My attempt to clarify made it even more confusing: '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.'
You meant could NOT maintain node correspondence. On 10/02/2009 09:37 AM, Donna Dierker wrote: > 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 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
