Yea, you need to do it in the two steps you mention. You can do that from one command line with something like bbregister --s subject --mov epi.nii --init-{fsl,header} --bold --int aascout.nii --o register.dat The --int is an "intermediate" volume. doug

Andrew Dumas wrote:

That did the trick, thank you! As for using bbregister, I haven't had any luck using bbregister for the partial volume EPIs... they're always off. We have a strange protocol where only the functionals get the 32-channel coil, so right before the EPIs get done I have an AAscout image. I've been using bbregister to align the FS MPRAGE scans with the AAscout (first frame), then using that registration on the EPIs. It seems to come out a LOT better than using bbregister on EPIs directly.

Andrew

On Tue, 2011-12-20 at 14:58 -0500, Douglas N Greve wrote:

...

Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or --talres 1 for 1mm isotropic) option. This will put it into an MNI305 space. So something like

mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o yourvolume.mni305.nii

If you did not create the register.dat with bbregister, I would strongly suggest it. It works really well on the partial volume files. If you do, you should specify your current register.dat as the init registration.

doug

Andrew Dumas wrote:

...

Hi,

I'm trying to move a bunch of partial FOV functional images (occipital cortex only with oblique coronal slices) into common space. For each subject, I have a registration file (register.dat) to register functional images to anatomicals, and I'd like to incorporate the talairach.xfm registration so that I have a matrix that registers the functional images to the mni305 volume. I've been using the following, but registrations aren't coming out properly:

mri_matrix_multiply -im register.dat -iim <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat

I'm checking them using tkregister2, but the results don't look great. Is there a better/easier way to do this? Thanks!

Andrew

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