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 <greve@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 < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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-bbrftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mc-bbr
cheers,
satra
On Mon, Dec 19, 2011 at 2:04 AM, Michael Waskom
<mwaskom@stanford.edu mailto:mwaskom@stanford.edu
<mailto:mwaskom@stanford.edu mailto:mwaskom@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 somuch
about the epi-anat registration, but what I would like to beable
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 slicefrom one
of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample thesource
voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deepenough
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 isdifferent I
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