ah in that case you need to multiply the affine stored in one session's bbreg with the inverse of the other bbreg from the target session and then use mri_vol2vol with the composite transform. note: only nearest or trilinear interp
cheers, satra On Tue, Dec 20, 2011 at 12:07 AM, Michael Waskom <mwas...@stanford.edu>wrote: > OK, cool, I'll look into this for the future. > > But back to my original question. If I already have data preprocessed with > several runs, each run motion-corrected within-session, and an affine > registration from each run's space to the anatomical determined by > bbregister, is there any way to use those transformation parameters to take > the function scans into a common space that retains the original voxel size? > > Michael > > > On Mon, Dec 19, 2011 at 1:34 PM, Satrajit Ghosh <sa...@mit.edu> wrote: > >> 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. 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> >>>> >>>> >>> >> >> _______________________________________________ >> 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 . 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