Hi Jesse, I doubt these have anything to do with talairach. Have you added control points? If not, I don't understand the cause of the local brightening that your images show in both the cerebellum and cortex in what is either the end of a white matter strand or in the gray matter itself.
cheers, Bruce On Fri, 22 Jan 2010, Jesse Bledsoe wrote: > Hello FreeSurfer experts, > > I have been reconstructing many brains and noticed that the surfaces are > quite bumpy. Here are a few things I have done to fix or understand more > about the consistently bumpy surfaces I seem to generate after > reconstruction: > > 1) Checked the talairach.xfm files with tkmedit and tkregister2 (it looked > fine in all planes) > 2) I have run mri_convert on original, talairach, and ac-pc aligned dicoms > (Bruce, you were right, there did not appear to be any improvement from the > original. Actually, the originals produced fewer surface errors). > > I have attached four .jpg images of white matter errors (bumps) in both > tksurfer and tkmedit views with the same white matter points. Can you tell > me if you see any errors in tkmedit that I am missing? I dont' seem to see > any considerable pial/white matter inconsistencies yet continue to produce > very bumpy surfaces. Also, why do some brains produce more bumps than > others? I realize that a bad talairach may cause errors but my talairachs > seem to be fine. > > Thanks in advance for all of your time, > > Jesse > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
