[caret-users] Missing landmarks

John Harwell john at pulvinar.wustl.edu
Fri Sep 19 09:08:24 CDT 2003


The "landmarks from flatting" file should be created each time the 
flattening of a full hemisphere is performed and consists of three 
borders that identify the dorsal region of the medial wall, the ventral 
region of the medial wall, and the location of the calarine sulcus.  
During the flattening process the medial wall border is cut into two 
pieces by the frontal cut and the calcarine cut.  If the medial wall, 
the calcarine cut, or the frontal cut are missing, named improperly 
(names other than MEDIAL.WALL, CalcarineCut, FrontalCut), or either of 
the calcarine or frontal cuts does not intersect the medial wall, that 
is the most likely cause of the landmarks from flattening border file 
not being created.

A file that should always be created when flattening a full hemisphere 
is named "TemplateCuts.<#nodes>.borderproj".  This contains the medial 
wall and all cuts made during the flattening of a full hemisphere.  You 
should be able to start the flattening process, and, at the point in 
the process where you are asked to update the medial wall and cuts, 
delete all borders, and then load this "TemplateCuts" border projection 
file.  Verify that the frontal and calcarine cuts intersect the medial 
wall and then proceed with the initial flattening.  The "landmarks from 
flattening" file should be created and it is not necessary to continue 
beyond the point of the initial flat surface being created.

John Harwell
john at v1.wustl.edu

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

On Friday, September 19, 2003, at 03:26 AM, 
johannes at pet.mpin-koeln.mpg.de wrote:

> Hi everyone,
> I'm registering a few brains to the human Colin atlas. In one of my
> subjects, the landmarks from flattening-file is missing. I guess I'll
> just create a new directory and flatten the hemisphere again, but I'd
> like to know if there is a known cause to this and how I can avoid that
> problem in future.
> Thanks for your help
> Johannes
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> caret-users at pulvinar.wustl.edu
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