mrtrix3.ResponseSD - Handling of multiple b-values

[kaitj]

Summary

When running ResponseSD() (and assuming EstimateFOD(), which has a similar input), current interface does not seem to handle multiple b-values (possibly due to the input max_sh defaulting to a single integer value).

Actual behavior

Get an error specifying the number of manually-defined lmax's does not match number of b-values (see last line).

Command:  dwi2mask /home/tkai/Desktop/tmp2/genACTTractography/act_preproc_wf/MRConvert/dwi.mif /home/tkai/Desktop/tmp2/genACTTractography/act_preproc_wf/dwi2response/dwi2response-tmp-U774DL/mask.mif
Command:  mrconvert /home/tkai/Desktop/tmp2/genACTTractography/act_preproc_wf/Generate5tt/5tt.mif /home/tkai/Desktop/tmp2/genACTTractography/act_preproc_wf/dwi2response/dwi2response-tmp-U774DL/5tt.mif
dwi2response: Changing to temporary directory (/home/tkai/Desktop/tmp2/genACTTractography/act_preproc_wf/dwi2response/dwi2response-tmp-U774DL/)
Command:  5ttcheck 5tt.mif
dwi2response: [ERROR] Number of manually-defined lmax's (1) does not match number of b-values (3)

Expected behavior

The lmax, if manually defined should allow for more than a single integer to match the number of b-values (e.g. -lmax 0,8,8 in this case), otherwise no default from the Nipype interface.

At the moment, I've forked a copy of nipype and made a temporary solution with the input max_sh passing the expected input as a string, removing the default to run without error.

How to replicate the behavior

Use of multi-shell dwi data with mrt.ResponseSD and algorithm 'msmt_5tt'.

Script/Workflow details

Current pipeline code is stored at https://github.com/kaitj/mrtpipelines

Platform details:

python3 -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"
{'nibabel_version': '2.2.1', 'numpy_version': '1.14.3', 'nipype_version': '1.0.4-dev+g5a96ea5', 'commit_source': 'repository', 'sys_version': '3.5.2 (default, Nov 23 2017, 16:37:01) \n[GCC 5.4.0 20160609]', 'traits_version': '4.6.0', 'scipy_version': '1.1.0', 'pkg_path': '/home/tkai/git/nipype/nipype', 'sys_platform': 'linux', 'commit_hash': '5a96ea5', 'networkx_version': '2.1', 'sys_executable': '/usr/bin/python3'}
1.0.4-dev+g5a96ea5

Execution environment

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