Hello experts
I'm running a multi shell diffusion sequence on a Varian 9.4 Tesla scanner looking at rodent brain data. I'm currently using a diffusion scheme with b=0, b=1000, and b=2000. My first volume is a b=0 volume, and I acquire a b=0 every tenth volume, and add three on the end (total of 123 volumes).
I use a 4 shot epi sequence and collect two averages.
To run topup I collect two separate scans with no diffusion weighting (i.e. b0) and phase encoding in opposite directions (AP, PA). I want to then run applytopup to my diffusion scans but have been unsuccessful in defining my parameters. I'm wondering how I would specify --inindex in this situation?
Any advice would be helpful
Patrick
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