External Email - Use Caution Thanks Bruce! I was not aware of this basic design decision.
If that is the case, will freesurfer disregard manual corrections to try to force inclusion of the hippocampus? I am using freesurfer to make cortical models for use with epilepsy surgery, and as the MTL is a common implant target, having the pial surface respect this structure is important. Aaron > On Apr 17, 2022, at 9:59 AM, Fischl, Bruce <bfis...@mgh.harvard.edu> wrote: > > Hi Aaron > > We explicitly exclude amygdala/hippocampus from the surface models since they > aren’t neocortical. Hippocampus of course has some internal structure that > could be modeled that way (and has been), but it is pretty tough to do > without significantly higher res data than we usually require and would > require a different algorithm than the pial surface one > > Cheers > Bruce > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Aaron Geller > Sent: Sunday, April 17, 2022 11:42 AM > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] pial surface vs aseg in MTL > > External Email - Use Caution > > Hi- > > A recurring issue with my recons is that the pial surface excludes the > hippocampal formation and associated MTL grey matter structures. A typical > image is attached. > > <image001.png> > > Aseg has clearly captured the location of these structures correctly, as > indicated by the coloring in freeview, > so I'm wondering: does freesurfer not use the aseg results when constructing > the pial surface? If not, can it be made to do so? Is there any workaround > other than manual correction of each pial surface? > > Interestingly, I have never seen freesurfer exclude the ventral midbrain (or > thalamus), though it seems to be in an analogous situation. > > Thanks, > > Aaron > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/149o4n-3DJoH958kDYBonEi-X2HJgUr748exW8_XahN8GzHdorcBlt3RCpJhg1SpjPkUeXOyApt2OaL2CuPDE0xFd3akPYdzIgIuqPogCMElV3VM6sc9Odkwpb7hO6ua00mruqutmqNFiLrQwjc8Gyi9CHAnBWGiXwgDm2wrpUrqbrtxv5Jdoaa24DDaJ8a6fxOtbF3D8Ddt_3EyisrcUe5YRbxvrlL9mxK63ccD_PjPjyR-rjzh9PYQ6RH5be0pkmvq1vUXo3dnakmR4kN6P7mDYk0rl9MwzZ8d8-1c-EAKnT1qOG36Tjy99kaWCyzQB/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/149o4n-3DJoH958kDYBonEi-X2HJgUr748exW8_XahN8GzHdorcBlt3RCpJhg1SpjPkUeXOyApt2OaL2CuPDE0xFd3akPYdzIgIuqPogCMElV3VM6sc9Odkwpb7hO6ua00mruqutmqNFiLrQwjc8Gyi9CHAnBWGiXwgDm2wrpUrqbrtxv5Jdoaa24DDaJ8a6fxOtbF3D8Ddt_3EyisrcUe5YRbxvrlL9mxK63ccD_PjPjyR-rjzh9PYQ6RH5be0pkmvq1vUXo3dnakmR4kN6P7mDYk0rl9MwzZ8d8-1c-EAKnT1qOG36Tjy99kaWCyzQB/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > The information in this e-mail is intended only for the person to whom it is > addressed. 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