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 . 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. > >
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