fiber tracts clustered around midbrain

[iliana-karipidis]

I am setting up a new DWI protocol and analyzing some pilot data (Philips scanner, 32 dirs, b=1,000 & 2,000, isotropic 2mm). Preprocessing was performed using qsiprep and qsirecon, output was reviewed and looks ok. The pyAFQ output looks incorrect, with all fiber tracts clustered around the midbrain. What went wrong?

This issue seems to be specific to this pilot data, processing single-shell data of another sequence (Philips scanner, 32 dirs, b=1,000, isotropic 2mm) worked well: