Hi All, There is a large variability between labs. An extensive effort has begun for produce a "Harmonized Protocol for Hippocampal Volumetry", see:
http://www.hippocampal-protocol.net/SOPs/index.html This group has been working on this goal for a few years. Good resources at their site, particularly showing differences between protocols. While the project is still ongoing, its interresting. -Timothy 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 > <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. If you believe this e-mail was sent to you in error and >>>>>>>> the >>>>>>>> e-mail >>>>>>>> contains patient information, please contact the Partners >> Compliance >>>>>>>> HelpLine at >>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent >> to >>>>>>>> you >>>>>>>> in error >>>>>>>> but does not contain patient information, please contact the >> sender >>>>>>>> and >>>>>>>> properly >>>>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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. If you believe this e-mail was sent to you in error and >> the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >> you >>>>>> in >>>>>> error >>>>>> but does not contain patient information, please contact the sender >> and >>>>>> properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >> in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >> > Timothy Brown email: timo...@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
