Dear Maria,
If you don't have CT of all the participants, I don't think it will be a good idea to use it for your project. Otherwise you will have different methods of co-registration within the same study. You can always perform the registration of the PET directly to the [15O]water PET template from SPM. In addition, the movement parameters are generally not included as regressors in the model, while I assume that up to some degree you can include them if you have enough degrees of freedom in your design and you expect a substantial effect of the registration method in the results of your analysis.
About the analysis it self, due to the characteristics of the PET studies it is not usual to perform a 1rst level analysis as is done in fMRI. One question here, do you have 12 PET different acquisitions per subject? That is not frequent at all. In one study that we performed in our department, we performed repeated acquisitions of [15O]water to the same patient, since we tested different conditions under the scanner, but with other tracers that [15O]water multiple PET acquisitions are extremely infrequent. Take into account that repeated measurements are not properly analyzed in SPM, so we used the
SwE toolbox for the analysis (maybe you can use in your design other tools such as GLM Flex).
If you provide some extra information of your design and radiotracer, I may give you more help.
