Thanks Donna, I'll use the F6.BOTH.withF99 dataset. I've had success loading individual surfaces into SUMA (after converting the files to ASCII), but haven't figured out how to load / display the curvature. Since this is probably more related to SUMA and figuring out how to properly load the data with SUMA, I'll follow up with the AFNI/SUMA folk for more help.
It also appears that SUMA is looking for a .params file. I generated one in Caret from File-> save data file (after loading the atlas spec). I assume this should be sufficient. Thanks! Mike On Oct 1, 2009, at 9:38 AM, Donna Dierker wrote: > Hi Mike, > > 1) F6 dataset: Probably only David knows for sure, but > Macaque.F6.BOTH.SURF-VOL.Std-MESH.73730 is dated 3/9/2007, while > Macaque.F6.BOTH.withF99-Data.Std-MESH.73730 is dated 8/16/2007. Since > they have many files in common, my guess is that the latter was > based on > the former, but has an important enhancement: > Macaque.F99UA1.COMPOSITE_PartititioningSchemes.73730.borderproj. It > has > the partitioning schemes not only in paint form, but also border form. > I'd use the latter. > > 2) SUMA interoperability: While John Harwell (our lab) has worked > with > Ziad Saad and Rick Reynolds (AFNI/SUMA orbit) on GIFTI, a neutral > surface file format akin to what NIfTI does for volumes, I don't think > you need to convert your surfaces to GIFTI in order for SUMA to read > them. Ziad has worked pretty hard to make SUMA read Caret surfaces > with > little tweaking. We did uncover some issues recently with the way > Caret > was writing AFNI .HEAD files, but sticking with NIfTI, where possible, > should avoid these problems. That said, both the datasets mentioned > above have AFNI volumes, so if you run into any alignment issues > between > the volume and the surface in SUMA, let us know. I don't necessarily > anticipate problems. > > Donna > > On 09/30/2009 03:15 PM, Michael Arcaro wrote: >> Hello, >> >> I'm interested in mapping some macaque fMRI data onto the macaque >> atlases, specifically the Lewis - Van Essen '00 atlas. I'm new to >> Caret and have a couple of basic questions: >> >> First, is there a recommended atlas dataset to use? (F6 or F99) From >> the tutorial, it sounds as if I would want to go with the F6 atlas. >> Assuming I go with the F6, what are the differences between: >> Macaque.F6.BOTH.SURF-VOL.Std-MESH.73730 >> Macaque.F6.BOTH.withF99-Data.Std-MESH.73730 >> Is there a reason to use one of these above the other? >> >> Second, I'm looking to import the atlas into SUMA to warp/align with >> my data. I'm having a bit of difficulty with this. From what I have >> read, SUMA can read Caret format. I was wondering if I need to >> convert >> any of the files into a different format for SUMA to read (or >> possibly >> rename the files). This may be more of a question for the SUMA folk, >> but I thought I'd see if anyone here is familiar with importing the >> atlases into SUMA. >> >> Thanks, >> Mike Arcaro >> _______________________________________________ >> 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
