diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index 4bf696e..c8405bc 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -45,23 +45,18 @@ jobs:
         run: |
           git config --global user.email "dummy@email.com"
           git config --global user.name "Dummy User"
-
       - name: install dependencies
         run: |
            sudo apt-get update
            sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
-
       - name: Run sccache-cache
         uses: mozilla-actions/sccache-action@v0.0.3
-
       - name: Get CMake
         uses: lukka/get-cmake@latest
         with:
           cmakeVersion: '3.16.3'
-
       - name: Print CMake version
         run: cmake --version
-
       - name: Clone latest MRtrix and switch to latest tag
         run: |
           mkdir $MRTRIX_HOME
@@ -71,10 +66,8 @@ jobs:
           git checkout pydra-usage-python-cmd
           git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-mrtrix3 release"
           git describe --abbrev=0
-
 # echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
 # git checkout $MRTRIX_VERSION
-
       - name: configure
         run: |
           cd $MRTRIX_HOME/src
@@ -88,40 +81,31 @@ jobs:
           -D CMAKE_C_COMPILER=clang \
           -D CMAKE_CXX_COMPILER=clang++ \
           -D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL
-
       - name: Build Mrtrix
         run: |
           cd $MRTRIX_HOME/src
           cmake --build build
-
       - name: Install Mrtrix
         run: |
           cd $MRTRIX_HOME/src
           cmake --install build
-
       - name: Set PATH Variable
         run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
-
       - name: Set LD_LIBRARY_PATH Variable
         run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
-
       - name: Change back to the root directory
         run: cd ..
-
       - name: Set up Python
         uses: actions/setup-python@v2
-
       - name: Install Python build dependencies
         run: |
           python -m pip install --upgrade pip
-
       - name: Install pydra-auto-gen requirements
         run: >
           pip install
           -e related-packages/fileformats
           -e related-packages/fileformats-extras
           -e .[dev,test]
-
       - name: Generate task specifications
         run: >
           ./generate.py
@@ -130,22 +114,18 @@ jobs:
           $MRTRIX_VERSION
           --log-errors
           --latest
-
       - name: Upload MRtrix3 install
         uses: actions/upload-artifact@v2
         with:
           name: MRtrix3
           path: ${{ env.MRTRIX_INSTALL}}
-
       - name: Upload auto-gen pydra
         uses: actions/upload-artifact@v2
         with:
           name: AutoGen
           path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
-
       - name: Write version file
         run: echo $MRTRIX_VERSION > mrtrix3_version.txt
-
       - name: Upload version file
         uses: actions/upload-artifact@v2
         with:
@@ -165,40 +145,32 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-
     - name: Download version file
       uses: actions/download-artifact@v2
       with:
         name: VersionFile
         path: mrtrix3_version.txt
-
     - name: Extract Mrtrix version
       run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
-
     - name: Download auto-gen pydra
       uses: actions/download-artifact@v2
       with:
         name: AutoGen
         path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
-
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
-
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-
     - name: Install build dependencies
       run: |
         python -m pip install --upgrade pip
-
     - name: Install Pydra
       run: |
         pip install ${{ matrix.pydra }}
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-
     - name: Install task package
       run: |
         pip install ${{ matrix.pip-flags }} "related-packages/fileformats"
@@ -221,66 +193,55 @@ jobs:
       run: |
           sudo apt-get update
           sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
-
     - name: Checkout code
       uses: actions/checkout@v2
-
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+    - name: Fetch tags
+      run: git fetch --prune --unshallow
     - name: Download version file
       uses: actions/download-artifact@v2
       with:
         name: VersionFile
         path: mrtrix3_version.txt
-
     - name: Extract Mrtrix version
       run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
-
     - name: Download auto-gen pydra
       uses: actions/download-artifact@v2
       with:
         name: AutoGen
         path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
-
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
-
     - name: Download MRtrix3 install
       uses: actions/download-artifact@v2
       with:
         name: MRtrix3
         path: ${{ env.MRTRIX_INSTALL}}
-
     - name: Make commands executable
       run: chmod +x ${{ env.MRTRIX_INSTALL }}/bin/*
-
     - name: Set PATH Variable
       run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
-
     - name: Set LD_LIBRARY_PATH Variable
       run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
-
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-
     - name: Install build dependencies
       run: |
         python -m pip install --upgrade pip
-
     - name: Install task package
       run: >
         pip install
         -e ./related-packages/fileformats
         -e ./related-packages/fileformats-extras
         -e '.[test]'
-
-    - name: Install dev branch of pydra until bugfix
-      run: pip install --upgrade git+https://github.com/nipype/pydra.git@typing-bugfixes
-
     - name: Test with pytest
       run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
-
     - uses: codecov/codecov-action@v1
       if: ${{ always() }}
 
@@ -304,7 +265,7 @@ jobs:
       run: twine check ./related-packages/fileformats/dist/*
     - name: Check for PyPI token on tag
       id: deployable
-      if: github.event_name == 'release'
+      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
       env:
         PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}"
       run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
@@ -336,7 +297,7 @@ jobs:
       run: twine check ./related-packages/fileformats-extras/dist/*
     - name: Check for PyPI token on tag
       id: deployable
-      if: github.event_name == 'release'
+      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
       env:
         PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}"
       run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
@@ -353,73 +314,58 @@ jobs:
     needs: [devcheck, test, deploy-fileformats, deploy-fileformats-extras]
     runs-on: ubuntu-latest
     steps:
-
     - name: Checkout repo
       uses: actions/checkout@v2
-
     - name: Set up Git user
       run: |
         git config --local user.email "action@github.com"
         git config --local user.name "GitHub Action"
-
     - name: Download version file
       uses: actions/download-artifact@v2
       with:
         name: VersionFile
         path: mrtrix3_version.txt
-
     - name: Extract Mrtrix version
       run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
-
     - name: Download auto-gen pydra
       uses: actions/download-artifact@v2
       with:
         name: AutoGen
         path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
-
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
-
     - name: Add auto-generated directory to git repo
       if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
       run: |
         git add pydra/tasks/mrtrix3/$SUBPKG_NAME
         git commit -am"added auto-generated version to make new tag for package version"
         git status
-
     - name: Get latest version tag
       id: latest_tag
       run: |
         git fetch --tags
         echo "TAG=$(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')" >> $GITHUB_OUTPUT
-
     - name: Overwrite the tag of release event with latest commit (i.e. including the auto directory)
       if: github.event_name == 'release'
       run: |
         git tag -d ${{ steps.latest_tag.outputs.TAG }};
         git tag -a ${{ steps.latest_tag.outputs.TAG }} -m"Tag used to create a pydra-mrtrix3 $MRTRIX_VERSION release";
-
     - name: Set up Python 3.11
       uses: actions/setup-python@v2
       with:
         python-version: 3.11
-
     - name: Install build tools
       run: python -m pip install --upgrade pip twine build
-
     - name: Build source and wheel distributions
       run: python -m build
-
     - name: Check distributions
       run: twine check dist/*
-
     - name: Upload sdist
       uses: actions/upload-artifact@v2
       with:
         name: SDist
         path: dist/*.tar.gz
-
     # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
     # Secrets are not accessible in the if: condition [0], so set an output variable [1]
     # [0] https://github.community/t/16928
@@ -430,7 +376,6 @@ jobs:
       env:
         PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
       run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi
-
     - name: Upload to PyPI
       if: steps.deployable.outputs.DEPLOY
       uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.gitignore b/.gitignore
index c55f867..a0713aa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -137,4 +137,7 @@ dmypy.json
 # Hatchling
 _version.py
 
+# Mac Garbage
+.DS_Store
+
 /pydra/tasks/mrtrix3/v3_0
diff --git a/pyproject.toml b/pyproject.toml
index ad2fb37..23d4949 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ description = "pydra-mrtrix3 contains Pydra task specifications for MRtrix3 tool
 readme = "README.rst"
 requires-python = ">=3.8"
 dependencies = [
-    "fileformats-medimage_mrtrix3 >=3.0.4a4",
+    "fileformats-medimage_mrtrix3 >=3.0.4a5",
     "numpy",
     "pydra >=0.23",
 ]
@@ -36,8 +36,7 @@ dev = [
     "click >=8.1.3",
     "tqdm",
     "attrs >=23.1.0",
-    "fileformats >= 0.8",
-    "fileformats-extras >= 0.2.1",
+    "fileformats-extras >= 0.12.1",
 ]
 doc = [
     "packaging",
diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py
index 1301188..c87918c 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py
@@ -1,4 +1,4 @@
-from fileformats.core import hook
+from fileformats.core import converter
 from fileformats.medimage.base import MedicalImage
 
 from fileformats.medimage_mrtrix3 import (
@@ -16,7 +16,7 @@
     in_out_file_kwargs = {}
 
 
-@hook.converter(
+@converter(
     source_format=MedicalImage,
     target_format=MrtrixImage,
     out_ext=MrtrixImage.ext,
@@ -40,7 +40,7 @@ def mrconvert(name, out_ext: str, **kwargs):
     return MrConvert(name=name, out_file="out" + out_ext, **kwargs)
 
 
-@hook.converter(
+@converter(
     source_format=MedicalImage,
     target_format=MrtrixImageHeader,
     out_ext=MrtrixImageHeader.ext,
diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py
index 4b9f9b5..e25d5da 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py
@@ -1,9 +1,10 @@
 import numpy as np
+from fileformats.core import extra_implementation
 from fileformats.medimage import DwiEncoding
 from fileformats.medimage_mrtrix3 import BFile
 
 
-@DwiEncoding.read_array.register
+@extra_implementation(DwiEncoding.read_array)
 def bfile_read_array(bfile: BFile) -> np.ndarray:
     return np.asarray(
         [[float(x) for x in ln.split()] for ln in bfile.read_contents().splitlines()]
diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py
index 7f58e5b..be543ee 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py
@@ -4,23 +4,23 @@
 from pathlib import Path
 import numpy as np
 from medimages4tests.dummy.nifti import get_image as get_dummy_nifti
-from fileformats.core import FileSet, SampleFileGenerator
+from fileformats.core import FileSet, SampleFileGenerator, extra_implementation
 from fileformats.medimage import MedicalImage, Nifti1
 from fileformats.medimage_mrtrix3 import ImageFormat
 
 
-@FileSet.generate_sample_data.register
+@extra_implementation(FileSet.generate_sample_data)
 def generate_mrtrix_sample_data(
     mif: ImageFormat,
     generator: SampleFileGenerator,
-) -> ty.Iterable[Path]:
+) -> ty.List[Path]:
     nifti = Nifti1(get_dummy_nifti(generator.dest_dir / "nifti.nii"))
     with mock.patch.dict(os.environ, {"MRTRIX_CLI_PARSE_ONLY": "0"}):
         mif = ImageFormat.convert(nifti)
     return mif.fspaths
 
 
-@MedicalImage.read_array.register
+@extra_implementation(MedicalImage.read_array)
 def mrtrix_read_array(mif: ImageFormat) -> np.ndarray:
     raise NotImplementedError(
         "Need to work out how to use the metadata to read the array in the correct order"
diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py
index a7594b6..2ef9f37 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py
@@ -3,15 +3,15 @@
 import math
 from pathlib import Path
 import typing as ty
-from fileformats.core import FileSet, SampleFileGenerator
+from fileformats.core import FileSet, SampleFileGenerator, extra_implementation
 from fileformats.medimage_mrtrix3 import Tracks
 
 
-@FileSet.generate_sample_data.register
+@extra_implementation(FileSet.generate_sample_data)
 def generate_tracks_sample_data(
     tracks: Tracks,
     generator: SampleFileGenerator,
-) -> ty.Iterable[Path]:
+) -> ty.List[Path]:
     """Generate a tracks file with a single straight track of length 10"""
     fspath = generator.dest_dir / "tracks.tck"
     timestamp = str(time.time() * 1e9 + time.process_time_ns())
diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml
index 7155dad..0ee7929 100644
--- a/related-packages/fileformats-extras/pyproject.toml
+++ b/related-packages/fileformats-extras/pyproject.toml
@@ -9,7 +9,7 @@ readme = "README.rst"
 requires-python = ">=3.8"
 dependencies = [
     "fileformats >= 0.8",
-    "fileformats-medimage-mrtrix3 >=3.0.4a4",
+    "fileformats-medimage-mrtrix3 >=3.0.4a5",
     "medimages4tests",
     "pydra >= 0.23.0",
 ]
diff --git a/related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py
index 74bbcff..287e9da 100644
--- a/related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py
+++ b/related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py
@@ -1,4 +1,3 @@
-from fileformats.core import hook
 from fileformats.core.mixin import WithAdjacentFiles
 from fileformats.medimage import DwiEncoding, Nifti1, NiftiGz, NiftiX, NiftiGzX
 from .image import ImageFormat, ImageHeader, ImageFormatGz
@@ -12,7 +11,6 @@ class BFile(DwiEncoding):
 
 # NIfTI file format gzipped with BIDS side car
 class WithBFile(WithAdjacentFiles):
-    @hook.required
     @property
     def encoding(self) -> BFile:
         return BFile(self.select_by_ext(BFile))
@@ -35,12 +33,12 @@ class NiftiGzXB(WithBFile, NiftiGzX):
 
 
 class ImageFormatB(WithBFile, ImageFormat):
-    pass
+    iana_mime = "application/x-mrtrix-image-format.b"
 
 
 class ImageFormatGzB(WithBFile, ImageFormatGz):
-    pass
+    iana_mime = "application/x-mrtrix-image-format+gzip.b"
 
 
 class ImageHeaderB(WithBFile, ImageHeader):
-    pass
+    iana_mime = "application/x-mrtrix-image-header.b"
diff --git a/related-packages/fileformats/fileformats/medimage_mrtrix3/image.py b/related-packages/fileformats/fileformats/medimage_mrtrix3/image.py
index 1a5c74c..1b4b587 100644
--- a/related-packages/fileformats/fileformats/medimage_mrtrix3/image.py
+++ b/related-packages/fileformats/fileformats/medimage_mrtrix3/image.py
@@ -1,6 +1,6 @@
-import typing as ty
 from pathlib import Path
-from fileformats.core import hook
+import typing as ty
+from fileformats.core import FileSet, extra_implementation
 from fileformats.generic import File
 from fileformats.application import Gzip
 from fileformats.core.mixin import WithMagicNumber
@@ -17,43 +17,6 @@ class BaseMrtrixImage(WithMagicNumber, fileformats.medimage.MedicalImage, File):
     magic_number = b"mrtrix image\n"
     binary = True
 
-    def read_metadata(self):
-        metadata = {}
-        with open(self.fspath, "rb") as f:
-            line = f.readline()
-            if line != self.magic_number:
-                raise FormatMismatchError(
-                    f"Magic line {line} doesn't match reference {self.magic_number}"
-                )
-            line = f.readline().decode("utf-8")
-            while line and line != "END\n":
-                key, value = line.split(": ", maxsplit=1)
-                if "," in value:
-                    try:
-                        value = [int(v) for v in value.split(",")]
-                    except ValueError:
-                        try:
-                            value = [float(v) for v in value.split(",")]
-                        except ValueError:
-                            pass
-                else:
-                    try:
-                        value = int(value)
-                    except ValueError:
-                        try:
-                            value = float(value)
-                        except ValueError:
-                            pass
-                if key in metadata:
-                    if isinstance(metadata[key], MultiLineMetadataValue):
-                        metadata[key].append(value)
-                    else:
-                        metadata[key] = MultiLineMetadataValue([metadata[key], value])
-                else:
-                    metadata[key] = value
-                line = f.readline().decode("utf-8")
-        return metadata
-
     @property
     def data_fspath(self):
         data_fspath = self.metadata["file"].split()[0]
@@ -67,7 +30,9 @@ def data_fspath(self):
 
     @property
     def data_offset(self):
-        return int(self.metadata["file"].split()[1])
+        fspath_and_offset = self.metadata["file"].split()
+        assert len(fspath_and_offset) <= 2
+        return int(fspath_and_offset[1]) if len(fspath_and_offset) > 1 else 0
 
     @property
     def vox_sizes(self):
@@ -81,8 +46,9 @@ def dims(self):
 class ImageFormat(BaseMrtrixImage):
 
     ext = ".mif"
+    iana_mime = "application/x-mrtrix-image-format"
 
-    @hook.check
+    @property
     def check_data_file(self):
         if self.data_fspath != self.fspath:
             raise FormatMismatchError(
@@ -97,15 +63,15 @@ def data_file(self):
 
 class ImageFormatGz(Gzip[ImageFormat]):
 
-    iana_mime = "application/x-image-format-gz"
+    iana_mime = "application/x-mrtrix-image-format-gz"
     ext = ".mif.gz"
 
 
 class ImageHeader(BaseMrtrixImage):
 
     ext = ".mih"
+    iana_mime = "application/x-mrtrix-image-header"
 
-    @hook.required
     @property
     def data_file(self):
         return ImageDataFile(self.data_fspath)
@@ -120,3 +86,46 @@ def __attrs_post_init__(self):
 class ImageDataFile(File):
 
     ext = ".dat"
+
+
+@extra_implementation(FileSet.read_metadata)
+def mrtrix_read_metadata(
+    mif: BaseMrtrixImage, selected_keys: ty.Optional[ty.Collection[str]] = None
+) -> ty.Mapping[str, ty.Any]:
+    metadata = {}
+    with open(mif.fspath, "rb") as f:
+        line = f.readline()
+        if line != mif.magic_number:
+            raise FormatMismatchError(
+                f"Magic line {line} doesn't match reference {mif.magic_number}"
+            )
+        line = f.readline().decode("utf-8")
+        while line and line != "END\n":
+            key, value = line.split(": ", maxsplit=1)
+            if "," in value:
+                try:
+                    value = [int(v) for v in value.split(",")]
+                except ValueError:
+                    try:
+                        value = [float(v) for v in value.split(",")]
+                    except ValueError:
+                        pass
+            else:
+                try:
+                    value = int(value)
+                except ValueError:
+                    try:
+                        value = float(value)
+                    except ValueError:
+                        pass
+            if key in metadata:
+                if isinstance(metadata[key], MultiLineMetadataValue):
+                    metadata[key].append(value)
+                else:
+                    metadata[key] = MultiLineMetadataValue([metadata[key], value])
+            else:
+                metadata[key] = value
+            line = f.readline().decode("utf-8")
+    if selected_keys:
+        metadata = {k: v for k, v in metadata.items() if k in selected_keys}
+    return metadata