Hi Reza,Hmmm. I can almost replicate this behavior. When I load CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, both the individual and atlas directory buttons are disabled, but Data File and Deformed File... are both enabled (see attached capture). I thought perhaps this might be because the deform_map was read-only, but I get the same behavior with a copy that is writeable. Normally, one can change the individual and atlas directories, as one must do when using a deform_map from one of our datasets (unless you're David Van Essen, in which case the paths work fine).
Using the Data File button, I could navigate to an input metric and successfully deform the data file. But if your buttons are disabled, then you might try using the following two caret commands to get the job done:
DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
caret_command -def-map-path \
<deformation-map-file> <source-path> <target-path>
SURFACE APPLY DEFORMATION MAP
caret_command -surface-deformation-apply \
<deformation-map-file> <file-type> \
<input-file> <output-file> \
[source-topo-file] [source-deformed-topo-file] \
[atlas-topo-file]
Deform a data file.
Note: "source-topo-file", "source-deformed-topo-file" and
"atlas-topo-file" are only required when deforming
coordinate files.
"file-type" is one of:
AREAL_ESTIMATION
BORDER_FLAT
BORDER_PROJECTION
BORDER_SPHERICAL
CELL
CELL_PROJECTION
COORDINATE
COORDINATE_FLAT
FOCI
FOCI_PROJECTION
LAT_LON
METRIC
PAINT
PROB_ATLAS
RGB_PAINT
SURFACE_SHAPE
TOPOGRAPHY
Donna
On 03/14/2007 03:11 AM, Reza Rajimehr wrote:
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, RezaReza, 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_mapOnce 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=6595051&archive_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=6595051&archive_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=6585200&dir_name=CARET_TUTORIAL_SEPT-06I 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. DavidThanks 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 mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
-- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
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