In my data-set I have observed that Freesurfer has a tendency to include some amygdala into the hippocampal head, despite a visible strip of alveus white-matter segregating hippocampus from amygdala in my images. Has this tendency been noticed by others? If so, has anyone found a non-manual correction? Best, - Josh
On Thu, Aug 2, 2012 at 7:37 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Fred > > 1. Yes, this has been done multiple times, including in our original 2002 > paper: > https://surfer.nmr.mgh.**harvard.edu/ftp/articles/**fischl02-labeling.pdf<https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf> > > 2. You can manually edit, but it's a lot more work. In the cortex minor > interventions can lead to large improvements in accuracy. Unfortunately we > have no such algorithm subcortically. That said, things are usually quite > accurate except in a small percentage of cases. > > cheers > Bruce > > > > On Wed, 1 Aug 2012, Fred Sanders wrote: > > Hi All, >> Two questions: >> >> 1. I am interested in subcortical gray matter volumes such as hippocampus, >> amygdala, & basal ganglia. Can someone recommend some good references >> looking at the accuracy of Freesurfer relative to the "gold standard" >> approach of hand-tracing these structures? >> >> 2. Most of the problems that require quality checks for Freesurfer relate >> to >> defining the cortical surface and the grey-white boundary. As far as I >> can >> tell, there is rarely a need to edit Freesurfer's definitions of >> subcortical >> gray. Am I correct in this? >> >> >> >> Thanks! >> Fred >> >> >> > _______________________________________________ > 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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