Hi Andrew
wow, that's pretty strange. The only thing I can think of that might recover this is to put pairs of control points in the white matter, one on either side of the boundary of your artifact. Or maybe it always affects the same slices and you can scale them up? I guess it depends on how variable it is
cheers Bruce
On Tue, 7 Mar 2017, Andrew D. Davis wrote:
Hello Freesurfer experts,
I have a dataset in which there is an artifact affecting many subjects. The problem is a greatly reduced signal at the top of the head. The images come from a GE scanner and it appears to have been caused by a configuration issue in the protocol. Sometimes this artifact impacts the cortical grey matter, as in the attached screenshot (showing T1.mgz after this subject was run through recon-all). In these cases the aseg.mgz is invalid in these superior areas, as the mask does not extend into the signal dropout area.
I'm wondering if anyone has an idea for correcting this issue, perhaps by adjusting parameters associated with Freesurfer's non-uniformity correction steps.
Thanks much for any suggestions, Andrew Davis
Inline image 1