Hi Jason,
Dr. Van Essen and I just discussed your question, and we'd like more
information about what you're trying to do. Often, there are easier
ways to accomplish goals than posters envision.
But to answer your question directly, no -- there are no published
materials for adapting the core6 landmarks. (We typically use more
landmarks for nonhuman primates, for whom variability is much less of an
issue. I often refer users to the old Caret 4.6 Tutorial Part II,
tutorial 8, Register Flat Maps, because I think it's a useful reference
-- even though we don't use the flat map registration as a method anymore.)
In principle, it's possible to add landmarks. In general, you would
need to do this for each of the 24 PALS_B12 hemispheres (12 left, 12 right):
1. Identify the landmark on the fiducial surface.
2. Draw the border (probably easiest on the PALS flat surface, using
the deformed folding as a shape underlay; we don't believe a composite
folding file is available in sumsdb, but we have them).
3. Project the border.
4. Load the PALS_B12 spherical surface, and save the border relative to
that surface.
5. Average the resulting borders to create an average PreCes target
border for each hemisphere; add this border to the Core6 landmarks to
generate a new landmark set -- let's call it Connolly7.
Before going down this path, we think you would benefit from a warm-up
exercise that might help you understand why the PreCes is not a core
seventh landmark; we believe its variability makes it difficult to
establish correspondence across subjects. Even where you can establish
clear guidelines that can be applied consistently, we think this
landmark will add more variance -- not reduce it.
To see this personally, download the PALS tutorial here:
http://sumsdb.wustl.edu/sums/directory.do?id=6332260
Go to scene 6A, Case1.R sulcal depth, four configurations.
Switch the D/C menu from Scene to Surface Shape.
Looking just at the very inflated and flat maps, toggle among the
deformed depth columns for each of the 12 PALS_B12 right hemispheres.
On each depth map, locate the PreCes on both the flat and very inflated
maps.
Note that the fiducial for Case 1 is shown in Window 3; since there
aren't preset scenes for each subject, you'll need to use File: Open
Data File: Coord file and navigate to your
CARET_HOME/data_files/fmri_mapping_files directory to load fiducial
coord files for the other PALS_B12 subjects. (For each hemisphere,
there is a coord file for each of the six atlas spaces we support; for
the purposes of this exercise, it doesn't matter which you choose, as
long as you get the right case number and make sure it's a right
hemisphere -- named like *.R.*.)
Case 1 has a nicely defined PreCes, so it won't be a problem. But
several of the other cases illustrate the nature of the correspondence
problem with this landmark. For registration purposes, we believe this
problem creates more problems than it solves.
But if you decide to go ahead and add additional landmarks, then we
recommend you register your data both ways: Using the Core6 and the
Connolly7. Once you get your data segmented and flattened, running
registration multiple ways is easy; just make sure you use a different
deformation prefix (fourth tab on the registration menu) and/or atlas
target directory. (I'd recommend separate atlas target spec files, if
not separate directories.) This way, you can compare the two and see
which results you prefer. You may find they both are helpful, but tell
you different things. Having the Core6 results will give you a way to
compare your results with those of other labs who have used the Core6
landmarks.
Happy morphing!
On 04/06/2006 01:02 PM, Jason D Connolly wrote:
Dear Caret-users,
Is there any information in the tutorials, manuals etc. that can
instruct us as to how to go about adapting the core6 landmarks to use
our own landmarks (in addition to the core6) for morphing to the PALS
atlas? We hope to use the precentral sulcus as an additional
registration landmark ...
Many thanks, Jason.
------------------------------------------------------------
Jason D. Connolly, PhD
Center for Neural Science, New York University
6 Washington Place Room 875, New York, NY 10003
cell:646.417.2937 lab:212.998.8347 fax:212.995.4562
http://www.psych.nyu.edu/curtislab/people/jasonconnolly.html
_______________________________________________
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.)
