Re: [caret-users] About Monkey to Human Deformation
Dear David, In the Apply Deformation Map dialog box, I specified the following items: 1) Deformation Map File: the 23-LDMK deform_map file 2) File Type: Metric 3) Flat Max Edge Length: 10.00 4) Metric Deformation: Nearest Node (not sure which one is better?) 5) Smooth One Iteration (Except Flat) The other buttons were not clickable (the dialog box does not allow me to use them). When I click the Apply button, I immediately receive the following error message: Deform Error Is deformation map file valid? You must select a data file for deformation. You must select the output name for the deformed file. I tried to apply deformation map from two different .spec files: 1) Macaque F99 atlas directory, which has deformed metric files (from individual macaque to F99). I added/appended the .deform_map file to this .spec file before applying deformation. 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06 directory). I added/appended my metric files to this .spec file before applying deformation. In both cases, I got the same error. Thanks for your helpful comments/suggestions, Reza Reza, On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote: Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map Once you have a deform_map file, you can use it to register data sets from monkey to human WITHOUT re-running a registration. This is done using the Surface: Deformation: Apply Deformation Map option. If you want to register paint files, metric files, and most other files, you don't need anything other than the deform_map file to get the job done, and the dialog window is fairly self- explanatory. If you want to register a border projection file or a coordinate file, then you need additional coordinate and topology files that are available as part of the Caret Sept_06 tutorial dataset: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051archive_name=COMPARE_PALS_MacaqueF99.73730.spec The only reason to actually re-run an interspecies registration is IF you don't like the particular set of landmarks used and you want to try your own. If so, you should start with borderproj files also in: http://sumsdb.wustl.edu/sums/archivelist.do? archive_id=6595051archive_name=COMPARE_PALS_MacaqueF99.73730.spec and make your additions and subtractions from there. See Part 4 of the latest Caret tutorial for more details on monkey- human comparisons. http://sumsdb.wustl.edu/sums/directory.do? id=6585200dir_name=CARET_TUTORIAL_SEPT-06 I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dialog box? Or there are other files that I should use? I also assume that the macaque F99 .spec file should be used in the Individual tab, and the human PALS .spec file should be used in the Atlas tab. See above. These steps should not be necessary for your purposes. I hope this helps. David Thanks for your help, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
[caret-users] About Monkey to Human Deformation
Dear caret-users, David Van Essen suggested me to use the following .deform_map file for deformation of macaque F99 to Human PALS: RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23- LDMK-VE.73730.spec.deform_map I specified this as my .deform_map file in the Spherical Parameters tab in the Spherical Surface Deformation dialog box. My question is what I should specify as .borderproj file. I have a borderproj file in my F99 directory (that I used for the registration of individual macaque to F99). I also have a borderproj file in my PALS directory (that I used for the registration of individual human to PALS). Should I use these borderproj files in the Individual and Atlas tabs in the Spherical Surface Deformation dialog box? Or there are other files that I should use? I also assume that the macaque F99 .spec file should be used in the Individual tab, and the human PALS .spec file should be used in the Atlas tab. Thanks for your help, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
Re: [caret-users] Flattening and Spherical Registration of the Monkey Brain
Dear Donna and David, Thank you for the helpful comments and suggestions. I successfully finished flattening of an individual human brain and its spherical registration to the human PALS atlas, and the registration is perfect. Now I want to start flattening of an individual monkey brain and its spherical registration to the macaque F99UA1 atlas. Before starting this process, I just wanted to make sure that I am using the correct (and the most up-to-date) files. In particular, I would appreciate if you provide me with the SumsDB links for the following files: 1) Macaque template cuts for flattening (border file and border color file). 2) Macaque landmarks for registration (border color file and border projection file). 3) F99UA1 atlas for registration (.spec, .deform_map, and sphere.coord files). 4) The complete F99UA1 atlas containing various .coord files (and other Caret files) for surface visualization. and a brief question about flattening: where is the location of temporal and frontal cuts on the macaque cortex, and how can I draw them? (i.e. where are the recommended start and end points for these cuts?) Thanks, Reza Hi Reza, The atlas target dataset you used was the right one, but it is a stripped down version that minimizes the number of files that get deformed from the atlas to the individual's directory. (Some people want to look at the atlas paint or border files on their individual's surface, so then you would need to put those files in the atlas target directory and add them to your atlas spec file; then, they would automatically deform to the individual's directory during registration.) Since you want to visualize on the atlas target, there's no need to re-register; rather, just download one or more of these datasets: PALS_B12.LEFT.STANDARD-SCENES.73730.spec http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595803 PALS_B12.RIGHT.STANDARD-SCENES.73730.spec http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595827 There are quite a few other options/documents listed here: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 You can move your deformed results to the extracted directory, or move the extracted files to your atlas target directory -- your choice. I tend to create separate right and left subdirectories under my atlas target directory, which has lots of files, but when I run registration I use the single parent atlas target directory. Often, we want to do group analysis of functional (metric) or anatomical (surface_shape) data; in these cases, we create composite metric or depth files. This command line utility (caret_command -help-full) can be helpful: caret_command -metric-or-shape-composite caret_command -metric-or-shape-composite-named-column If you're going to use the tools under Attributes: Metric and Surface Shape Statistical Operations, then the spec files above lack the distortion metrics and OPEN topo files included in these analysis datasets: * Visualization/Analysis spec LEFT: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486316 * Visualization/Analysis spec RIGHT: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6486393 Most of the tests can be run using the caret_command utility. Donna On 02/21/2007 01:25 AM, Reza Rajimehr wrote: Dear caret-users, I did the spherical registration of an individual human brain to the human PALS atlas. I used the following dataset as the target atlas brain: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499 A new deformed .spec file has been generated. However, it has only one new surface, which is a deformed sphere. I would like to visualize the functional activities of the individual brain on the atlas brain (e.g. on the atlas flat map). Should I download a more elaborate PALS dataset and add them to the current directory? If so, should I redo the spherical registration, or the new PALS surfaces (e.g. inflated, flattened, ...) will be automatically linked to the deformed spherical surface that I already have? Thanks, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
[caret-users] A Question about Spherical Registration
Dear caret-users, I did the spherical registration of an individual human brain to the human PALS atlas. I used the following dataset as the target atlas brain: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499 A new deformed .spec file has been generated. However, it has only one new surface, which is a deformed sphere. I would like to visualize the functional activities of the individual brain on the atlas brain (e.g. on the atlas flat map). Should I download a more elaborate PALS dataset and add them to the current directory? If so, should I redo the spherical registration, or the new PALS surfaces (e.g. inflated, flattened, ...) will be automatically linked to the deformed spherical surface that I already have? Thanks, Reza Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
[caret-users] Macaque-Human Deformation and Registration
Dear caret-users, We have done an fMRI experiment in macaques and humans. The anatomicals of macaques and humans have been fully reconstructed in FreeSurfer. The functionals have been also analyzed in FreeSurfer/FS-FAST. We have successfully imported some reconstructed surfaces (e.g. inflated surface) and functional .w files into Caret using freesurfer2caret.sh (more specifically, we have imported one macaque cortex, and the spherical average of 10 human cortices into Caret). Now we want to deform/register the macaque cortex to the human cortex in Caret to see whether the functional activity patterns are topographically aligned across species, and therefore test possible homologies (something similar to Orban, Van Essen, Vanduffel - TICS 2004 - Fig. 4). I had some questions regarding this analysis, and I would really appreciate any comments or suggestions: 1) It is recommended to do this analysis in the spherical space. We have spherical surfaces of macaques and humans in the FreeSurfer format. Is there any way to import the spherical surfaces from FreeSurfer to Caret? Similarly, is there any way to import the flattened patches from FreeSurfer to Caret? 2) For the macaque-human registration, should I deform my monkey's cortex/hemisphere to the macaque F99 atlas, and my human's cortex/hemisphere to the human PALS atlas, and then deform F99 to PALS? Or, I can directly deform the monkey's cortex to the human's cortex without using the atlases? 3) It would be great if you also refer me to the most up-to-date documentation/tutorial describing the macaque-human deformation analysis. Thank you, Reza - Tootell/Vanduffel Lab Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED]
