Before you give up you could try running distortion correction on each of those volumes before you try averaging/motion correction again...
On Wed, 2 Feb 2005, Margaret Duff wrote:
The one using the orig is really horrible looking, very distorted and rotated. I tried using the brain volume, and it looks better, but also has a rimming/shadowing effect.
On Wed, 2 Feb 2005, Evelina Busa wrote:
Hi Margaret,
How does the talairach transform look?
On Wed, 2 Feb 2005, Margaret Duff wrote:
Hello, I am trying to reconstruct brains of patients who had one structural scan during each of 2 visits, a month apart. I averaged the two images together, but since they are from different visits, they look very badly lined up. It looks like there is one image and another image overlaid and shifted by a cm or so. These are clearly wrong and will not work but I was wondering if it was OK to run freesurfer with only one of the images, or if there was a way to line these two images up better so they can be combined? Thanks, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer