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FreeSurfer BBR is generally slightly more accurate than FLIRT BBR, probably because of the much higher quality surface being used (i.e. the FLIRT BBR makes a quick white matter surface based on a FAST segmentation, whereas FreeSurferıs white matter surface is based on a lot more processing). For HCP Minimal Preprocessing Pipelines where we cared about getting the alignment right down to submm levels, we used both (FLIRT BBR first and then FreeSurfer BBR). Whether or not it is better to use the field map with FLIRT BBR or apply it before depends on how good of a field map to EPI registration you can get outside of FLIRT BBR vs a field map to structural registration (and EPI to structural registration) inside FLIRT BBR (i.e. epi_reg). Generally one does a better job inside of FLIRT BBR, but this is not always the case. Also, it can be harder to debug what is going wrong when the steps are not separated (is my registration not good because the distortion correction is not good, or because the EPI to structural registration is not good?). I actually prefer using spin echo field maps (phase reversed spin echo images matched to the gradient echo EPI acquisition) and topup, as these have the same distortion as the gradient echo EPIs and can be very precisely registered (EPI to matching spin echo image) without the complication of using the structural image as an intermediate. Then one can use BBR on the undistorted EPI image. This keeps each step separate for debugging and ³easy² for the algorithms involved to achieve robustly. Peace, Matt. From: Julia Huntenburg <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Wednesday, April 16, 2014 at 9:25 AM To: <[log in to unmask]> Subject: [FSL] flirt -bbr -fieldmap compared to flirt -bbr / freesurfer bbregister Dear list, Concerning the usage of flirt with bbr cost function and a fieldmap I was wondering if there is any experience on: 1. how different it is to use the flirt -fieldmap option as compared to unwarping with the fieldmap first and using flirt -bbr afterwards? (-- and related: How exactly is the fieldmap applied in this implementation?) 2. how the FSL bbr implementation compares to freesurfer bbregister? E.g. if I use the freesurfer segmentation with flirt -bbr, would that give me similar results as bbregister? Any thoughts or experience (even if anecdotal) would be highly appreciated! Many thanks, Julia