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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