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

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