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]>//
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