The only thing I'd add to John's advice is that the text editor part is for identifying which borders are dups -- not for deleting them. You can delete them from the border file, but then you'll need to tweak other lines. For example, the number of borders is in a line by itself right after the EndHeader line. If you don't delete from the end, then you'll need to reindex the border numbers. Typically, if you use the text editor to find the dup borders, it's easier to then use Layers: Borders: Delete border with mouse to delete the "top" one.

Problems like this can occur when borderproj files mistakenly get loaded twice. For example, say you somehow have a borderproj loaded with just the medial wall and calcarine borders. Then if you append a borderproj file that also includes those landmarks, now you have dup borders. This is where the Append and Replace buttons are important when loading borderproj files.


On 03/01/2007 04:44 PM, John Harwell wrote:

Since it states that there are 16 border with 14 border names, that seems to indicate that there are multiple borders with the same name. You can correct this by loading the border projection file into a text editor, finding the duplicate borders, and deleting them duplicate that you do not need. It may require trial and error to determine which of the duplicate borders to delete so be sure to back up your file before editing it.

Good Luck.

John Harwell

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.    Box 8108
St. Louis, MO 63110   USA

On Mar 1, 2007, at 4:22 PM, Reza Rajimehr wrote:

Hi caret-users,

I am doing a spherical registration of the individual monkey brain to the F99UA1 atlas, and I am experiencing a problem. I drew 14 landmarks on the individual flat coord, did border projection, and saved it as a borderproj file. When checking the borderproj file by ? in the individual spec file,
it confirms that it has 14 borders, and there are 14 border names. I
selected the same landmarks on the atlas flat coord, deleted the rest of
the borders, did border projection, and saved it as a borderproj file.
When checking the borderproj file by ? in the atlas spec file, it says
that there are 16 borders. However, there are only 14 border names in the
? box. It seems that there are 2 additional landmarks on the atlas brain
that are not visible to me in the Caret window and have no name. I get an error when doing the deformation, complaining that the number of landmarks
in the individual and atlas brains are different.

Thanks for any help,


Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

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