Hi Sheeva, The pial surface is not designed to include the hippocampus and amygdala.
Quoting from http://www.freesurfer.net/fswiki/FsTutorial/OutputData : There are regions where the surfaces are not intended to be accurate that you should be aware of: * Areas around the hippocampus and amygdala. The surfaces will not completely include or exclude certain subcortical regions. These inaccuracies can be ignored as subcortical regions are excluded from the cortical measures and subcortical volume is measured by the aseg, not the surfaces. cheers, -MH On Mon, 2011-09-12 at 17:04 -0400, Sheeva Azma wrote: > Dear Freesurfer List, > > I am using recon-all to measure cortical thickness in a population of > Alzheimer's patients and I have noticed that in many patients the pial > surface does not include the whole brain. This seems to be because > there are hippocampal lesions that are dark spots in the image which > throw off the segmentation. I have tried adding control points, but > that is only for the white matter boundary, and so I was wondering if > you could provide any insight as to how to correct the pial surface so > that the entire hippocampus is included. I have attached an example > image from tkmedit showing the pial and white boundaries. > > Thank you, > Sheeva Azma > _______________________________________________ > 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
