Hi Lucas
the problem can be one of definitions. For example the FreeSurfer
definition of the thalamus extends into the lateral thalamic nuclei that
look a lot like wm, whereas others don't necessarily. Thus it's hard to
compare apples to apples.
cheers
Bruce
On Mon, 29 Aug 2011, Anderson Winkler wrote:
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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