Thank you Bruce, this is helpful. Matthew
On Wed, Oct 1, 2014 at 5:41 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Matthew > > 1. Sorry, we have little experience with this and I would be worried that > even the fully collected hemisphere will have different results than if > the whole brain/head had been acquired since there are global steps like > linear alignment. > > 2. The label definitions come from various CMA papers from the 90s. I'll cc > Dave Kennedy who might know, but you can also check out the refs in the > Neuon paper > > cheers > Bruce > > > On Tue, 30 Sep 2014, Matthew Sacchet wrote: > > > Hi all, > > I was hoping to gain insight regarding two questions associated with the > use > > of FreeSurfer's aseg (Fischl, Neuron 2002): > > > > 1. I have been using aseg to assess volumetric differences across > > populations. For one of our individuals a portion of the right hemisphere > > was not fully collected. The entirety of the subcortical structures we > are > > interested in were collected (I've attached an image to this message, not > > sure if images propagate to the list...). Will the lack of whole-brain > > coverage bias the segmentation for the hemisphere that was not fully > > collected? I'm assuming that the fully covered hemisphere's data will be > ok. > > > > 2. Regarding the "ventral diencephalon" region that is segmented using > aseg, > > is there a 'gold standard' citation that describes what anatomical > > structures are included in this region? Previously on the FreeSurfer list > > serve there was mention from Anderson Winkler that the VD includes "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)", but no citation was given. In Glahn et > al. > > (Biological Psychiatry 2012 71, 6-14) it is stated that the VD mostly > > includes the hypothalamus, but again, as far as I can tell, a citation is > > not offered. > > > > Any help would be appreciated, thank you, > > > > Matthew > > > > > > > > > > > > > _______________________________________________ > 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. > > >
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