Fiberfox Phantoms to MRTrix3

Dear MRTrix users and developers,

I’m trying to use mrtrix on phantoms generated by FiberFox. Unfortunetly, this program (part of MITK-Difussion) generates as output a *.dwi file. I tried to open it as text file and has something which makes me think is like an *.nrrd file. I’m trying to covnert it to a format MRTrix can deal with. DOes any of you have experience in those phantoms? Maybe someone know about another DWI simulator more friendly with MRTrix?

Thanks everybody :slight_smile:

Hi @mandorra,

I haven’t used FiberFox hands-on myself, but I’d be looking for ways to export it to a NIfTI… that’s a pretty common format, and MRtrix handles it very well out of the box. I’ve seen diffusion challenges/competitions based on FiberFox phantoms, where NIfTI files were supplied… so at least it has been done in some way. :slight_smile:



Based on my little experience on FiberFox, there is a way to export data in Nifti format with MitkDiffusion:

In MitkDiffusion, open the *.dwi file that you have generated using FiberFox, right-click on your *.dwi file, choose ‘save’, and change the ‘files of type’ from ‘Diffusion Weighted Images’ into ‘Nifti’. That shall give you a *.nii file. From there, you can play the data with MRtrix.


Many thanks for your replies. I think this solve the issue.