Dwifslpreproc: unequal number of b0 images

Dear MRtrix users,

I wrote a post in August about the preprocessing of non-standard DWI data set but I haven’t received an answer yet. I have a data set with 158 images (AP phase encoding) that composed of multi-shell DWI volumes and 14 b0 volumes that are interspersed among the DWIs. In addition, a set of 3 b0 volumes with PA phase encoding was collected for distortion correction with topup. Thus, the number of b0 images in both AP and PA sets doesn’t match. Is there any recommendation how to proceed in this case? I’m considering two approaches:

  1. to average b0 in both phase encoding directions and to use a pair of such averaged images for dwifslpreproc.

  2. to extract the first b0 from main AP data set and to extract one b0 (with best quality) from PA and to use this pair for correction in dwifslpreproc.

Does anyone have an experience of handling such data? Would be grateful for your help or opinion on the preprocessing step.

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I have very similar data, and I always do the second option. Note that if you do an average before eddy correction, the results are likely to be blurry and suboptimal.

Best regards,


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