Hello,
We have some signal dropout at the top of the brain in some scans,
possibly similar to Rutvik Desai's 02/18/10 post. However, in our case,
FreeSurfer is not including any of the regions affected by the dropout
in both its subcortical segmentation and cortical parcellation. Instead,
FreeSurfer essentially begins to treat the gray/white boundary as the
CSF/gray surface, and classifies white matter as gray matter. The
severity of this issue seems to correlate with how severe the dropout
is.
I have tried running nu_correct (normalization) for up to 256
iterations. This produces a noticeable effect when visualizing the
volumes in tkmedit, but has no effect on FreeSurfer's output. I can
upload a sample subject, if desired. We are using FreeSurfer 5.0 x64 on a
Sun Grid Engine operating servers running CentOS 4.5.
Thank you,
Victor Yee