Re: [Freesurfer] Hippocampal Sub field segmentation (fwd)

-- On 11/17/11 12:46 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: >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? >> >> Koen >> >> >> On 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 >> alandarkenergy@gmail.com >>> 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 >> alandarkenergy@gmail.com >>>>> wrote: >>>>>> Thanks Shashwath. >>>>>> >>>>>> On Wed, Nov 16, 2011 at 2:04 PM, Shashwath >> shashwath123@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 >> alandarkenergy@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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