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>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>> 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> > > 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 > > -- > 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 >
_______________________________________________ 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.
