Rishi,
A couple of points to add to Donna's.
1) The 'Core 6' landmarks refer specifically to human cortex, not the
macaque. The calcarine sulcus has a rather different configuration
in the macaque (especially in posterior regions).
2) If your objective is to make a calcarine cut to reduce distortions
during flattening, Donna's comments should suffice.
3) If your objective is to register an individual macaque to the
macaque F99 atlas, you should use a macaque-specific set of
registration landmarks. The number of suitable landmarks is actually
larger than for humans because there is much greater consistency of
the folding patterns.
Instructions for macaque-specific within-species registration are
available in Caret Tutorial 11 (Part 3). This tutorial is somewhat
outdated, as it was written for Caret 4.6. Nonetheless, the section
on landmark selection and drawing should nonetheless get you on the
right track.
Tutorial document:
http://brainmap.wustl.edu/caret Tutorials and documentation for
Caret 4.6:
Caret User's Guide and Tutorial Part 2 (PDF) For use with Tutorial
data sets 5 to 11
Tutorial 11 dataset:
http://sumsdb.wustl.edu/sums/directory.do?
id=6135715&dir_name=TUTORIAL_11_REGISTER_FREESURFER_SURFACES_TO_MACAQUE_
ATLAS
I hope this helps.
David
On Mar 22, 2007, at 1:17 PM, Donna Dierker wrote:
Rishi,
See inline replies below.
Donna
On 03/22/2007 10:45 AM, Rishi Kalwani wrote:
hi,
in the core6 landmark website it says not to draw the calcarine
sulcus if it makes a hard ventral turn.....
This means as it extends from the medial wall toward the occipital
pole.
the CaSu on my monkey makes a ventral turn below the medial wall,
but it's about 20-30 degrees off from the medial wall......should
i draw the full extent of the CaSu?
This isn't too uncommon. Your calcarine border/cut MUST intersect
the medial wall, or the Caret demons will visit you. If your
calcarine sulcus starts curving ventrally as it approaches the
medial wall, almost parallel with the parahippocampal gyrus for a
while, then you'll need to deviate from the fundus and cross over
to the medial wall, near the margins of the cortex inferior to the
splenium.
The attached captures range_inflated.jpg and range_fiducial.jpg
show my best guess of the ballpark intersection location. I'm
copying Erin Reid, who draws many more monkey borders than I do.
Other monkey people may also weigh in here if I'm off.
does the CaSu nearly stretch to the most ventral extent of the
surface?
Not at either end. I'm not sure I understand what you mean. (Some
captures with well-placed ID nodes will help me get it if my
captures don't clear things up.)
also, a separate problem is that when i press the apply button in
the DRAW Borders dialog and begin to click the left mouse button
to trace the medial wall on the surface in the main window, it
doesn't show me a border being drawn.....is there something else i
need to do?
This used to happen when you somehow rotated a flat surface, such
as the compressed medial wall surface. Slight rotations that
aren't evident to the user can prevent draw borders from working
properly. Hitting Toolbar: R (reset) usually fixes the problem
(but undoes any zooming/panning). But I thought John added a
warning if you applied draw borders and there was a rotation to the
surface. How old is your Caret version? I thought you just got a
new version, but I'm not certain.
thanks
rishi
<range_inflated.jpg>
<range_fiducial.jpg>
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