See inline below. On 10/01/2009 02:34 PM, Michael Arcaro wrote: > Hi Donna, > > Thanks for the heads up. I'm was a bit confused as to the differences > between Caret and Surefit datasets. I tried using SUMA's Make_Spec > script for Caret surfaces. I noticed that I had to rename the files > slightly for the program to recognize the .coord and .topo files. > > I also had to edit the SUMA .spec file. When, I initially included > both F6 and F99 datasets, the node correspondence between surfaces was > lost. By creating .spec files that only load F6 or F99 surfaces, node > correspondence is maintained when switching between surfaces (within > F6 or F99 datasets) in SUMA. > Hmmm. No clue there, but I bet Ziad would have some ideas. > The next issue was mapping on the curvature. As you suggested, > extracting the curvature column and making a 1D.dset did the trick. > Interestingly, this 1D.dset file works for both F6 and F99 datasets > and appears to have proper mapping for surfaces in both datasets. This > seems a bit odd since I could maintain node correspondence when > switching between F6 and F99 surfaces in the same .spec file. > I think you mean "could maintain node correspondence when switching between F6 and F99 surfaces in the same .spec file," based on my understanding of your previous paragraph.
Again, I can't explain what you saw in the paragraph preceding my "Hmmm" response above. But I can explain why the 1D works for both: David took great pains to register both F6 and F99 to the standard 73730 mesh. Thank David Van Essen. > I also extracted the border projections into a .1D.dset which maps > onto the surfaces fine. It's a bit of a hack job, but I haven't found > any tutorials on SUMA on how to properly load .paint or .borderproj > files. This also seems to properly map onto both F6 and F99 datasets. > This is a first to my knowledge. I'm not sure how SUMA handles borders. > This is what I really care about. I hope to use the SUMA tools to warp > the F6 dataset and my own datasets into a standard / aligned space. > Are you using something like the Argall, et. al. method to register your subjects? > All my data is on the surface. I don't think I will need to project > back into volume space, so the point of origin should not be an issue > for me. > > Mike > > > On Oct 1, 2009, at 2:24 PM, Donna Dierker wrote: > > >> Mike, >> >> Just as a heads up, when SUMA was first developed, Caret and SureFit >> were separate. (SureFit generated segmentations and surfaces; Caret >> displayed, flattened, and registered surfaces.) In those days, >> SureFit's origin was at the lower left corner of the cropped bounding >> box. When SureFit merged into Caret, there was a migration from voxel >> space to coordinate space, and the origin moved to the AC (or whatever >> the origin in the volume fed to Caret for segmentation). If SUMA >> translates the surface by some parameters defined in the .params file, >> you'll see major misalignment between surface and volume. I think >> Ziad >> has a work-around for this -- perhaps a flag added to the coord header >> to indicate it is post-SureFit. The F6 and F99 datasets are post- >> SureFit. >> >> It is possible that you'll need to convert the surface shape file to >> ASCII ; strip the header; and extract the curvature column into a "1D" >> file. But it is worth posting to the AFNI message board. >> >> Donna >> >> On 10/01/2009 12:34 PM, Michael Arcaro wrote: >> >>> 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
