Hi Margaret,
mri_motion_correct calls the mni rigid body alignment code. Use it as:
mri_motion_correct <output> <in 1> <in 2> ...
cheers, Bruce
p.s. you still are probably better off just using one volume. There's no difference in processing, but more manual intervention will probably be needed.
On Thu, 3 Feb 2005, Margaret Duff wrote:
Hi, Both images are from here on the old bay 2 scanner, they just occurred 1 month apart. Could you describe a little for me how to use mri_motion_correct and how it differs from setup structural scans in csurf? I checked the wiki, but it did not have tons of info. Also, what are the major differences in using only one scan as opposed to two for the reconstruction? Thanks for your help, Margaret
On Wed, 2 Feb 2005, Bruce Fischl wrote:
Hi Margaret,
what are you using to align them? If they are from different sites, then they may not be possible to really align, due to differences in shims, read-out directions and bandwidth. Reconning with a single image is certainly doable (we've done hundreds), but is more labor intensive.
cheers, Bruce
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
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