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 <legg...@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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