Hi Donna,
context: advances in streamlining FreeSurfer and Caret processing
(PALS_B12.LR.zip).
goal: I have my subject's T1 ran through FreeSurfer's recon-all. for
this same subject i want to use Caret to obtain native space sulcal
depth maps. thereafter i want to take this Caret native space
Thanks for information, but I must confess I don't understand why you
create the sphere first. I thought the procedure for atlases was to make a
surface, then resample it as a standard mesh, then do spherical morphing
etc. Is the idea instead to create the fiducial surface, do spherical
Yes It is possible!
http://brainvis.wustl.edu/wiki/index.php/Caret:Download
if you use Freesurfer_to_PALS-B12 Pipeline you will get all surfaces in
caret and it gives you the shape file (sulci pattern) in *.shape format
and deformation map (fs to caret or caret to fs).
It also gives you
Tim - what you say is interesting.
I have actually wondered about node spacing in fiducial surfaces registered
to F99 via macaque.sphere6.
It's not always 100% super straight forward to register (without lots of
crossovers and issues). I'm fairly pleased with what I have. the matches
are quite
Hi Tristan,
As you know, the target keeps moving. If you haven't done so, read this paper:
http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr290.long
It's been a while since I read it, and I noticed one of the sumsdb links was
bad, but this looks like the right thing:
It's possible, but this isn't what preborder.sh does. First, its depth maps
are generated from a version of the midthickness that has been stereotaxically
registered to WashU's 711-2B space (because this is what the probabilistic
volumes representing the sulci are in). But also it has already
Creating the sphere may not be the first step, but the key thing about an
atlas is that all of the subjects used to generate the atlas need to be on
the same mesh, with subject landmarks occupying the same or nearby node
numbers. Native meshes from freesurfer do not have this property, nor to
