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
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