Hi Lucas,
It seems you are looking at the FreeSurferColorLUT.txt. Not all these
labels are in the aseg.mgz file. Try looking at the aseg.stats file, in
the subdirectory stats of each directory of your subjects. The labels
there are the ones in the aseg.mgz, and have friendly names.
For the segmentation, FS still works voxelwise, but it's objective is to
identify each structure as a whole, whereas SPM and FSL/FAST attempt to
classify each voxel as being GM, WM or CSF.
A short description of the method in FS is here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream
You may want also to have a look at this paper:
http://dx.doi.org/10.1016/S0896-6273(02)00569-X
Hope this helps!
All the best,
Anderson
On 29/08/11 03:38, Lucas Eggert wrote:
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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