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
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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
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