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Hi Ben, Yes, if run without fieldmap, epi_reg only takes two steps: 1. Run fast on the anatomical image to get a WM segmentation (this step is skipped if you provide a WM segmentation). The FAST output is cleaned up at the end of the script 2. Run flirt with BBR as the cost function. If run with a fieldmap, the registration procedure becomes a lot more complicated, but the final result of a registration from an EPI image to a structural is the same. Cheers, Michiel > On 29 Aug 2018, at 20:15, Ben M <[log in to unmask]> wrote: > > Hi Michiel, > > Thank you, that was very helpful. I tried to find out more about epi_reg but I couldn't find much information in the FSL website. Does epi_reg use BBR that you suggested I use? > > Best, > Ben > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1