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UKFTractography for NIFTI
UKFTractography works with only NRRD/NHDR images. To make it work with NIFTI images, you can use our conversion scripts. Specifically, you need nhdr_write.py that will write an associated header for a NIFTI image, may the latter be 4D (diffusion) or 3D (structural). After writing the headers, provide them as inputs to UKFTractography command e.g.
UKFTractography --dwiFile dwi.nhdr --maskFile mask.nhdr --seedsFile mask.nhdr --tracts tract.vtk
If you are working on Slicer, select the above headers as inputs.
NOTE You will need Python 3 interpreter for conversion package. Once you have that interpreter, you can just do:
pip install git+https://github.com/pnlbwh/conversion.git
After installation completes:
nhdr_write.py --help
On the other hand, if you use our pipeline pnlNipype, the accompanied ukf.py script will work with NIFTI images seamlessly.