Hi Lucas,
To know if a given structure is gray or white matter you can look in any reasonable anatomy textbook. 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.
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.
Hope this helps!
All the best,
Anderson
On 28/08/11 02:53, Lucas Eggert wrote:
Dear List,
I recently posted the message you see below.
I currently compare the segmentation results of different segementation algorithms and FreeSurfer always yields the least accurate results. Because I still have difficulties to decide which of the labels in the aseg.mgz files should be considered gray matter, I have the feeling, the bad results I am getting for FreeSufer might be caused by not including all relevant gray matter segments.
So, I would very much appreaciate any help on deciding which of the labels in the aseg.mgz file belong to gray matter!
With kind regards Lucas Eggert
-------- Original-Nachricht -------- Betreff: [Freesurfer] How to determine gray matter in the aseg.mgz Datum: Tue, 03 May 2011 17:26:55 +0200 Von: Lucas Eggert leggert@Uni-Osnabrueck.DE An: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Dear Experts,
I would like to generate a gray matter mask using the aparc+aseg.mgz file.
Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify).
Or is there a easier way to create a gray matter mask?
Thank you very much in advance!
Best regards, Lucas Eggert
-- Lucas Eggert, M.Sc. Institute of Cognitive Science University of Osnabrueck Albrechtstrasse 28 D-49076 Osnabrueck Germany
Phone: +49-541-969-44-28 Website:http://www.cogsci.uni-osnabrueck.de/~leggert/
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