segmentation vs parcellation: Segmentation appears to mean identifying and assigning voxels to a label which maps to a gross structure like thalamus, left cortex, etc. Parcellation appears to mean the same but for mappings at higher resolution, e.g. L V1. Is this correct?
surface vs volume: My questions here arise from differences in the results of extracting labels when using mri_cor2label vs mri_annotation2label. Spot checks of mri_cor2label results show sets of pixels on a 1 mm grid which fill the volume associated with the label. I have been assuming that this is "volume" although volume also refers to what is captured in the .mgz files.
Spot checks of mri_annotation2label results show sets of pixels which appear to delineate boundaries or "surfaces" of the gray matter (--surface orig), white matter ( --surface white) or pia (--surface pial). There appears to a similar switch in the help text for mri_cor2label, i.e. -surf subject hemi <surf>, but it appears to specify the nature of the input rather than that of the output as does the -surface switch in mri_annotation2label. This leads to my next question regarding the input "volume" but first, is what I've said correct so far? An addition concern that I have is that "surface" may be used in reference to a projection onto the sphere.
input volumes: Here I have only tried the .mgz files contained in directory ${FREESURFER_HOME}/subjects/NNN/mri . Which of these files are useful as input to mri_cor2label for outputting .label files that are likely to accurately fill the structures to which the label corresponds? What I mean here is which ones represent the end-points of a processing stream and which ones are intermediates? I understand that the intermediates are likely useful given that they are being saved in the standard processing streams.
If I load them into freeview, specify the standard color map, and place the cursor on the cerebellum, I can see which ones give the right answer, e.g. aparc.a2009, wmparc, aparc+aseg, aseg.auto, and which don't, e.g. filled, wm.seg, wm, rh.ribbin, brain, brain.finalsurfs, T1, orig (of course). But "filled", for instance, does appear to provide a good segementation of the left and right supra-tentorial white matter although the colors (right=127; left=255) do not map to those names in the standard color table.
Regards,
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text