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.
