Using --t2 and --bold will always give identical results. If there is not much G/W contrast in the MRA (and there probably isn't), then you can try using the pial surface instead (maybe more GM/CSF contrast). Use --surf pial --t1. Use --t1 here because the GM will probably be brighter than CSF.
doug On 08/20/2014 04:54 PM, SHAHIN NASR wrote: > Hi Surfers > I want to use bbregister to register my MRA scans to the > structural scans. The first attempts by using these parameters came > out OK but not perfect: > > bbregister --s <Subject_ID> --mov MRA.nii --init-fsl --reg > register.dat --bold > > However, there are obvious problems around frontal areas. > > I have to admit that one of the reasons for this imperfect > registration may be that MRA scans do not cover the whole brain. > However, they still cover a large portion of it. I was wondering if > there is any argument in bbregister command that may help me improve > the quality. It is very fine if it increases the registration time. > > Regards > > P.S.: using --t2 in bbregister (instead of --bold) generated the same > outcome but --t1 was completely off. > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
