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 <fischl@nmr.mgh.harvard.edu> 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




--
Jesse Bledsoe, M.A.
Clinical Psychology
Assistant Director, Consortium for Neurodevelopmental Study
Department of Psychiatry
Michigan State University
321 W. Fee Hall
East Lansing, MI 48824
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