Reza,
Did you press the "Data File..." button to choose an input metric
file for deformation? The Apply Deformation Map Dialog requires the
user to select one specific data file for deformation, it does not
deform all of the files automatically which is done as part of the
spherical registration.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Mar 14, 2007, at 3:11 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,
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=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-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]
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********************************
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]
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