Yes, the --o option for bbregister will map the functional to the output space. Instead use mri_vol2vol with the --inv option to apply an already existing registration to map the anatomical into the functional space. I have not used fnirt that much, so I'm not sure about the implications. I assume fnirt would need a functional-to-anatomical registration, if so, then using bbregister to compute that would be a good idea. You can get an FSL-compatible registration using

tkregister2 --mov func.nii --fstarg --reg register.dat --fslregout fsl.mat --noedit

doug

On 02/13/2014 11:24 AM, Shantanu Ghosh wrote:

Hi Trang,

Have you tried the --o <outvol> flag with bbregister to save the desired coregistered output? (where outvol is the "mov" or moving volume)

Thanks. Shantanu

On Wed, February 12, 2014 4:51 pm, qtnguyen@nmr.mgh.harvard.edu wrote:

...

Hi all,

We're conducting the registration using bbregister that gives us a registration matrix (a .dat file) BUT the original structural file remains intact, i.e. the registered output can be viewed but not stored. Can we store the co-registered structural image as a .nii file? And if so, how? We are using the Connectivity Toolbox that requires structural data to be coregistered with functional data, and there is no way we can feed in the .dat file.

Also, what are your thoughts on first using bbregister for linear coregistration, and then use fnirt on the output to get nonlinear coregistration? We ask this because we are working on a younger population (ages 8-25) with autism spectrum disorder and the data is affected by motion. Should we also be using --init-fsl instead of --init-spm if we want to use fnirt?

Thank you for your help,

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