[Freesurfer] mri_vol2vol not downsampling when applying a morph and a rigid registration matrix

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