Dataset Requirements

PyDesigner can process input DWIs in NifTi (.nii), compressed NifTi (.nii.gz), MRTrix3 file format (.mif), and DICOM (.dcm) file formats. With the exception of .mif and .dcm filetypes, all other input formats are required to be accompanied with .bval, .bvec, and .json files.

Note: With the exception of extensions, all files additional accompanying a DWI need to have the same name as DWI. For example, the input DWI file DKI_64_dir.nii will be accompanied by DKI_64_dir.bval, DKI_64_dir.bvec and DKI_64_dir.json files

Separate or Combined Shells

Having B-value shells in separate or single 4D volumes doesn’t matter as long as each 4D DWI has it’s own accompanying files.


Every DWI will NEED a .json file of the same name; PyDesigner will refuse to process any input that fails to meet this criterion. This behavior is intentional to prevent unintentional corrections from being exectuted when they are incompatible. Users must create a JSON file if their DICOM to NifTi conversion software fails to create it.

PyDesigner primarily looks for partial Fourier information within a JSON information. This information if encoded in the fields PartialFourier; or PhaseEncodingSteps and AcquisitionMatrixPE. Users need to have have these fields at the bare minimum to process DWIs.