Aaron,
Donna's email covers the key technical issues. I have some
clarifications to add regarding the semantics of what we mean by the
term 'fiducial' surface.
We consider that the term 'fiducial' is applicable to ANY surface
configuration that 'captures' the shape of a given hemisphere, with
all of its glorious convolutions. By this convention, the gray/
white surface, the pial surface, and the mid-thickness (~layer 4)
surface are all 'fiducial' sub-types.
Also, a given hemisphere can have fiducial surface representations in
more than one 3D space - the native space, an AC-PC aligned space,
and a standard stereotaxic space (e.g., SPM99, AFNI-tlrc).
If there is any possibility of ambiguity it is advisable to identify
the fiducial sub-type and space explicitly. In Caret, when saving a
coordinate file, you are asked to specify its type (fiducial,
inflated, etc.) and its coordinate frame. We do not currently
include the option of specifying pial vs mid-thickness vs gray-white
('smoothwm') [but that may change], so if you are dealing with
FreeSurfer-generated files, we recommend that you include this
information in the file name and/or comment to allow disambiguation.
David VE
On Feb 13, 2006, at 10:58 AM, Donna Hanlon wrote:
Hi Aaron,
The caret_file_convert command below will just convert lh.orig to
Caret -- not average lh.orig with lh.pial. John Harwell recently
wrote a command line utility, caret_command, for this an other
purposes. If you're willing to wait until tomorrow morning, I'm
planning to write a script that uses caret_command,
caret_file_convert, etc. to streamline the steps in part 3 of the
NIH tutorial (http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6459772). When this is available, I'll post to caret-
users, because there are others interested in doing the same thing.
The old Caret 4.6 tutorial part II (http://brainmap.wustl.edu/caret/
pdf/CARET_UsersGuide.03-06.Part-II.pdf) covered Freesurfer-to-Caret
conversion, but it reflects the old interface. The NIH tutorial
(http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6459688) is
the next best thing, but I think this script will be what you want.
Donna
On 02/13/2006 10:12 AM, Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I’ve just started using caret, and am trying to convert
freesurfer data. To do so, I used the following command suggested
in the caret_file_convert help file:
caret_file_convert -sc -is FSS lh.orig.asc -os CARET
fiducial.coord closed.topo FIDUCIAL CLOSED -spec file.spec -hem LEFT
As I understand it, fiducial.coord should be a surface halfway
between fs’s white and pial surfaces. However, on the test subject
I did, it looks the same to me as the white matter surface, so I
wanted to make sure what I did was correct.
Also, is there a tutorial or help website for converting from
freesurfer to caret? Thanks,
-Aaron-
//Aaron L. Goldman//
//Kelly Contractor//
//Genes, Cognition and Psychosis Program, NIMH//
//Building 10, Room 3C108//
//Phone: (301) 435-0944//
//Email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>//
---------------------------------------------------------------------
---
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
