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Author: Akiko Ikkai (---.NYU.EDU)
Date: 02-21-08 11:49
Hello,
I have a question about how I could map stats on surface created in Caret.
Each suubject's anatomical is first registered in MNI space, and then segmented and flattened using Caret's SureFit. It is then morphed into Colin atlas space using 6 landmarks. Deformation matrix is created here.
For EPI, I ran 3dDeconvolve to get beta coefficients for each covariates, for each subject. Using 3dbucket, betas for the covariates of interest are extracted and put into one HEAD/BRIK. Our goal is to run 3dANOVA3 and project the stats onto surface (apply the deformation matrix), but I wonder when this should be applied.
I guess my options are
1. morph betas, run 3dANOVA, and then project the stats onto surface
2, register betas into MNI space, run 3dANOVA, morph stats, and then project the morphed stats onto surface.
the first option sounds more intuitive, but I'm not sure about the AFNI-Caret file type compatibility, ot there might be better approach to this problem...
Any suggestions?
Thanks in advance! Akiko
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Author: Donna Dierker (---.wustl.edu)
Date: 02-25-08 10:20
Hi Akiko,
You've got surfaces, so take advantage of them. Run your group analysis in surface-land. Take a look at Ziad's slides here, paying particular attention to slide 23:
http://afni.nimh.nih.gov/pub/dist/edu/latest/suma/Surface-Cross-Subject.html
I think many users still do their individual analysis in volume-land, but then map and do group analysis in surface-land. You can use either AFNI's tools (may need the secret environment variable to enable "1D" processing using the normal 3d* tools), or Caret's (caret_command). If you're used to AFNI anyway, there may be some advantage to learning SUMA and doing your analysis with 1D files.
The Van Essen Lab no longer recommends use of Colin as a registration target; we now recommend the PALS_B12 atlas target. Your landmarks will work, with minor tweaking.
Caret5 Spherical Registration Core 6 Landmark Set
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html
PALS atlas tutorial
http://sumsdb.wustl.edu/sums/directory.do?id=707139
Donna
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Author: rick reynolds (---.nimh.nih.gov)
Date: 02-25-08 10:47
Hi Donna,
Thanks for the nice comment.
I would just like to note that in AFNI, the prefered method
for analyzing data on the surface is to use .niml.dset files,
which can be read and written just like any other AFNI datasets.
Those files can be created via the vol2surf program or interface,
just like the old .1D files (-out_niml MY_DSET.niml.dset).
- rick
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