Dcm2niix interface: Add mvecs output

[pvelasco]

Summary

dcm2niix produces .mvec files for Bruker DW images, to indicate that the polarity of those vectors is undefined (see here).

However, the Dcm2niix interface does not include those files.

Actual behavior

When converting a Bruker DW dataset using dcm2niix, the output includes .nii.gz, .json, .bval and .mvec files. However the interface outputs are:

>>> output.outputs
bids = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.json
bvals = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.bval
bvecs = <undefined>
converted_files = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.nii.gz

Expected behavior

either:

>>> output.outputs
bids = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.json
bvals = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.bval
bvecs = <undefined>
mvecs = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.mvec
converted_files = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.nii.gz

or:

>>> output.outputs
bids = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.json
bvals = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.bval
bvecs = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.mvec
converted_files = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.nii.gz

I'm more inclined to the first option, to be more explicit, and let the application using the interface handle it (e.g., making output.outputs.bvecs = output.outputs.mvecs if that is OK, or otherwise deal with it).

How to replicate the behavior

>>> from nipype.interfaces.dcm2nii import Dcm2niix
>>> root_dir = '/home/pvelasco/data/samples/bruker_dti/'
>>> converter = Dcm2niix()
>>> converter.inputs.source_dir = root_dir + 'dicom/1'
>>> converter.inputs.output_dir = root_dir + 'nifti'
>>> converter.inputs.bids_format = True
>>> output = converter.run()
>>> output.outputs
bids = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.json
bvals = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.bval
bvecs = <undefined>
converted_files = /home/pvelasco/data/samples/bruker_dti/nifti/1_DTI_EPI_seg_30dir_sat_20210928080241_130001.nii.gz

>>> import os
>>> os.listdir(root_dir + 'nifti')
['1_DTI_EPI_seg_30dir_sat_20210928080241_130001.nii.gz', '1_DTI_EPI_seg_30dir_sat_20210928080241_130001.bval', '1_DTI_EPI_seg_30dir_sat_20210928080241_130001.mvec', '1_DTI_EPI_seg_30dir_sat_20210928080241_130001.json']

Script/Workflow details

(see above)

Platform details:

{'commit_hash': 'cdfe679a4',
 'commit_source': 'repository',
 'networkx_version': '3.0',
 'nibabel_version': '5.0.1',
 'nipype_version': '1.8.6.dev0',
 'numpy_version': '1.24.2',
 'pkg_path': '/home/pvelasco/code/utils/nipype/nipype',
 'scipy_version': '1.10.1',
 'sys_executable': '/home/pvelasco/.pyenv/versions/3.10.4/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.10.4 (main, Nov 10 2022, 13:47:31) [GCC 7.5.0]',
 'traits_version': '6.3.2'}

Execution environment

Choose one

• My python environment outside container