I think the most likely issue is still mis-sorting: DWIConvert requires that all files to be converted are from the same series (or at least identical acquisition parameters) and alone in one folder. You could try this script to do the sorting first:
That said, if the data is from a Prisma or newer scanner, then I’m not sure if DWIConvert fully supports it yet. Please let us know the following tag information: (0008,0070) (0008,1090) (0018,1020)
e.g.:
(0008,0070) LO [SIEMENS] # 8, 1 Manufacturer
(0008,1090) LO [Verio] # 6, 1 ManufacturerModelName
(0018,1020) LO [syngo MR B17] # 12, 1 SoftwareVersions
If you are using a Prisma or newer scanner version, then it would be very helpful if you are able to share phantom data – that’s the fastest way for me and @hjmjohnson to be able to fix problems and update supported versions.