Dear Anderson Winkler,
thank you very much for your quick response and your very helpful
comments!
To know if a given structure is gray or white matter you can look
in any reasonable anatomy textbook.
That is ture, of course; however, my problem is rather to match
labels like "LeftmOg" in the aseg.mgz file to anatomical
structures.
In any case, the question itself is somewhat
ill-posed, because some of the subcortical structures have
heterogeneous tissue composition and can't really be labeled
entirely as gray matter, even macroscopically. The most notable
examples are perhaps the thalamus and hippocampus, but the same
applies to other structures too.
That is totally true. Nevertheless, for a comparison between
different segmentation methods, if you would like to compare e. g.
total gray matter volume, it is important to know, which of the
labels should rather be regarded as gray matter and which should be
regarded as something else. But as you mention below, a direct
comparison between different segmentation methods might not be valid
--- Thanks for this important hint!
But then, I am a bit suprised, anyway: I am not familiar with the
method used by FreeSurfer for (sub)cortical segmentation; but could
you, in simple words describe shortly, how FreeSurfer does the
segmentation, if not voxel-vise, that is, how does FreeSurfer define
a whole structure (see your comment below)? That would be of great
help for the upcoming discussion of the results for the evaluation
of different segmentation methods.
Anyway, if you really want to make a hard distinction, you can
call then caudate, putamen, pallidum, amygdala, accumbens,
hippocampus and thalamus as gray matter. The region defined as
ventral diencephalon is very heterogeneous and I would not
classify it either as GM or WM, as it includes mamillary bodies,
tuber cinereum/infundibulum (but not hypophysis), some
hypothalamic nuclei near the lateral and inferior walls of the 3rd
ventricle and sometimes fragments of the optic tracts (but not
chiasm, which has its own label). It also includes parts of the
mesencephalon (e.g. part of the cerebral crux, part of the
substantia nigra and rubra).
Importantly, if you are comparing algorithms, you have to be sure
they are reporting the same thing. For instance, it's fairly
common to run SPM or FSL/FAST segmentation, then sum the GM voxels
within a region defined from an atlas. If you do this for, say,
caudate or thalamus, you'll get the volume of what the algorithm
classified as GM within the structure you selected. FreeSurfer
(and, e.g. FSL/FIRST), on the other hand, will segment and report
the volume of the structure as a whole, including all what it
contains. A direct comparison, thus, is not valid.
With kind regards
Lucas Eggert