Sorry, I guess it's not clear what I'm hoping to do. Because I'm going to use this data for mvpa, I don't want to resample into 1x1x1 voxels or go onto the surface. But I have multiple runs that I want to use, so I need there to be a voxel-to-brain correspondence across the different runs.
Michael On Mon, Dec 19, 2011 at 12:46 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > 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<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<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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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> >> >> <http://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> >> >> <http://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:freesur...@nmr.mgh.** >> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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> > >
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