Error with mrtrix3 dwidenoise

#1

Hi, I’m trying to run mrtrix3 dwidenoise but I keep getting an error saying that -fslgrad is not an option in dwidenoise

import nipype.interfaces.mrtrix3 as mrt
denoise = mrt.DWIDenoise()
denoise.inputs.in_file = 'data_dwi.nii.gz'
denoise.inputs.in_bval 'bvals'
denoise.inputs.in_bvec = 'bvecs'
denoisee.run()

Standard error:
dwidenoise: [ERROR] unknown option "-fslgrad"
Return code: 1
#2

Hi @mri ,

Can you try running it without providing the in_bval and in_bvec options? Those 2 options are inherited from the Mrtrix3BaseInputSpec but aren’t needed for running dwidenoise.

#3

Thanks @Michael_Joseph, it works without providing in_bval and in_bvec.