Graham Wideman wrote:
Doug:
Thanks for your quick reply -- but I still have some big holes in understanding, probably because I'm having a hard time digesting the mri_aparc2aseg's wiki page.
There's also the --help (might be the same thing).
For the ribbon-related parameters we seem to have the 3 choices:
no ribbon param ... or ... --ribbon ...or... --noribbon
Actually, if you do not spec a ribbon, then it is the same as --noribbon, which means that it uses the aseg-based ribbon.
The Description presumably applies to using no ribbon parameter, and describes that *both* aseg *and* the surface-derived ?h.ribbon are used. If that's the case, then what does the --ribbon arg add?
Turns off using the surface-based ribbon.
It goes on to say "This can be turned off with --noribbon". What can be turned off? Use of ?h.ribbon? Or relabeling of the "unknown" voxels to zero (ie: aparc+aseg would have them labeled as "cortex").
Finally, for my task where I hope to ignore aseg entirely, is my solution to fake up an aseg volume filled with "cortex" voxels, and use that for input? (And I'm not seeing an argument to tell mri_aparc2aseg to use a different aseg...).
Yes, that should work. You can use the ?h.ribbon files (change the values to 3 so aparc2aseg knows it's cortex).
doug
Thanks,
Graham
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