Hi caret-users,
Our tutorials remain fractured while we attend to other priorities, and
recently several labs outside wustl.edu are interested in using Caret to
register Freesurfer-generated surfaces. Therefore, now seems like a
good time to provide a roadmap to guide you through the maze of web
pages and tutorials.
First, read this page specifying our core 6 landmark set:
Caret5 Spherical Registration Core 6 Landmark Set
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html
This page supersedes figures and datasets cited in the tutorials below.
Second, consider applying an affine transform to your surfaces before
generating depth and registering to PALS_B12. Many scientists are very
skeptical about this step, and I concede that it is not appropriate for
all analyses. As a practical matter, however, it does make drawing
registration borders more difficult if the surface is not at least AC-PC
aligned. Before you do a lot of work, please read this document:
Reasons to Affine Register Volumes Before Segmenting in Caret
http://brainvis.wustl.edu/help/why_normalize_input
Contact me about your particular situation if you are unsure about what
to do or how to do it. Also feel free to share your concerns about it.
Third, follow the flattening and registration tutorials with your
dataset, but use the PALS_B12 atlas target (linked from the core 6 page
above) in lieu of the colin target. Flattening is really registration
part I; it is the easiest way to draw the medial wall and calcarine
borders, and the flat map makes drawing the other registration borders
easier:
Flattening
http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Segment.pdf
page 30
Registration
http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf
page 55
One probable "gotcha" is that the Flattening tutorial assumes you have
segmented in SureFit, so you have inflated and ellipsoid surfaces. If
you are importing Freesurfer surfaces, then an imported Freesurfer
inflated surface can function as an ellipsoid for flattening purposes,
and my freesurfer2caret.sh script imports this surface as a Caret
ellipsoid surface for this reason. However, most of the gaps in the
core6 landmarks page are relative to the SureFit-generated inflated
surface, and the Freesurfer surface won't work for this purpose.
Therefore, you must generate an inflated (not very inflated) surface for
this purpose (Surface: Geometry: Generate Inflated and Ellipsoid from
Fiducial). Currently, there is no "inflate_surface" command line
utility, but I will ask John to add this to his crowded wish list.
Lastly, users new to Caret and PALS may also find this tutorial helpful:
PALS_ATLAS_TUTORIAL
http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260
Donna Hanlon
