You'll have to try and see how fast it would be.
First time the command on the shell, then time it from matlab.
SPM certainly has registration tools that may be fast enough it should not be too hard to put the volumes you have into their structures. But I have no idea how that would be done.
Also, if you describe what you are trying to achieve in greater detail there may be other solutions. For example, if you need speed because you are doing real-time imaging, then you should do the registration before you get the volumes into matlab. That can be easily done with afni ....
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