It will output a register.dat for each frame. You can extract the frame from the time series (mri_convert --frame ), apply the reg with mri_vol2vol or mri_vol2surf, then concatenate the results back into a time series (mri_concat) doug
Michael Waskom wrote: > Hi Satra and Doug, > > That script is good to know about. But, from what I can tell, it > looks like it will output a timeseries in the same space as the > original template (each frame gets transformed with a combination of > the matrix specifying its registration to the anatomical and the > inverse of the matrix specifying the registration from the template to > the anatomical). So this might give me somewhat better motion > correction, but it won't give me a common space across runs. > > Best, > Michael > > On Mon, Dec 19, 2011 at 7:26 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > That may or may not do what you want. I think that version keeps the > functional data in the functional space. It would be better to > register > each TR to the anat, then simply sample each TR to the anatomical > space > (volume or surface) rather than going back into functional space. > doug > > > Satrajit Ghosh wrote: > > hey mike, > > > > take a look at: > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr > > > > cheers, > > > > satra > > > > > > > > On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom > <mwas...@stanford.edu <mailto:mwas...@stanford.edu> > > <mailto:mwas...@stanford.edu <mailto:mwas...@stanford.edu>>> wrote: > > > > Hi Doug, > > > > Is it possible to use the bbregister parameters to resample a > > functional image such that it is in register with the anatomical > > image but retains the epi geometry? I actually don't care so > much > > about the epi-anat registration, but what I would like to be > able > > to do is motion correct and otherwise preprocess my timeserieses > > within session* and then move different sessions into a common > > volumetric space for analysis. As I have great faith in > > bbregister, ideally the transformation would be determined with > > this method (I suspect it is superior to picking a slice > from one > > of the sessions to use as a motion correction target across all > > sessions). Additionally, I would prefer not to upsample the > source > > voxels either into 1x1x1 anatomical geometry or to surface > > vertices. Unfortunately, my affine understanding isn't deep > enough > > for me to figure this out myself. > > > > Does that make sense, and (if so) do you have any ideas? > > > > Thanks! > > Michael > > > > * Here i use "session" in the sense of "run", which is > different I > > think from FSFast terminology so apologies for any confusion. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
