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 <k...@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? > > Koen > > > On Thu, Nov 17, 2011 at 12:18 PM, Joshua Lee <jki...@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 <alandarkene...@gmail.com> > > wrote: > >> > >> Thanks Koen. > >> > >> On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput > >> <k...@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 < > alandarkene...@gmail.com> > >>> wrote: > >>> > Thanks Shashwath. > >>> > > >>> > On Wed, Nov 16, 2011 at 2:04 PM, Shashwath <shashwath...@gmail.com> > >>> > 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 <alandarkene...@gmail.com > > > >>> >> 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 person to > >>> >> > whom > >>> >> > it is > >>> >> > addressed. 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