Fantastic! Thanks again for all your help! Best,
Elise On Mon, Dec 7, 2009 at 5:10 PM, John Harwell <[email protected]>wrote: > Hi Elise, > > You can make the flat maps in Caret. There is a tutorial for flattening > available at http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation. > > Typically in the Van Essen laboratory, it is our practice to average the > pial and smooth white matter surfaces to create a surface that approximates > layer 4. This can be done from the command line (caret_command > -surface-average) or though the Caret5 GUI using File Menu->Surface Create > Average Coordinate File. > > Good luck, > > John > > > On Dec 7, 2009, at 3:07 PM, Dickinson, Annelise (NIH/NIMH) [F] wrote: > > > 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!! > > > > -Elise > > > > > > On 12/1/09 1:59 PM, "John Harwell" <[email protected]> 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. > > > > John > > > > > > > > ***************************************************** > > Annelise Dickinson > > Post-Bac IRTA > > Laboratory of Brain and Cognition, NIMH/NIH/DHHS > > Building 10, Room 4C212 > > 10 CENTER DR MSC 1366 > > BETHESDA MD 20892-1366 > > ***************************************************** > > Phone: (301) 435-4941 > > FAX: (301) 402-0921 > > E-Mail : [email protected] > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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