ok, great. so let's say I have a linear transformation or a full warp field to go between the freesurfer processed image and the unprocessed brain. is there a way that I can propagate onto the unprocessed image the entire freesurfer contents including the "mri" and "label" and everything else, using the warp? The processed image has extensive manual edits, so I basically just want to transfer everything over.
Thanks Bruce! -David On Thu, Feb 26, 2015 at 6:05 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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 >
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