Hi Svetlana,
Depending on which version of Caret you're running, you may need to
download a more recent version of this script:
http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh
login pub
password download
This version replaces the " -hem" flag in the caret_file_convert steps
with " -struct" (not sure exactly when this change took effect in
caret_file_convert). Thanks to Johannes Klein for pointing this out.
Note that I haven't tested this script.
In an attempt to be more clear, I also replaced these lines:
CASES="ED EF EG FH FK FL FM FN"
CASES="FH"
... with this one:
CASES="MYSUBJECT_01 MYSUBJECT_02 MYSUBJECT_03"
Earlier this year, the gracious folks in Bob Cox's AFNI group at NIH
provided us some Freesurfer cases from an old Mike Beauchamp study, for
the purposes of importing them into Caret, so this is what the "ED EF EG
..." cases are. The second line (CASES=FH) is just overriding the
previous line, having the effect of running the script solely on case FH
(e.g., probably to troubleshoot something).
In your case, you would replace this line:
CASES="MYSUBJECT_01 MYSUBJECT_02 MYSUBJECT_03"
... with this one:
CASES="sub01"
Then, cd to the directory containing sub01 and run the script.
If you don't care about sulcal depth, then comment out the
generate_depth lines near the end of the script to greatly reduce
run-time. (Even if you're doing an anatomical study, you might use
Freesurfer's convexity metric, rather than sulcal depth. In this case,
you'll need to add a few more lines to convert the curvature-like
convexity file to Freesurfer ASCII, and then into a Caret surface_shape
file. I believe this is the *h.sulc file; please correct me if I'm wrong.)
On 08/01/2006 06:42 AM, Svetlana Georgieva wrote:
Hi Donna,
Since I am a new caret user and trying to convert some freesurfer flat
maps your script 'freesurfer2caret.sh.rev' sound grate to me. Could
you please explain me haw exactly to run this script. Is it working
under freesurfer?
If I would like to run it for one subject (for example ‘sub01’) what
should I write in the following rows?
CASES="ED EF EG FH FK FL FM FN"
CASES="FH"
Thanks,
Svetlana
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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
