diff --git a/.circleci/config.yml b/.circleci/config.yml
index 0c171241..bf707248 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -74,8 +74,7 @@ jobs:
       - run:
           name: Initiate versioning
           command: |
-            python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                                  setuptools_scm_git_archive pip twine docutils
+            python3 -m pip install -U build hatch hatchling pip twine docutils
 
             pip install /tmp/src/eddymotion[all]
 
diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
index 1f9246da..c0f1a005 100755
--- a/.github/workflows/contrib.yml
+++ b/.github/workflows/contrib.yml
@@ -11,15 +11,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-      - name: Install flake8
-        run: python -m pip install flake8
-      - name: Check EddyMotion
-        run: python -m flake8 src
+          python-version: 3
+      - name: Lint EddyMotion
+        run: pipx run flake8-pyproject
diff --git a/.github/workflows/docs-build-pr.yml b/.github/workflows/docs-build-pr.yml
index 48faa369..fc96c4e2 100644
--- a/.github/workflows/docs-build-pr.yml
+++ b/.github/workflows/docs-build-pr.yml
@@ -7,11 +7,11 @@ on:
 
 jobs:
   build:
-    if: "(github.repository_owner != 'nipreps') && !contains(github.event.head_commit.message, '[skip ci]')"
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -39,10 +39,11 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --no-cache-dir "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+        pip install -U build hatch pip
         pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1
 
     - name: Build docs
       run: |
-          python -m setuptools_scm  # Generate _version.py file
+          python -m hatch build --hooks-only
           make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html
diff --git a/.github/workflows/docs-build-update.yml b/.github/workflows/docs-build-update.yml
index bf73fa7c..a3be07b4 100644
--- a/.github/workflows/docs-build-update.yml
+++ b/.github/workflows/docs-build-update.yml
@@ -42,12 +42,13 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --no-cache-dir "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2"
+        pip install -U build hatch pip
         pip install -r docs/requirements.txt
+        python -m hatch version | tail -n1
 
     - name: Build docs
       run: |
-          python -m setuptools_scm  # Generate _version.py file
+          python -m hatch build --hooks-only
           make -C docs/ SPHINXOPTS="-W" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html
 
     - name: Push created tag to gh-pages
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index b3b6a132..0e583523 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -16,19 +16,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        pip: ["pip==21.2", "pip~=22.0"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Fetch all tags (for setuptools_scm to work)
-      run: |
-        /usr/bin/git -c protocol.version=2 fetch --tags --prune --unshallow origin
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+        fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v1
+    - uses: actions/cache@v4
       with:
         path: $HOME/.cache/pip
         key: pip-cache-v1
@@ -39,20 +38,18 @@ jobs:
       run: |
         python -m venv /tmp/buildenv
         source /tmp/buildenv/bin/activate
-        python -m pip install -U build "setuptools >= 45" wheel "setuptools_scm >= 6.2" \
-                              setuptools_scm_git_archive pip twine docutils
+        pip install -U build hatch pip twine
         
         python -m build -s -w
         python -m twine check dist/eddymotion-*
 
         mv dist /tmp/package
-        rm -rf eddymotion.egg-info/
 
         # Interpolate version
         if [[ "$GITHUB_REF" == refs/tags/* ]]; then
           TAG=${GITHUB_REF##*/}
         fi
-        THISVERSION=$( python -m setuptools_scm )
+        THISVERSION=$( python -m hatch version | tail -n1 | xargs )
         THISVERSION=${TAG:-$THISVERSION}
         echo "Expected VERSION: \"${THISVERSION}\""
         echo "THISVERSION=${THISVERSION}" >> $GITHUB_ENV
@@ -61,7 +58,7 @@ jobs:
       run: |
         python -m venv /tmp/pip
         source /tmp/pip/bin/activate
-        python -m pip install -U "setuptools >= 45" "setuptools_scm >= 6.2" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install .
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -72,7 +69,7 @@ jobs:
       run: |
         python -m venv /tmp/install_sdist
         source /tmp/install_sdist/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install /tmp/package/eddymotion*.tar.gz
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
@@ -83,7 +80,7 @@ jobs:
       run: |
         python -m venv /tmp/install_wheel
         source /tmp/install_wheel/bin/activate
-        python -m pip install -U "setuptools >= 45" "${{ matrix.pip }}"
+        pip install -U pip
         python -m pip install /tmp/package/eddymotion*.whl
         INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 86f118e6..00000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,12 +0,0 @@
-recursive-exclude .circleci/ *
-recursive-exclude .docker/ *
-recursive-exclude .github/ *
-recursive-exclude .git/ *
-recursive-exclude .maint/ *
-recursive-exclude docs/ *
-recursive-exclude test/ *
-
-exclude .*
-exclude Dockerfile
-
-recursive-include src/eddymotion/config *.*
diff --git a/docs/index.rst b/docs/index.rst
index 4e6dbd0b..848e3cc2 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,6 +1,8 @@
 .. include:: links.rst
 .. include:: ../README.rst
    :end-line: 29
+.. include:: ../README.rst
+   :start-line: 34
 
 
 .. image:: _static/eddymotion-flowchart.svg
diff --git a/docs/requirements.txt b/docs/requirements.txt
index e27fcc66..85f17b2c 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,6 +1,7 @@
 attrs >= 20.1.0
-furo ~= 2021.10.09
+furo >= 2024.01.29
 matplotlib >= 2.2.0
 packaging
-sphinx ~= 4.2
+sphinx >= 4.5
 sphinxcontrib-apidoc
+nireports
diff --git a/pyproject.toml b/pyproject.toml
index 78a60e81..317a96e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,15 +1,183 @@
 [build-system]
-requires = [
-    "setuptools >= 45",
-    "setuptools_scm[toml] >= 6.2",
-    "wheel"
-]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools_scm]
-write_to = "src/eddymotion/_version.py"
-write_to_template = """\
-\"\"\"Version file, automatically generated by setuptools_scm.\"\"\"
-__version__ = "{version}"
-"""
-fallback_version = "0.0"
+requires = ["hatchling", "hatch-vcs", "nipreps-versions"]
+build-backend = "hatchling.build"
+
+
+[project]
+name = "eddymotion"
+description = "Pure python eddy-current and head-motion correction for dMRI, an extension of QSIprep's SHOREline algorithm (Cieslak, 2020) to multiple diffusion models."
+readme = "README.rst"
+authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Image Recognition",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+license = "Apache-2.0"
+requires-python = ">=3.8"
+dependencies = [
+    "dipy>=1.3.0",
+    "joblib",
+    "nipype>= 1.5.1, < 2.0",
+    "nitransforms>=21.0.0",
+    "nireports",
+    "numpy>=1.17.3",
+    "nest-asyncio>=1.5.1",
+    "scikit-image>=0.14.2",
+    "scipy>=1.8.0",
+]
+dynamic = ["version"]
+
+[project.urls]
+Documentation = "https://www.nipreps.org/eddymotion"
+Home = "https://github.com/nipreps/eddymotion"
+NiPreps = "https://www.nipreps.org/"
+
+[project.optional-dependencies]
+doc = [
+    "attrs >= 20.1.0",
+    "furo >= 2024.01.29",
+    "matplotlib >= 2.2.0",
+    "nbsphinx",
+    "packaging",
+    "pydot >= 1.2.3",
+    "pydotplus",
+    "sphinx >= 4.5",
+    "sphinx-argparse",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-apidoc ~= 0.3.0",
+    "sphinxcontrib-napoleon",
+    "sphinxcontrib-versioning"
+]
+
+dev = [
+    "black",
+    "flake8",
+    "flake8-pyproject",
+    "isort",
+    "pre-commit",
+    "pre-commit-hooks",
+]
+
+plotting = ["nilearn"]
+
+resmon = ["psutil >=5.4"]
+
+popylar = ["popylar >= 0.2"]
+
+test = [
+    "coverage",
+    "pytest >= 4.4",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-xdist >= 1.28"
+]
+
+# Aliases
+docs = ["eddymotion[doc]"]
+tests = ["eddymotion[test]"]
+all = ["eddymotion[doc,test,dev,plotting,resmon,popylar]"]
+
+#
+# Hatch configurations
+#
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.sdist]
+exclude = [".git_archival.txt"]  # No longer needed in sdist
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/eddymotion"]
+# exclude = [
+#     "eddymotion/tests/data",  # Large test data directory
+# ]
+
+
+[tool.hatch.version]
+validate-bump = true
+source = "vcs"
+raw-options = { version_scheme = "nipreps-calver" }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/eddymotion/_version.py"
+
+#
+# Developer tool configurations
+#
+
+[tool.black]
+line-length = 99
+target-version = ['py39']
+skip-string-normalization = true
+exclude = '''
+# Directories
+/(
+    \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | venv
+  | _build
+  | build
+  | dist
+)/
+'''
+
+[tool.isort]
+profile = 'black'
+skip_gitignore = true
+
+[tool.flake8]
+max-line-length = 99
+doctests = false
+exclude = ["*build/", "docs/"]
+select = "C,E,F,W,B,B950"
+ignore = "N802,N806,W503,E203"
+per-file-ignores = [
+    "*/__init__.py: F401",
+    "docs/conf.py: E265",
+    "/^\\s*\\.\\. _.*?: http/: E501"
+]
+
+[tool.pytest.ini_options]
+pythonpath = "src/ test/"
+norecursedirs = [".*", "_*"]
+addopts = "-v --doctest-modules"
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+
+
+[tool.coverage.run]
+branch = true
+concurrency = 'multiprocessing'
+omit = [
+    '*/tests/*',
+    '*/__init__.py',
+    '*/conftest.py',
+    'src/eddymotion/_version.py'
+]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_lines = [
+    'raise NotImplementedError',
+    'warnings\.warn',
+]
+
+[tool.codespell]
+# nd - import scipy.ndimage as nd
+# mapp, reson -- Mapp. and Reson. abbreviations in citation
+ignore-words-list = 'nd,mapp,reson'
+skip = """
+./.git,*.pdf,*.svg,*.min.js,*.ipynb,ORIGINAL_LICENSE,\
+./docs/source/_static/example_anatreport.html"""
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100755
index c75129a8..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,125 +0,0 @@
-[metadata]
-name = eddymotion
-author = Derek Pisner
-author_email = nipreps@gmail.com
-classifiers =
-    Development Status :: 3 - Alpha
-    Intended Audience :: Science/Research
-    Topic :: Scientific/Engineering :: Image Recognition
-    License :: OSI Approved :: Apache Software License
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-description = Pure python eddy-current and head-motion correction for dMRI, an extension of QSIprep's SHOREline algorithm (Cieslak, 2020) to multiple diffusion models.
-license = Apache License, Version 2.0
-long_description = file:README.rst
-long_description_content_type = text/x-rst; charset=UTF-8
-maintainers = The NiPreps developers
-maintainer_email = nipreps@gmail.com, dpysalexander@gmail.com
-url = https://github.com/nipreps/eddymotion
-
-[options]
-python_requires = >=3.8
-setup_requires =
-    setuptools >= 45
-    setuptools_scm >= 6.2
-    wheel
-install_requires =
-    dipy>=1.3.0
-    joblib
-    nipype>= 1.5.1, < 2.0
-    nitransforms>=21.0.0
-    nireports
-    numpy>=1.17.3
-    nest-asyncio>=1.5.1
-    scikit-image>=0.14.2
-    scipy>=1.8.0
-test_requires =
-    codecov
-    coverage
-    pytest
-packages = find_namespace:
-package_dir=
-    = src
-include_package_data = True
-zip_safe = True
-
-[options.packages.find]
-where = src
-include = eddymotion*
-exclude =
-    test
-    test.*
-
-[options.package_data]
-eddymotion.config =
-    *.json
-
-[options.exclude_package_data]
-* = test
-
-[options.extras_require]
-doc =
-    nbsphinx
-    packaging
-    pydot >= 1.2.3
-    pydotplus
-    sphinx >= 2.1.2
-    sphinx-argparse
-    sphinx_rtd_theme
-    sphinxcontrib-apidoc ~= 0.3.0
-    sphinxcontrib-napoleon
-    sphinxcontrib-versioning
-docs =
-    %(doc)s
-plotting = nilearn
-resmon = psutil >=5.4
-popylar = popylar >= 0.2
-style =
-    flake8 >= 3.7.0
-test =
-    pytest >= 4.4
-    pytest-xdist >= 1.28
-    pytest-env
-    pytest-cov
-    coverage
-tests =
-    %(test)s
-dev =
-    black~=22.3
-    flake8~=4.0
-    isort~=5.10
-    pre-commit
-    pre-commit-hooks
-    %(docs)s
-    %(test)s
-all =
-    %(doc)s
-    %(resmon)s
-    %(popylar)s
-    %(tests)s
-    %(dev)s
-
-[flake8]
-max-line-length = 99
-doctests = False
-exclude=
-    *build/
-    docs/
-select = C,E,F,W,B,B950
-ignore = N802,N806,W503,E203
-putty-ignore =
-    */__init__.py : +F401
-    docs/conf.py : +E265
-    /^\s*\.\. _.*?: http/ : +E501
-
-[tool:pytest]
-pythonpath = src/ test/
-norecursedirs = .* _*
-addopts = -v --doctest-modules
-doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE
-env =
-    PYTHONHASHSEED=0
-filterwarnings =
-    ignore::DeprecationWarning
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 5c773cf1..00000000
--- a/setup.py
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env python
-"""eddymotion's PEP518 setup.py shim."""
-from setuptools import setup
-
-if __name__ == "__main__":
-    """ Install entry-point """
-    setup()
diff --git a/src/eddymotion/__init__.py b/src/eddymotion/__init__.py
index 90e1b6f0..dd1f0ac7 100644
--- a/src/eddymotion/__init__.py
+++ b/src/eddymotion/__init__.py
@@ -27,6 +27,4 @@
 __copyright__ = "Copyright 2021, The eddymotion developers"
 __url__ = "https://github.com/nipreps/EddyMotionCorrection"
 
-DOWNLOAD_URL = (
-    f"https://github.com/nipreps/{__packagename__}/archive/{__version__}.tar.gz"
-)
+DOWNLOAD_URL = f"https://github.com/nipreps/{__packagename__}/archive/{__version__}.tar.gz"
diff --git a/src/eddymotion/data/dmri.py b/src/eddymotion/data/dmri.py
index dfefd01a..55d634a5 100644
--- a/src/eddymotion/data/dmri.py
+++ b/src/eddymotion/data/dmri.py
@@ -228,9 +228,7 @@ def from_filename(cls, filename):
         """Read an HDF5 file from disk."""
         with h5py.File(filename, "r") as in_file:
             root = in_file["/0"]
-            data = {
-                k: np.asanyarray(v) for k, v in root.items() if not k.startswith("_")
-            }
+            data = {k: np.asanyarray(v) for k, v in root.items() if not k.startswith("_")}
         return cls(**data)
 
 
diff --git a/src/eddymotion/data/pet.py b/src/eddymotion/data/pet.py
index 44a97b89..4591962d 100644
--- a/src/eddymotion/data/pet.py
+++ b/src/eddymotion/data/pet.py
@@ -132,9 +132,7 @@ def from_filename(cls, filename):
         """Read an HDF5 file from disk."""
         with h5py.File(filename, "r") as in_file:
             root = in_file["/0"]
-            data = {
-                k: np.asanyarray(v) for k, v in root.items() if not k.startswith("_")
-            }
+            data = {k: np.asanyarray(v) for k, v in root.items() if not k.startswith("_")}
         return cls(**data)
 
 
diff --git a/src/eddymotion/data/utils.py b/src/eddymotion/data/utils.py
index 4d5e00d3..07cdd329 100644
--- a/src/eddymotion/data/utils.py
+++ b/src/eddymotion/data/utils.py
@@ -28,9 +28,7 @@ def apply_affines(nii, em_affines, output_filename=None):
 
     for ii, bvecnii in enumerate(nib.four_to_three(nii)):
         xfms = nt.linear.Affine(em_affines[ii])
-        transformed_nii[..., ii] = np.asanyarray(
-            (~xfms).apply(bvecnii, reference=nii).dataobj
-        )
+        transformed_nii[..., ii] = np.asanyarray((~xfms).apply(bvecnii, reference=nii).dataobj)
 
     nii_t_img = nii.__class__(transformed_nii, nii.affine, nii.header)
 
diff --git a/src/eddymotion/estimator.py b/src/eddymotion/estimator.py
index 7efff9d0..137b6dba 100644
--- a/src/eddymotion/estimator.py
+++ b/src/eddymotion/estimator.py
@@ -95,18 +95,16 @@ def fit(
         n_iter = len(models)
         for i_iter, model in enumerate(models):
             reg_target_type = (
-                "dwi"
-                if model.lower() not in ("b0", "s0", "avg", "average", "mean")
-                else "b0"
+                "dwi" if model.lower() not in ("b0", "s0", "avg", "average", "mean") else "b0"
             )
 
             # When downsampling these need to be set per-level
             bmask_img = None
             if dwdata.brainmask is not None:
                 _, bmask_img = mkstemp(suffix="_bmask.nii.gz")
-                nb.Nifti1Image(
-                    dwdata.brainmask.astype("uint8"), dwdata.affine, None
-                ).to_filename(bmask_img)
+                nb.Nifti1Image(dwdata.brainmask.astype("uint8"), dwdata.affine, None).to_filename(
+                    bmask_img
+                )
                 kwargs["mask"] = dwdata.brainmask
 
             if hasattr(dwdata, "bzero") and dwdata.bzero is not None:
@@ -203,9 +201,7 @@ def fit(
                         if bmask_img:
                             registration.inputs.fixed_image_masks = ["NULL", bmask_img]
 
-                        if dwdata.em_affines is not None and np.any(
-                            dwdata.em_affines[i, ...]
-                        ):
+                        if dwdata.em_affines is not None and np.any(dwdata.em_affines[i, ...]):
                             reference = namedtuple("ImageGrid", ("shape", "affine"))(
                                 shape=dwdata.dataobj.shape[:3], affine=dwdata.affine
                             )
@@ -243,9 +239,7 @@ def fit(
         return dwdata.em_affines
 
 
-def _advanced_clip(
-    data, p_min=35, p_max=99.98, nonnegative=True, dtype="int16", invert=False
-):
+def _advanced_clip(data, p_min=35, p_max=99.98, nonnegative=True, dtype="int16", invert=False):
     """
     Remove outliers at both ends of the intensity distribution and fit into a given dtype.
 
diff --git a/src/eddymotion/model/__init__.py b/src/eddymotion/model/__init__.py
index e2eb4565..7e32df8b 100644
--- a/src/eddymotion/model/__init__.py
+++ b/src/eddymotion/model/__init__.py
@@ -22,12 +22,12 @@
 #
 """Data models."""
 from eddymotion.model.base import (
-    ModelFactory,
     AverageDWModel,
     DKIModel,
     DTIModel,
-    TrivialB0Model,
+    ModelFactory,
     PETModel,
+    TrivialB0Model,
 )
 
 __all__ = (
diff --git a/src/eddymotion/model/base.py b/src/eddymotion/model/base.py
index e0e8d2e9..fe8aca40 100644
--- a/src/eddymotion/model/base.py
+++ b/src/eddymotion/model/base.py
@@ -22,9 +22,10 @@
 #
 """A factory class that adapts DIPY's dMRI models."""
 import warnings
-from joblib import Parallel, delayed
+
 import numpy as np
 from dipy.core.gradients import gradient_table
+from joblib import Parallel, delayed
 
 
 def _exec_fit(model, data, chunk=None):
@@ -97,7 +98,11 @@ def __init__(self, gtab, S0=None, mask=None, b_max=None, **kwargs):
         # Setup B0 map
         self._S0 = None
         if S0 is not None:
-            self._S0 = np.clip(S0.astype("float32") / S0.max(), a_min=1e-5, a_max=1.0,)
+            self._S0 = np.clip(
+                S0.astype("float32") / S0.max(),
+                a_min=1e-5,
+                a_max=1.0,
+            )
 
         # Setup brain mask
         self._mask = mask
@@ -124,9 +129,7 @@ def __init__(self, gtab, S0=None, mask=None, b_max=None, **kwargs):
         from importlib import import_module
 
         module_name, class_name = model_str.rsplit(".", 1)
-        self._model = getattr(
-            import_module(module_name), class_name
-        )(_rasb2dipy(gtab), **kwargs)
+        self._model = getattr(import_module(module_name), class_name)(_rasb2dipy(gtab), **kwargs)
 
     def fit(self, data, n_jobs=None, **kwargs):
         """Fit the model chunk-by-chunk asynchronously"""
@@ -136,9 +139,7 @@ def fit(self, data, n_jobs=None, **kwargs):
 
         # Select voxels within mask or just unravel 3D if no mask
         data = (
-            data[self._mask, ...]
-            if self._mask is not None
-            else data.reshape(-1, data.shape[-1])
+            data[self._mask, ...] if self._mask is not None else data.reshape(-1, data.shape[-1])
         )
 
         # One single CPU - linear execution (full model)
@@ -154,8 +155,7 @@ def fit(self, data, n_jobs=None, **kwargs):
         # Parallelize process with joblib
         with Parallel(n_jobs=n_jobs) as executor:
             results = executor(
-                delayed(_exec_fit)(self._model, dchunk, i)
-                for i, dchunk in enumerate(data_chunks)
+                delayed(_exec_fit)(self._model, dchunk, i) for i, dchunk in enumerate(data_chunks)
             )
         for submodel, index in results:
             self._models[index] = submodel
@@ -182,10 +182,7 @@ def predict(self, gradient, **kwargs):
         if n_models == 1:
             predicted, _ = _exec_predict(self._model, gradient, S0=S0, **kwargs)
         else:
-            S0 = (
-                np.array_split(S0, n_models) if S0 is not None
-                else [None] * n_models
-            )
+            S0 = np.array_split(S0, n_models) if S0 is not None else [None] * n_models
 
             predicted = [None] * n_models
 
@@ -345,10 +342,7 @@ def fit(self, data, *args, **kwargs):
         self._shape = data.shape[:3]
 
         # Convert data into V (voxels) x T (timepoints)
-        data = (
-            data.reshape((-1, data.shape[-1]))
-            if self._mask is None else data[self._mask]
-        )
+        data = data.reshape((-1, data.shape[-1])) if self._mask is None else data[self._mask]
 
         # A.shape = (T, K - 4); T= n. timepoints, K= n. knots (with padding)
         A = BSpline.design_matrix(x, self._t, k=self._order)
@@ -357,17 +351,12 @@ def fit(self, data, *args, **kwargs):
 
         # One single CPU - linear execution (full model)
         if n_jobs == 1:
-            self._coeff = np.array([
-                cg(ATdotA, AT @ v)[0] for v in data
-            ])
+            self._coeff = np.array([cg(ATdotA, AT @ v)[0] for v in data])
             return
 
         # Parallelize process with joblib
         with Parallel(n_jobs=n_jobs) as executor:
-            results = executor(
-                delayed(cg)(ATdotA, AT @ v)
-                for v in data
-            )
+            results = executor(delayed(cg)(ATdotA, AT @ v) for v in data)
 
         self._coeff = np.array([r[0] for r in results])
 
diff --git a/src/eddymotion/viz.py b/src/eddymotion/viz.py
index 38d112b0..eeeaee88 100644
--- a/src/eddymotion/viz.py
+++ b/src/eddymotion/viz.py
@@ -49,11 +49,13 @@ def plot_dwi(dataobj, affine, gradient=None, **kwargs):
         nb.Nifti1Image(dataobj, affine, None),
         vmax=vmax,
         cut_coords=cut_coords,
-        title=r"Reference $b$=0"
-        if gradient is None
-        else f"""\
+        title=(
+            r"Reference $b$=0"
+            if gradient is None
+            else f"""\
 $b$={gradient[3].astype(int)}, \
-$\\vec{{b}}$ = ({', '.join(str(v) for v in gradient[:3])})""",
+$\\vec{{b}}$ = ({', '.join(str(v) for v in gradient[:3])})"""
+        ),
         **kwargs,
     )
 
@@ -289,8 +291,7 @@ def plot_carpet(
     segment_labels=None,
     detrend=False,
 ):
-    """
-    Return carpet plot using niworkflows carpet_plot
+    """Return carpet plot using niworkflows carpet_plot
 
     Parameters
     ----------
@@ -305,10 +306,8 @@ def plot_carpet(
     output_file : :obj:`string`
         Path to save the plot
     segment_labels : :obj:`dict`
-        Dictionary of segment labels
-        e.g. {'Cerebral_White_Matter': [2, 41],
-              'Cerebral_Cortex': [3, 42],
-              'Ventricle': [4, 14, 15, 43, 72]}
+        Dictionary of segment labels, mapping segment name to list of integers
+        e.g. {'Cerebral_White_Matter': [2, 41], ...}
     detrend : :obj:`bool`
         niworkflows plot_carpet detrend flag
 
@@ -328,9 +327,7 @@ def plot_carpet(
     nii_data_div_b0 = dw_data / bzero[..., np.newaxis]
 
     sort_inds = np.argsort(
-        gtab.bvals[~gtab.b0s_mask]
-        if sort_by_bval
-        else np.arange(len(gtab.bvals[~gtab.b0s_mask]))
+        gtab.bvals[~gtab.b0s_mask] if sort_by_bval else np.arange(len(gtab.bvals[~gtab.b0s_mask]))
     )
     nii_data_div_b0 = nii_data_div_b0[..., sort_inds]
 
@@ -351,9 +348,7 @@ def plot_carpet(
             for label in labels:
                 indices = np.array([], dtype=int)
                 for ii in segment_labels[label]:
-                    indices = np.concatenate(
-                        [indices, np.where(segmentation_masked == ii)[0]]
-                    )
+                    indices = np.concatenate([indices, np.where(segmentation_masked == ii)[0]])
                 segments[label] = indices
 
     else:
@@ -372,9 +367,7 @@ def plot_carpet(
     )
 
 
-def get_segment_labels(
-    filepath, keywords, delimiter=" ", index_position=0, label_position=1
-):
+def get_segment_labels(filepath, keywords, delimiter=" ", index_position=0, label_position=1):
     """
     Return segment labels for plot_carpet function
 
diff --git a/test/test_estimator.py b/test/test_estimator.py
index b592fe57..84a77475 100644
--- a/test/test_estimator.py
+++ b/test/test_estimator.py
@@ -77,4 +77,4 @@ def test_ANTs_config_b0(datadir, tmp_path, r_x, r_y, r_z, t_x, t_y, t_z):
 
     coords = xfm.reference.ndcoords.T
     rms = np.sqrt(((xfm.map(coords) - xform.map(coords)) ** 2).sum(1)).mean()
-    assert  rms < 0.8
+    assert rms < 0.8