[caret-users] Import Freesurfer flat maps into Caret?

Dickinson, Annelise (NIH/NIMH) [F] dickinsona at mail.nih.gov
Mon Dec 7 15:07:42 CST 2009

Hi Dr. Harwell,

Oh wow, that looks interesting! Hmmm I'll talk this all over with my post-doc as soon as I can-but thank you so so much for all your help and advice and please do let me know if you'd like any more information or data files from us at all.

My post-doc's goal is to use Caret's atlases for a retinotopy experiment-do you suggest simply making the flat maps themselves in Caret? If so, would you happen to know the answer to the following question: Should the Fiducial surface for flattening in Caret be set as the FreeSurfer smoothwm (this is suggested in Beauchamp's Caret OpenWetWare flattening wiki) or another FreeSurfer dataset such as pial or orig? We just want to make sure we are catching all the appropriate brain tissue in the flat surface (since FreeSurfer's segmetation creates different types of files from Caret's).

Please let me know if you have any insights on this issue, and thank you again!!


On 12/1/09 1:59 PM, "John Harwell" <john at brainvis.wustl.edu> wrote:

Hello Elise,

I examined the FreeSurfer patch file and it appears to be in a different format than FreeSurfer patch files we have had in the past.  While I can change caret so that it does not crash, I am unable to determine the organization of the file so that it can be read.  You will need to run the command "mris_convert -p  lh.cort.patch.flat.try1  lh.cort.patch.flat.try1.asc" to convert the file to ascii format which caret is able to read.  While caret is then able to read the patch file, the surface from the patch file does not look correct.


Annelise Dickinson
Post-Bac IRTA
Laboratory of Brain and Cognition, NIMH/NIH/DHHS
Building 10, Room 4C212
BETHESDA  MD  20892-1366
Phone: (301) 435-4941
FAX:   (301) 402-0921
E-Mail : dickinsona at mail.nih.gov

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