Hi David yes, you can use bbregister to do the rigid alignment, then use it as initialization for mri_nl_align. I would think you are better off doing the surface recons and using cvs though. It's only computer time....
cheers Bruce On Wed, 25 Feb 2015, David Grayson wrote: > Hey Bruce, > Thanks for responding. I would actually prefer nonlinear. I did not mention > it, but the aseg data that I have is on a distortion-corrected T1 image, > whereas the unprocessed image I want to warp onto is the same scan but not > corrected for distortion. The distortions are nonlinear. I was hoping there > might be a way to get a warp field to go between the two images without > running both images through the recon-all pipeline. Are there any other > possible tools? > > Thanks! > -David > > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > Is there any reason you need it to be nonlinear? I would think > bbregister and mri_vol2vol would do the trick > Cheers > Bruce > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson > <dgray...@ucdavis.edu> wrote: > > > > Hi freesurfers, > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image > on the same subject. I would like to use a purely > intensity-based nonlinear volumetric registration to do this, to > save time and complication. I understand I can do this if I have > a .m3z warp file. > > > > My question is, how can I get this warp file? I have tried > using mri_cvs_register with the --step3 option, but that appears > to only work after the surface-based registrations have been > carried out. I haven't found another tool to do this yet. > > > > Are there any ideas? Thank you very much for your time. > > > > -David > > _______________________________________________ > > 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 > > > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
