yes, I do think it's causing the bumps, and also leading to inaccuracy in the surface locations. Usually these are associated with susceptibility artifacts, but not usually in those locations, so I'm not sure what's going on Bruce
On Sun, 24 Jan 2010, Jesse Bledsoe wrote: > Hi Bruce, > > I have not added control points. There may be something with the MRI > acquisition that I can try and figure out. I did not have these problems > with a different magnet so I will see if there may be an MR acquisition > difference causing the intensity problems. Is that what you think is causing > the bumps? The brightening at the white matter boundary? > > Thanks again, > > Jesse > > On Sun, Jan 24, 2010 at 12:06 PM, Bruce Fischl > <[email protected]>wrote: > >> 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
