[caret-users] Macaque Landmarks

[Donna Dierker]

On 08/27/2008 05:05 PM, MCLAREN, Donald wrote:
> Does anyone have instructions for drawing the macaque landmarks?
Donald,

There is no monkey-specific registration tutorial since 2003 (Caret 
4.6), and that one was using now obsolete flat-based registration.  But 
Figure 8.5, p. 37 
(http://brainmap.wustl.edu/caret/pdf/CARET_UsersGuide.03-06.Part-II.pdf) 
shows the landmark labels of the major sulci on the flat map, which is 
still useful for drawing borders for spherical registration.

Monkey registration differs from human registration as follows:

1. You are not limited to the Core 6 landmarks.  Macaque anatomy is much 
less variable than human anatomy is, so many more landmarks can be used. 
Use as many as are provided in the atlas target dataset's borderproj 
file (the ones named like "LANDMARK*"), but if one or more landmarks 
leaves you feeling uncertain about the correspondence between source and 
target, then delete that landmark in both source and target borderproj 
files.  (Save the modified target borderproj by a different filename, 
e.g., "Macaque.F99UA1.R.LANDMARK_xPS.35946.borderproj" to denote that 
the PS landmark was deleted.)

2. Use this target dataset:

Macaque.F99UA1.REGISTER-with-INDIVIDUAL.73730.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6589983

All three borderproj options in this dataset can be used for both right 
and left hems, since they are averages of both.  See attached listing of 
the comments and landmark borders listed in each borderproj file.  For 
discussion of the target options, see the September 2006 tutorial:

http://sumsdb.wustl.edu/sums/directory.do?dir_id=6585200

3. There is no monkey equivalent of the "Caret5 Spherical Registration 
Core 6 Landmark Set" page 
(http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html).  
Since macaques are less variable than humans, it is easier to establish 
correspondence between source and target -- even at the landmark 
terminations.  As described in 1 above, delete/trim any landmarks where 
correspondence is shaky.

4. For monkey to human landmarks, see Part 4 of the Sept 2006 tutorial 
(link above). The notes near the top of p. 62 are especially relevant.

Though not different from human, remember:

* Use spherical registration -- not flat.

* Source and target borderproj files must have the same number of 
borders, and they must be named identically.

Donna