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GalKepler opened this issue Jul 31, 2023 · 0 comments · Fixed by #3596
Closed

Error in Mrtrix3's DWIPreproc #3595

GalKepler opened this issue Jul 31, 2023 · 0 comments · Fixed by #3596

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@GalKepler
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Summary

The _list_outputs method of DWIPreproc tries to set up an input called "export_grad_mrtrix", which should be "out_grad_mrtrix", causing it to fail.

Actual behavior

AttributeError: 'DWIPreprocInputSpec' object has no attribute 'export_grad_mrtrix'

Expected behavior

No AttributeError raising when running DWIPreproc...

How to replicate the behavior

from nipype.interfaces import mrtrix3 as mrt

dwipreproc = mrt.DWIPreproc(rpe_options="pair", align_seepi=True,)
dwipreproc.inputs.pe_dir = "j-"
dwipreproc.inputs.in_epi = "path_to_epi"
dwipreproc.inputs.dwi_file = "path_to_dwi"
dwipreproc.run()

Platform details:

{'commit_hash': 'c31d206',
 'commit_source': 'repository',
 'networkx_version': '2.8.4',
 'nibabel_version': '4.0.1',
 'nipype_version': '1.8.6',
 'numpy_version': '1.23.0',
 'pkg_path': '/home/zvi/Projects/connectome_plasticity/venv/lib/python3.9/site-packages/nipype',
 'scipy_version': '1.8.1',
 'sys_executable': '/home/zvi/Projects/connectome_plasticity/venv/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.9.14 (main, Sep  7 2022, 23:43:29) \n[GCC 9.4.0]',
 'traits_version': '6.3.2'}

Execution environment

  • My python environment outside container
@GalKepler GalKepler changed the title Error to Mrtrix3's DWIPreproc Error in Mrtrix3's DWIPreproc Jul 31, 2023
@GalKepler GalKepler mentioned this issue Jul 31, 2023
Merged
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FIX: DWIPreproc issue GalKepler/nipype
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@GalKepler