Compatibility with nibabel 4.0.0

[HippocampusGirl]

Actual behavior

nipype uses the now removed nibabel.trackvis interface, which leads to a ModuleNotFoundError.

nipype/nipype/interfaces/mrtrix/convert.py

Line 8 in f4343d6

from nibabel.trackvis import HeaderError

│     ---- (full traceback above) ----
│     File "/usr/local/miniconda/lib/python3.10/site-packages/fmriprep/cli/workflow.py", line 82, in build_workflow
│         retval["workflow"] = init_fmriprep_wf()
│     File "/usr/local/miniconda/lib/python3.10/site-packages/fmriprep/workflows/base.py", line 64, in init_fmriprep_wf
│         single_subject_wf = init_single_subject_wf(subject_id)
│     File "/usr/local/miniconda/lib/python3.10/site-packages/fmriprep/workflows/base.py", line 304, in init_single_subject_wf
│         func_preproc_wf = init_func_preproc_wf(bold_file)
│     File "/usr/local/miniconda/lib/python3.10/site-packages/fmriprep/workflows/bold/base.py", line 419, in init_func_preproc_wf
│         bold_sdc_wf = init_sdc_estimate_wf(fmaps, metadata,
│     File "/usr/local/miniconda/lib/python3.10/site-packages/sdcflows/workflows/base.py", line 154, in init_sdc_estimate_wf
│         from .fmap import init_fmap2field_wf
│     File "/usr/local/miniconda/lib/python3.10/site-packages/sdcflows/workflows/fmap.py", line 29, in <module>
│         from .gre import init_fmap_postproc_wf, init_magnitude_wf
│     File "/usr/local/miniconda/lib/python3.10/site-packages/sdcflows/workflows/gre.py", line 17, in <module>
│         from niflow.nipype1.workflows.dmri.fsl.utils import cleanup_edge_pipeline
│     File "/usr/local/miniconda/lib/python3.10/site-packages/niflow/nipype1/workflows/dmri/__init__.py", line 4, in <module>
│         from . import camino, mrtrix, fsl, dipy
│     File "/usr/local/miniconda/lib/python3.10/site-packages/niflow/nipype1/workflows/dmri/mrtrix/__init__.py", line 3, in <module>
│         from .diffusion import create_mrtrix_dti_pipeline
│     File "/usr/local/miniconda/lib/python3.10/site-packages/niflow/nipype1/workflows/dmri/mrtrix/diffusion.py", line 5, in <module>
│         from nipype.interfaces import mrtrix as mrtrix
│     File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/mrtrix/__init__.py", line 36, in <module>
│         from .convert import MRTrix2TrackVis
│     File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/mrtrix/convert.py", line 6, in <module>
│         import nibabel.trackvis as trk
└─    ModuleNotFoundError: No module named 'nibabel.trackvis'

Expected behavior

There should not be an error.

My suggestions

• Update the requirements.txt to indicate a lack of compatibility with nibabel 4.0.0,

nipype/requirements.txt

Line 4 in f4343d6

nibabel>=2.1.0

• Find out where the removed interfaces were used, and replace them.

How to replicate the behavior

I'm skipping this for now, because I think the issue is obvious from the code. If I'm mistaken, please let me know and I will edit to add some steps.

Script/Workflow details

This happens when using fMRIPrep LTS with HALFpipe.

Platform details:

I am skipping this for now, since I believe the issue is unrelated to my platform. Please let me know if you require this information.

Execution environment

Container downloaded from https://download.fmri.science/singularity/halfpipe-halfpipe-latest.sif

[effigies]

I think it makes more sense to make it a runtime error instead of import time. Most people will not be using this interface. So we move the import into the method that calls it, and wrap it with a try/except ImportError to give a more helpful error message.

[HippocampusGirl]

Thank you :-)