hi michael, so for each frame of every session you get a bbreg file and the script ends up aligning the volumes to some reference. all you need to do is propagate that reference across your sessions. you might for example want this to be the middle volume of your entire experiment.
cheers, satra On Mon, Dec 19, 2011 at 10:18 PM, Michael Waskom <mwas...@stanford.edu>wrote: > 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. 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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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