Would manually changing the intensities in brain volume using the configure volume brush tool in tkmedit help? Shoudl white matter be re-labelled as 255? What would be a good value for grey matter?
-----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/20/2005 2:19 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Autorecon re-processing probably susceptibility problems. Try putting some control points in the wm, but there may not be enough g/w contrast to get good surfaces. On Tue, 20 Sep 2005, Fornito, Alexander wrote: > > Sorry, I missed it - forgive my absent mindedness :( > > Onto a more valid problem (I hope!), I've had trouble segmenting the > olfactory sulcus on some of my images. The wm wolume seems to segment well, > but the orig and/or white surface doesn't follow this. Rather than enter the > olfacoty sulcus, only partially enters it. I was curious as to why the > orig/white surface would not follow the surface of the wm volume, and if > there is anyway to fix it? > Thanks, > Alex > > -----Original Message----- > From: Doug Greve [mailto:[EMAIL PROTECTED] > Sent: Tue 9/20/2005 4:03 AM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Autorecon re-processing > > does your version not tell you these things when you run -help? > > > > Fornito, Alexander wrote: > >> HI, >> Just wanted to check a few things re: re-running autorecon. >> I'm guessing that re-running autorecon with the -pial flag re-runs >> make_final_surfaces, which takes about 4-6 hours (correct?). >> What is re-run when the -wm and -cp flags are used, and how long do they >> take? >>> From what I understand, -cp would require re-running everything from >>> intensity normalization on, including the subcortical segmentation, while >>> -wm would require re-running the topology fixer and final surfaces. >> Does this sound about right? >> Thanks, >> Alex >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
