Hi Freesurfers,
I am struggling to get mri_vol2vol to downsample when I apply an inverse
morph and an inverse registration matrix.
Specifically, I am bringing a volume in cvs_avg35 space back into an
individual subject's functional space. I have already registered the
subject's functional to their anatomical using bbregister and registered
the subject's anatomical to cvs_avg35 space using mri_cvs_normalize. Here
is the mri_vol2vol call that I am using to move a volume from cvs space to
native functional space:
mri_vol2vol --targ $roi_in_cvs_space \
--mov $func_vol_file \
--reg-final $bbreg_file \
--inv \
--inv-morph \
--m3z $morph_file \
--o $roi_in_native_func_space \
--interp nearest \
--noDefM3zPath
This call seems to register the cvs space to the native functional
space accurately -- the mask that I am projecting is in a reasonable
position in the functional space. However, the voxel size for this output
volume is not the same size as the functional voxels. The voxel size is
still the same as the size in cvs space. (Or it could be the anatomical
space, since both are 1 mm isotropic.)
My question: How do I get mri_vol2vol to downsample? I have no problem
getting mri_vol2vol to downsample from native anatomical to native
functional by applying the inverse of the bbregister-generated matrix, but
I am struggling to get the appropriate downsampling here. Any suggestions?
And FYI: I'm using this version of
freesurfer: freesurfer-Linux-centos4_x86_64-dev-20120104.
Thanks in advance!
Best,
Alex Kell
Kanwisher Lab Manager
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