Hi Joshua
I'll cc Jean Augustinack and Stephan Heckers, who I know have opinions on this issue :)
cheers Bruce
On Thu, 17 Nov 2011, Joshua Lee wrote:
There is great variability between the different segmentation protocols used by different research groups, and I think people are eager for a standard to facilitate comparison and replication. By becoming part of Freesurfer, I suspect that your segmentation algorithm will become that standard.
Luckily, I think it is one of truest I've seen to conforming to the Duvernoy atlas. Whether Duvernoy's work is the appropriate standard I am not qualified to say, but he does seem to be cited quite often as the basis for the various protocols in the wild. However, there might still be some differences between Duvernoy and the scheme used by the Freesurfer subfield segmentation.
Particularly, Duvernoy seems to indicate that in the head and the tail CA1 seems to be the only subfield present in the anterior 1/3 of the head and posterior 1/3 of the tail. Looking coronally, subiculum seems to extend further laterally in the head and tail than in the body of the hippocampus. Lastly, CA1 seems to continue further medially on the superior side of the hippocampus in the head and tail than in body. CA3, by my reading of Duvernoy, seems to be tiny in the head and tail.
All these are fairly minor points. Still, I wouldn't mind some comments on these observations, as they were changes I have been proposing to make in the segmentation protocol used in my lab.
Best,
Joshua
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Thu, Nov 17, 2011 at 9:30 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote: Hi Joshua,
I'm not a neuroanatomist so I can't really answer that question. My aim has just been to replicate what a human expert has given us as segmentation examples on a number of different subjects. I know that different labs follow very different conventions for labeling the subfields manually. Perhaps someone else can chime in? KoenOn Thu, Nov 17, 2011 at 12:18 PM, Joshua Lee jkilee@ucdavis.edu wrote:
At least by my reading of the Duvernoy Human Hippocampus atlas, the
most
anterior and posterior extents of the hippocmapus (perhaps just a
slice at
the tips in most scans) are almost entirely composed of the CA1
subfield.
Thoughts?
Joshua
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis
On Thu, Nov 17, 2011 at 6:46 AM, Alan Francis
wrote:
Thanks Koen.
On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput koen@nmr.mgh.harvard.edu wrote:
The answer is close to what Shashwath suggested, except that the "Hippocampus" segmentation is really computed at the same time as
all
the other subfields. For unfortunate reasons, the tail of the hippocampus that is not further subdivided in our manual training segmentations was called "Hippocampus" for lack of other good
names -
it really should have been "Part of the Hippocampus Tail that We Didn't Subdivide Manually".
If you want to compute the total volume of the hippocampus, you'll need to add the volume of this part, though..
Hope this helps,
Koen
On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis
wrote:
Thanks Shashwath.
On Wed, Nov 16, 2011 at 2:04 PM, Shashwath
wrote:
Alan- I believe the label "hippocampus" here refers to the
remaining
hippo segment after the algorithm has completed labelling of all
subfields.
In essence this would not be a measure that conveys very
meaningful info.
Sent from my iPhone
On Nov 16, 2011, at 1:01 PM, Alan Francis
wrote:
> Hi Koen and FreeSurfers: > > I have a 3T dataset that has undergone processing using 5.1.
I have
> also > run the Hippo sub fields command. Here are my results: > > [root@NeuroImage-Gamma mri]#
kvlQuantifyPosteriorProbabilityImages
> $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt > posterior_right_* > posterior_Right-Hippocampus.mgz > > volumeInVoxels: > right_CA1: 2473.34 > right_CA2-3: 7530.08 > right_CA4-DG: 4160.99 > right_fimbria: 520.14 > right_hippocampal_fissure: 376.772 > right_presubiculum: 2780.65 > right_subiculum: 4230.04 > Right-Hippocampus: 2277.69 > > My question is : Since these are "subfields" of the
Hippocampus,
> should > not the sum of all subregions be equal the volume of the
Right
> Hippocampus? > > Thanks so much! > > Alan Francis > > Beth Israel Deaconess Medical Center, BOSTON > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the
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