Dear Catriona,
I am not sure if you have already received some help on your questions outside this email list but I will try answer some questions.
Regarding 2: The attenuation maps has to be provided in STIR interfile format and the normalisation file can be used directly from the scanner. On the github repository in SIRF_data/examples/PET/mMR/ you find examples for a mu map and normalisation file. You can then simply load the attenuation map using attn_image = pSTIR.ImageData(attn_file_name). For more information and details please see: examples/Python/PET/reconstruct_from_listmode.py.
Regarding 3: For PET you will have to reconstruct each dynamic synogram one after the other. For MR it strongly depends what kind of MR acquisition you simulated. There are some specific dynamic reconstruction pipelines available from gadgetron but they are mainly 2D.
Regards,
Christoph
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