[Freesurfer] transforming functional volumes to MNI without resampling

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Hi,

I'm trying to register and transform some raw functional data (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low res dimensions.

I have tried: bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl --bold mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg --no-resample --nearest mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg --no-resample

And this looks pretty good, but not perfect... the functional data is oriented correctly but the brain seems to be a centimeter or two smaller in multiple dimensions, see:

http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png

I'm not too surprised since the MNI brain is blurry and oddly round, but presumably there is a way to do this transformation more accurately. I've run mri_cvs_register for this subject using the --mni flag:

mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir

And for other applications I use this m3z file to transform volumes between MNI orig.mgz and individual subject orig.mgz, but is there a way to use it to transform functional data to MNI space while keeping the functional dimensions?

I could do:

mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --reg register.dof6.lta --nearest --o template-in-anat.nii.gz

mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz --mov template-in-anat.nii.gz --m3z $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o template-in-MNI-m3z.nii.gz --nearest

But not only is this unideal because it requires upsampling the functional data to 256x256x256, it also gets these funky wavy distortions:

http://web.mit.edu/dsbeeler/www/images/m3z-mni.png

Any thoughts are appreciated, thanks!

-DB