Fantastic, thank you SO much! I should have known...in FreeSurfer that's exactly how things work also--you must open a full surface before opening the flat patch.
That's the first I've heard of GIFTI, which sounds wonderful--I'll definitely ask my post-docs if they know more about it! Hope you have a great weekend, and thanks so much again! -Elise ________________________________________ From: John Harwell [[email protected]] Sent: Wednesday, November 25, 2009 12:50 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Import Freesurfer flat maps into Caret? Hi Elsie, Yes Caret5 can read FreeSurfer files. You will need to know if the file is ASCII (usually ends with "asc") or binary. You will also need to know if the file is a "patch" file which usually has "patch" in its name. If the file is a patch file, you must open it AFTER opening a non-patch file such as an "orig" file. In Caret5: * Select File Menu->Open Data File. * Set the File Type to "Free Surfer Ascii Surface File" or "Free Surfer Binary Surface File". Select your file and press the Open Button. On the command line, using caret_command (run caret_command -file- convert for help information): Convert the free surfer surface into closed topology and fiducial coordinate files. Create a spec file for a left cortex. -file-convert -sc -is FSS lh.orig.asc -os CARET fiducial.coord \ closed.topo FIDUCIAL CLOSED -spec file.spec - struct LEFT Convert the free surfer patch into cut topology and flat coordinate files. Create or add to the spec file as left cortex. Write the coord and topo files in text format. -file-convert -sc -is FSP lh.oc.flat.asc lh.orig.asc \ -os CARET flat.coord cut.topo FLAT CUT -spec file.spec \ -struct LEFT -outtext By the way, there is a committee (GIFTI, www.nitrc.org/projects/gifti) that has developed a common surface file format for neuroimaging file formats. Both Caret and FreeSurfer are part of this committee. In the not too distant future you, and others, should be able to use the GIFTI format for your data and move between different neuroimaging software applications without having to do any file format conversion. ----------------------------------- John Harwell [email protected] Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave Box 8108 Saint Louis, MO 63110 On Nov 25, 2009, at 10:34 AM, Dickinson, Annelise (NIH/NIMH) [F] wrote: > Hello, > > Sorry in advance if the answer to this question is already up > somewhere! > > I was just wondering if there is any way to import flat maps made in > Freesurfer into Caret for viewing and editing? If so, how would this > process be carried out? > > Please let me know, thanks so much and happy Thanksgiving! > > Best, > > Elsie > > ***************************************************** > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
