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
