The hyper-intensity in the DWIs is caused by a compression of signal due to EPI susceptibility distortions. Without having the requisite image data to correct said distortions, there’s likely nothing you can do about the hyper-intensity itself on a per-subject basis; at least not without grossly altering the quantitative behaviour of AFD…
The relevant fixels could be masked from the FBA analysis using a combination of a manually-defined ROI and the voxel2fixel command to produce a fixel analysis mask, and then providing this to fixelcfestats via the-mask` option.