Hi Donna, Thanks for your quick response. I gatehred from the tutorial that Caret generates a fiducial surface from the freesurfer surfaces, which is what I'd like to do. Do I have to import the orig and pial surfaces for this. What do I do after this? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED]
________________________________ From: [EMAIL PROTECTED] on behalf of Donna Hanlon Sent: Sat 17/12/2005 12:56 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Tutorial troubles Hi Alex, I recognize your name from other mailing lists, but don't recall you posting on caret-users before -- welcome! Yes, this post reminds me of our need to update the old Caret 4.6 Tutorial 11 (Freesurfer-to-Caret), because this is something several users are going to want to do (e.g., so you can register your Freesurfer-generated surfaces using Caret's landmark-based registration algorithm, which is useful in ways that differ from Freesurfer's intensity/convexity-based registration algorithm). At some point, both tools may support multiple registration algorithms, but I'm guessing this is a ways off. Reading this passage, it's amazing how little I recall of the way Caret 4.6 used to work. ;-) But I don't think this step is necessary in Caret5. The smoothing will operate on the surface in the main window, whatever surface that is (presumably the rh.orig.asc surface). One thing that bears attention from David, my boss, however, is whether it is generally good practice to import both the rh.orig.asc and rh.pial.asc surfaces, and then use the Surface: Create Average Coord File, the result of which should be more like our SureFit-generated fiducial surfaces. I suppose this depends on what your objectives are, but David feels it is important to aim for layer 4, because then the surface area along gyral crests is not underestimated and the area along sulcal fundi is not overestimated. Since many of our analysis techniques depend on surface area, this is an important consideration for us. Please bear with our current state of documentation. We're juggling many priorities right now, but at some point we will turn our attention to updating the tutorials. Users who update them for us get stickers. ;-) Seriously, if you run into more trouble, let us know, because other users will soon feel your pain. Donna On 12/16/2005 01:55 AM, Fornito, Alexander wrote: >Hi, >I'm new to Caret and have just downloaded version 5.3. >I'm trying to work with surfaces generated in freesurfer, and have been >following the tutotial, but have become stuck at a point where I think the new >version differs to older ones. >After improting the surfaces and smoothing it, the tutorial (p. 71) says >Select Surface: Load AUXconfig into REFconfig. >The config files (?) did not come up before, so i don't know what this refers >to. Also, I can't seem to find anything that might resemble this option in the >usrface (or any other) pull-down menu. >Any help on how to proceed is much appreciated. My goal is to used caret >registration with freesurfer surfaces. >Thanks, >Alex > >Alex Fornito >M.Psych/PhD (clin. neuro.) candidate >Melbourne Neuropsychiatry Centre and Department of Psychology >The University of Melbourne >[EMAIL PROTECTED] > > >_______________________________________________ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
