The best thing is to follow the instructions in recon-all -help. recon-all will automatically use mri_motion_correct2. Basically, you just need to put your two scans in mri/orig/001 and mri/orig/002. However, if there is an artifact (as Ev suggests), then you'll have to use just one of the scans.
doug 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 > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
