I have a question that how to register simultaneous brain&cord fmri to an MNI152-PAM50-template? Now, I could only separately register the brain fmri to the MNI and cord to PAM50. Then merge the brain and cord fmri to MNI152-PAM50-template each volume. At last merge all the volumes to an 4D. This takes a lot of time, I wonder if there is a better solution? Thanks~
The brain and the spinal cord have very different motion patterns. Brain motion is well described by rigid motion (TxTyTzRxRyRz) while the spine, being an articulated object, is best described by axial slice-wise TxTyRz transformations (i.e. one different transformation per slice). So, you could always try to find a single transformation that prevents you from splitting brain/spine, but that might be suboptimal with regard to motion correction performance. For example, you could apply a slice-wise TxTyRx to your entire volume, but then you might miss RxRy motion from the brain.
When you say that separating the brain and spinal cord scans “takes a lot of time”, did you mean computation time or human time? Because all this can be automatized, so human time should not be involved here. Wrt. computational time, I think it actually takes less time than a full-FOV slice-wise transformation, because rigid transformations (which would be applied to the brain) are very quick to estimate, and you only need a single transformation for the brain, as opposed to ~20-30 (depending on your image resolution) if you were to include the brain for the slice-wise approach.
Thanks for your reply. Now I understand.