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feat: Replace c3d_affine_tool with a ConvertAffine interface (#3464)
Upgrading convert3d leads to segfaults, which means that we are playing a game of cat and mouse with ANTs, libitk and convert3d. It's not worth it just to convert FSL affines to ITK, when we can do this with nitransforms. The existing niworkflows `ConcatenateXFMs` interface does not quite do the job, since it assumes that `.mat` is an ITK binary affine, so I create a `ConvertAffine` interface. This replaces the `fsl2itk_fwd`, `fsl2itk_inv` and `invt_bbr` nodes, and moves the `lta_to_fsl` node to the section it is connected in. This PR could go further and stop using `LTAConvert` as well, but I intend this to be a narrow replacement. The main logical difference is that I only convert the `mri_coreg` output to FSL format if FLIRT is going to run; otherwise, I convert its output directly to ITK to avoid converting twice.
2 parents f3464b5 + a254756 commit 40e3770

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‎REFERENCES.md

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| nibabel | https://doi.org/10.5281/zenodo.60808 | https://github.com/nipy/nibabel/ |
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| nilearn | https://doi.org/10.3389/fninf.2014.00014 | https://github.com/nilearn/nilearn/ |
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| nipype | https://doi.org/10.3389/fninf.2011.00013 https://doi.org/10.5281/zenodo.581704 | https://github.com/nipy/nipype/ |
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| convert3d | | https://sourceforge.net/projects/c3d/ |
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| **Graphics**
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| seaborn | https://doi.org/10.5281/zenodo.883859 | https://github.com/mwaskom/seaborn |
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| matplotlib 2.0.0 | https://doi.org/10.5281/zenodo.248351 | https://github.com/matplotlib/matplotlib |

‎docs/installation.rst

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- FSL_ (version 6.0.7.7)
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- ANTs_ (version 2.5.1)
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- AFNI_ (version 24.0.05)
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- `C3D <https://sourceforge.net/projects/c3d/>`_ (version 1.4.0)
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- FreeSurfer_ (version 7.3.2)
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- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.14.0)
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- `connectome-workbench <https://www.humanconnectome.org/software/connectome-workbench>`_ (version 1.5.0)

‎env.yml

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# Try to remove this ASAP
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# https://github.com/conda-forge/ants-feedstock/issues/19
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- libitk=5.4.0
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# Workflow dependencies: Convert3d
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- convert3d=1.4
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# Workflow dependencies: Connectome Workbench
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- connectome-workbench-cli=2.0
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# Workflow dependencies: FSL (versions pinned in 6.0.7.13)

‎fmriprep/interfaces/conftest.py

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from pathlib import Path
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from shutil import copytree
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import pytest
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from .tests.data import load
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try:
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from contextlib import chdir as _chdir
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except ImportError: # PY310
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os.chdir(cwd)
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@pytest.fixture(scope='module')
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@pytest.fixture
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def data_dir():
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return Path(__file__).parent / 'tests' / 'data'
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with load.as_path() as data_dir:
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yield data_dir
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@pytest.fixture(autouse=True)
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def _docdir(request, tmp_path):
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# Trigger ONLY for the doctests.
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doctest_plugin = request.config.pluginmanager.getplugin('doctest')
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if isinstance(request.node, doctest_plugin.DoctestItem):
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copytree(Path(__file__).parent / 'tests' / 'data', tmp_path, dirs_exist_ok=True)
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with load.as_path() as data_dir:
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copytree(data_dir, tmp_path, dirs_exist_ok=True)
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# Chdir only for the duration of the test.
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with _chdir(tmp_path):

‎fmriprep/interfaces/nitransforms.py

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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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#
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# Copyright 2025 The NiPreps Developers <[email protected]>
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# We support and encourage derived works from this project, please read
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# about our expectations at
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#
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# https://www.nipreps.org/community/licensing/
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#
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"""Wrappers of NiTransforms."""
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from pathlib import Path
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from nipype.interfaces.base import (
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BaseInterfaceInputSpec,
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File,
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SimpleInterface,
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TraitedSpec,
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traits,
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)
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from nipype.utils.filemanip import fname_presuffix
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class _ConvertAffineInputSpec(BaseInterfaceInputSpec):
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in_xfm = File(exists=True, desc='input transform piles')
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inverse = traits.Bool(False, usedefault=True, desc='generate inverse')
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in_fmt = traits.Enum('auto', 'itk', 'fs', 'fsl', usedefault=True, desc='input format')
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out_fmt = traits.Enum('itk', 'fs', 'fsl', usedefault=True, desc='output format')
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reference = File(exists=True, desc='reference file')
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moving = File(exists=True, desc='moving file')
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class _ConvertAffineOutputSpec(TraitedSpec):
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out_xfm = File(exists=True, desc='output, combined transform')
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out_inv = File(desc='output, combined transform')
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class ConvertAffine(SimpleInterface):
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"""Write a single, flattened transform file."""
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input_spec = _ConvertAffineInputSpec
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output_spec = _ConvertAffineOutputSpec
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def _run_interface(self, runtime):
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from nitransforms.linear import load as load_affine
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ext = {
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'fs': 'lta',
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'itk': 'txt',
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'fsl': 'mat',
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}[self.inputs.out_fmt]
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in_fmt = self.inputs.in_fmt
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if in_fmt == 'auto':
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in_fmt = {
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'.lta': 'fs',
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'.mat': 'fsl',
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'.txt': 'itk',
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}[Path(self.inputs.in_xfm).suffix]
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reference = self.inputs.reference or None
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moving = self.inputs.moving or None
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affine = load_affine(self.inputs.in_xfm, fmt=in_fmt, reference=reference, moving=moving)
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out_file = fname_presuffix(
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self.inputs.in_xfm,
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suffix=f'_fwd.{ext}',
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newpath=runtime.cwd,
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use_ext=False,
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)
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self._results['out_xfm'] = out_file
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affine.to_filename(out_file, moving=moving, fmt=self.inputs.out_fmt)
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if self.inputs.inverse:
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inv_affine = ~affine
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if moving is not None:
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inv_affine.reference = moving
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out_inv = fname_presuffix(
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self.inputs.in_xfm,
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suffix=f'_inv.{ext}',
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newpath=runtime.cwd,
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use_ext=False,
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)
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self._results['out_inv'] = out_inv
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inv_affine.to_filename(out_inv, moving=reference, fmt=self.inputs.out_fmt)
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return runtime

‎fmriprep/interfaces/tests/data/__init__.py

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from acres import Loader
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load = Loader(__spec__.name)

‎fmriprep/interfaces/tests/data/mri_coreg-c3d-invert.txt

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#Insight Transform File V1.0
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#Transform 0
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Transform: MatrixOffsetTransformBase_double_3_3
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Parameters: 0.9999895968880486 -0.004093655352697662 -0.0020605942003409524 0.004033765542180662 0.9995917628463604 -0.028289559719570527 0.0021755887788865217 0.028280980403387748 0.9995979209696005 -0.31051619074750103 -0.7081012785638218 0.4403933958178312
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FixedParameters: 0 0 0

‎fmriprep/interfaces/tests/data/mri_coreg-c3d.txt

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#Insight Transform File V1.0
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#Transform 0
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Transform: MatrixOffsetTransformBase_double_3_3
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Parameters: 0.9999893987506181 0.0040337317156719996 0.0021755595966243754 -0.00409368802815685 0.999591499554368 0.02828093916460761 -0.0020606207364131553 -0.028289577997839488 0.9995973713325053 0.3124110873946151 0.6940861236277449 -0.4608878232636471
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FixedParameters: 0 0 0

‎fmriprep/interfaces/tests/data/mri_coreg-lta_convert-invert.txt

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#Insight Transform File V1.0
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#Transform 0
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Transform: AffineTransform_double_3_3
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Parameters: 0.99998968839645386 -0.0040936507284641266 -0.0020606310572475195 0.0040338016115128994 0.99959170818328857 -0.028289616107940674 0.0021755544003099203 0.028280943632125854 0.99959772825241089 -0.31053543090820312 -0.70811450481414795 0.440399169921875
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FixedParameters: 0 0 0

‎fmriprep/interfaces/tests/data/mri_coreg-lta_convert.mat

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0.99994755 0.00549713 -0.00865372 -5.78189802
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-0.00323471 0.97014636 0.24249923 -15.33529091
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0.00972842 -0.24245842 0.97011328 103.01686096
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0.00000000 0.00000000 0.00000000 1.00000000

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