know if you're willing to share it. Unfortunately, the cutting code we have is just some ad hoc python scripts at this stage. It would be interesting to see if we could clean it up and redo it in C++ for Caret, but like you we have other priorities. Thanks, Tristan On Tue, Jan 18, 2011 at 16:24, David Van Essen vanes...@wustl.edu wrote: Tristan, On Jan 17, 2011, at 6:56 AM, Tristan Chaplin wrote: Hi, I'm working on constructing brain models from histological sections with cortical areas demarcated. Until now we've been writing our own progrms to achieve this. I'd like to start to use Caret for more of this work so non-programmers can do it and our data is more compatible with other datasets, but I've got a few questions. Firstly, with regards to drawing a contour of the cortical mid-thickness, the tutorial suggests that you just estimate this visually when drawing the contours. I was wondering, is there a standard procedure or set of tools for calculating the mid-thickness given the pial and GM/WM boundaries? Not for histological contours. Unless the mapping between white and pial surfaces has already been determined (e.g., via Freesurfer automated segmentation) computing the midthickness is a very hard problem. In practice, we generally achieve a reasonable outcome by drawing a contour along the estimated midpoint between the white matter and pial contours in a given section, modulated by the fact that histological layer 4 tends towards the pial side in gyri and near the white matter side near sulcal fundi. Unless your histological sections are exceptionally well aligned (overcoming tissue distortions during histology), the inaccuracies associated with imperfect midthickness determination are likely to be small on average relative to the typical between-section misalignment. Finally on this front, Erin Reid in my lab has been doing contour-based reconstructions on a couple of recent projects and has been helping to update the old tutorial. If you have specific technical questions, you can contact her: Erin Reid e...@brainvis.wustl.edu Secondly, with regards to marking cortical areas, normally we would represent the area boundaries as points in space (cells in Caret I believe) and using our own programs, project to the nearest mesh node. Then, for a given cortical area, we would use the Dijkstra algorithm to cut out the cortical area by finding the shortest path between it's boundary points. Sounds nice. However it seems that in Caret the method is to view the projected cells on a flat map, and draw a border around it to create a paint file. Yes, except that Caret now permits borders to be drawn on inflated or other closed surfaces, thereby obviating the problems along the cuts in flat maps. Is there a more precise way, perhaps similar to the one I described, of doing it in Caret? Not at present. It would be nice to have this as an automated process/algorithm, but given other priorities it is not something we are likely to undertake in the near future. If you have C++ code that can do it, let us know if you're willing to share it. David VE Thanks, Tristan ___ 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] Calculating mid-thickness and accurately drawing borders
Hi, I'm working on constructing brain models from histological sections with cortical areas demarcated. Until now we've been writing our own progrms to achieve this. I'd like to start to use Caret for more of this work so non-programmers can do it and our data is more compatible with other datasets, but I've got a few questions. Firstly, with regards to drawing a contour of the cortical mid-thickness, the tutorial suggests that you just estimate this visually when drawing the contours. I was wondering, is there a standard procedure or set of tools for calculating the mid-thickness given the pial and GM/WM boundaries? Secondly, with regards to marking cortical areas, normally we would represent the area boundaries as points in space (cells in Caret I believe) and using our own programs, project to the nearest mesh node. Then, for a given cortical area, we would use the Dijkstra algorithm to cut out the cortical area by finding the shortest path between it's boundary points. However it seems that in Caret the method is to view the projected cells on a flat map, and draw a border around it to create a paint file. Is there a more precise way, perhaps similar to the one I described, of doing it in Caret? Thanks, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Importing VTK polygon CELL_DATA in Caret
Thanks I'll check that out. I can write a program to convert between two data formats if Caret has some appropriate file format. Something where you can assign data to the mesh polygons, so you can then say colour the surface in caret with that data, as you would if it was mean curvature etc. I was hoping it was the cell file? FYI The problem is I need to cut and then flatten some surface models that have data associated with the polygons. The thing is if I import to Caret, that polygon data is not kept anywhere. Then when I cut the surface and flatten, there are less polygons than there used to be, so when I save the it back as a VTK file I can't even cross reference it to the original VTK file to look up the polygon data. Therefore I need to hang on to this data whilst cutting and flattening. Thanks, Tristan On Tue, Sep 28, 2010 at 23:12, Donna Dierker do...@brainvis.wustl.eduwrote: It sounds like you have two kinds of VTK data: The surfaces, and the cell data. You can certainly import VTK surfaces into Caret, using either the File: Open Data File option, or caret_command (command line utility). I don't know about VTK cell data. Our whole lab is in all-day meetings today and tomorrow, so it might be Thursday before we can check on this. Enter caret_command -help-full /tmp/caret_command.txt at a terminal window and use a text editor to read /tmp/caret_command.txt and search for file-convert. (If you're on Windows, you'll need to adjust this command accordingly.) Hi, I'm pretty new to Caret, so far I've just been using it for reconstruction from histological slices and flattening. I have some pre-existing VTK surface models in which the polygons have some data associated with them, e.g. number tracer labelled cells, visuotopic information etc. In the VTK text file format, it's called CELL_DATA. When I load these surfaces into Caret, it seems this data is not preserved anywhere. However Caret does seem to support this VTK feature when exporting - if I colour the surface with a overlay of the mean curvature and save a VTK file, I see that it writes out the colouring as CELL_DATA in the VTK file. My question is, how do I import this polygon data into Caret surfaces? I'm thinking I need to import it as a different Caret file, such as a Cell file. Is that correct? Should I generate a separate file using the information at http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html ? Thanks, Tristan ___ 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] Importing VTK polygon CELL_DATA in Caret
Hi, I'm pretty new to Caret, so far I've just been using it for reconstruction from histological slices and flattening. I have some pre-existing VTK surface models in which the polygons have some data associated with them, e.g. number tracer labelled cells, visuotopic information etc. In the VTK text file format, it's called CELL_DATA. When I load these surfaces into Caret, it seems this data is not preserved anywhere. However Caret does seem to support this VTK feature when exporting - if I colour the surface with a overlay of the mean curvature and save a VTK file, I see that it writes out the colouring as CELL_DATA in the VTK file. My question is, how do I import this polygon data into Caret surfaces? I'm thinking I need to import it as a different Caret file, such as a Cell file. Is that correct? Should I generate a separate file using the information at http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html ? Thanks, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
