diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index 94ffe4c..9d936fa 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -112,6 +112,8 @@ jobs:
           -e related-packages/fileformats
           -e related-packages/fileformats-extras
           -e .[dev,test]
+      - name: Install development Pydra
+        run: pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax
       - name: Generate task specifications
         run: >
           ./generate.py
@@ -138,59 +140,12 @@ jobs:
           name: VersionFile
           path: mrtrix3_version.txt
 
-  devcheck:
-    needs: [generate]
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.8, 3.11]  # Check oldest and newest versions
-        pip-flags: ['', '--editable']
-        pydra:
-        - 'pydra'
-        - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Download version file
-      uses: actions/download-artifact@v4
-      with:
-        name: VersionFile
-        path: mrtrix3_version.txt
-    - name: Extract Mrtrix version
-      run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
-    - name: Download auto-gen pydra
-      uses: actions/download-artifact@v4
-      with:
-        name: AutoGen
-        path: pydra/tasks/mrtrix3/${{ 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"
-        pip install ${{ matrix.pip-flags }} ".[dev]"
-        python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-        python -c "import pydra.tasks.mrtrix3.$SUBPKG_NAME"
-        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-
   test:
     needs: [generate]
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.11]
+        python-version: [3.11, 3.13]
     defaults:
       run:
         shell: bash -l {0}
@@ -246,13 +201,15 @@ jobs:
         -e ./related-packages/fileformats
         -e ./related-packages/fileformats-extras
         -e '.[test]'
-    - name: Test with pytest
-      run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
-    - uses: codecov/codecov-action@v2
-      if: ${{ always() }}
+    - name: Install development Pydra
+      run: pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax
+    # - name: Test with pytest
+    #   run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
+    # - uses: codecov/codecov-action@v2
+    #   if: ${{ always() }}
 
   deploy-fileformats:
-    needs: [devcheck, test]
+    needs: [test]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
@@ -323,9 +280,8 @@ jobs:
         password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
         packages-dir: ./related-packages/fileformats-extras/dist
 
-
   deploy:
-    needs: [devcheck, test, deploy-fileformats, deploy-fileformats-extras]
+    needs: [test, deploy-fileformats, deploy-fileformats-extras]
     runs-on: ubuntu-latest
     steps:
     - name: Checkout repo
diff --git a/generate.py b/generate.py
index f832195..833ae27 100755
--- a/generate.py
+++ b/generate.py
@@ -7,6 +7,7 @@
 import typing as ty
 from importlib import import_module
 import logging
+import tempfile
 from traceback import format_exc
 import re
 from tqdm import tqdm
@@ -15,9 +16,10 @@
 import black.parsing
 from fileformats.core import FileSet
 from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, ImageOut, Tracks
-from pydra.engine.helpers import make_klass
-from pydra.engine import specs
+from pydra.design import shell
+from pydra.utils.typing import MultiInputObj
 from pydra.utils import add_exc_note
+from pydra.engine.helpers import list_fields
 
 
 logger = logging.getLogger("pydra-auto-gen")
@@ -176,7 +178,7 @@ def auto_gen_mrtrix3_pydra(
     manual_path = output_dir / "pydra" / "tasks" / "mrtrix3" / "manual"
     if manual_path.exists():
         for manual_file in manual_path.iterdir():
-            manual_cmd = manual_file.stem[:-1]
+            manual_cmd = manual_file.stem
             if not manual_cmd.startswith(".") and not manual_cmd.startswith("__"):
                 manual_cmds.append(manual_cmd)
 
@@ -205,9 +207,9 @@ def auto_gen_mrtrix3_pydra(
 
     # Write init
     init_path = output_dir / "pydra" / "tasks" / "mrtrix3" / pkg_version / "__init__.py"
-    imports = "\n".join(f"from .{c}_ import {pascal_case_task_name(c)}" for c in cmds)
+    imports = "\n".join(f"from .{c} import {pascal_case_task_name(c)}" for c in cmds)
     imports += "\n" + "\n".join(
-        f"from ..manual.{c}_ import {pascal_case_task_name(c)}" for c in manual_cmds
+        f"from ..manual.{c} import {pascal_case_task_name(c)}" for c in manual_cmds
     )
     init_path.write_text(f"# Auto-generated, do not edit\n\n{imports}\n")
 
@@ -267,20 +269,29 @@ def auto_gen_cmd(
         code_str = code_str.replace(f"{old_name}_output", f"{cmd_name}_output")
         code_str = re.sub(r"(?<!\w)5tt_in(?!\w)", "in_5tt", code_str)
     try:
-        code_str = black.format_file_contents(
-            code_str, fast=False, mode=black.FileMode()
-        )
-    except black.report.NothingChanged:
-        pass
-    except black.parsing.InvalidInput:
-        if log_errors:
-            logger.error("Could not parse generated interface for '%s'", cmd_name)
-            logger.error(format_exc())
-            return []
-        else:
-            raise
+        try:
+            code_str = black.format_file_contents(
+                code_str, fast=False, mode=black.FileMode()
+            )
+        except black.report.NothingChanged:
+            pass
+        except black.parsing.InvalidInput:
+            if log_errors:
+                logger.error(
+                    "Could not parse generated interface (%s) for '%s'", cmd_name
+                )
+                logger.error(format_exc())
+                return []
+            else:
+                raise
+    except Exception as e:
+        tfile = Path(tempfile.mkdtemp()) / (cmd_name + ".py")
+        tfile.write_text(code_str)
+        e.add_note(f"when formatting {cmd_name}")
+        e.add_note(f"generated file is {tfile}")
+        raise e
     output_path = (
-        output_dir / "pydra" / "tasks" / "mrtrix3" / pkg_version / (cmd_name + "_.py")
+        output_dir / "pydra" / "tasks" / "mrtrix3" / pkg_version / (cmd_name + ".py")
     )
     output_path.parent.mkdir(exist_ok=True, parents=True)
     with open(output_path, "w") as f:
@@ -301,9 +312,12 @@ def auto_gen_cmd(
 def auto_gen_test(cmd_name: str, output_dir: Path, log_errors: bool, pkg_version: str):
     tests_dir = output_dir / "pydra" / "tasks" / "mrtrix3" / pkg_version / "tests"
     tests_dir.mkdir(exist_ok=True)
-    module = import_module(f"pydra.tasks.mrtrix3.{pkg_version}.{cmd_name}_")
-    interface = getattr(module, pascal_case_task_name(cmd_name))
-    task = interface()
+    module = import_module(f"pydra.tasks.mrtrix3.{pkg_version}.{cmd_name}")
+    definition_klass = getattr(module, pascal_case_task_name(cmd_name))
+
+    input_fields = list_fields(definition_klass)
+    output_fields = list_fields(definition_klass.Outputs)
+    output_fields_dict = {f.name: f for f in output_fields}
 
     code_str = f"""# Auto-generated test for {cmd_name}
 
@@ -324,9 +338,8 @@ def test_{cmd_name.lower()}(tmp_path, cli_parse_only):
 
     task = {pascal_case_task_name(cmd_name)}(
 """
-    input_fields = attrs.fields(type(task.inputs))
-    output_fields = attrs.fields(make_klass(task.output_spec))
 
+    field: shell.arg
     for field in input_fields:
         if field.name in (
             "executable",
@@ -335,6 +348,7 @@ def test_{cmd_name.lower()}(tmp_path, cli_parse_only):
             "quiet",
             "info",
             "nthreads",
+            "additional_args",
             "config",
             "args",
         ):
@@ -355,12 +369,12 @@ def get_value(type_):
                 value = "True"
             elif type_ is Path:
                 try:
-                    output_field = getattr(output_fields, field.name)
+                    output_field = output_fields_dict[field.name]
                 except AttributeError:
                     pass
                 else:
                     output_type = output_field.type
-                    if ty.get_origin(output_type) is specs.MultiInputObj:
+                    if ty.get_origin(output_type) is MultiInputObj:
                         output_type = ty.get_args(output_type)[0]
                     if ty.get_origin(output_type) in (list, tuple):
                         output_type = ty.get_args(output_type)[0]
@@ -369,7 +383,7 @@ def get_value(type_):
                 value = f"{output_type.__name__}.sample()"
             elif ty.get_origin(type_) is ty.Union:
                 value = get_value(ty.get_args(type_)[0])
-            elif ty.get_origin(type_) is specs.MultiInputObj:
+            elif ty.get_origin(type_) is MultiInputObj:
                 value = "[" + get_value(ty.get_args(type_)[0]) + "]"
             elif ty.get_origin(type_) and issubclass(ty.get_origin(type_), ty.Sequence):
                 value = (
@@ -386,8 +400,8 @@ def get_value(type_):
 
         if field.default is not attrs.NOTHING:
             value = field.default
-        elif "allowed_values" in field.metadata:
-            value = repr(field.metadata["allowed_values"][0])
+        elif field.allowed_values:
+            value = repr(field.allowed_values[0])
         else:
             value = get_value(field.type)
 
diff --git a/pydra/tasks/mrtrix3/manual/mrcalc.py b/pydra/tasks/mrtrix3/manual/mrcalc.py
new file mode 100644
index 0000000..27ae7c9
--- /dev/null
+++ b/pydra/tasks/mrtrix3/manual/mrcalc.py
@@ -0,0 +1,291 @@
+import typing as ty
+from pathlib import Path  # noqa: F401
+from enum import Enum
+from fileformats.generic import File, Directory  # noqa: F401
+from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from pydra.engine import specs
+from pydra.design import shell
+from pydra.utils.typing import MultiInputObj
+
+
+class MrCalcOp(Enum):
+    abs = "abs"  # return absolute value (magnitude) of real or complex number
+    neg = "neg"  # negative value
+    add = "add"  # add values
+    subtract = "subtract"  # subtract values
+    multiply = "multiply"  # multiply values
+    divide = "divide"  # divide values
+    modulo = "modulo"  # modulo operation
+    min = "min"  # minimum value
+    max = "max"  # maximum value
+    lt = "lt"  # less than comparison
+    gt = "gt"  # greater than comparison
+    le = "le"  # less than or equal to comparison
+    ge = "ge"  # greater than or equal to comparison
+    eq = "eq"  # equal to comparison
+    neq = "neq"  # not equal to comparison
+    if_ = "if"  # if-else condition
+    replace = "replace"  # replace values
+    sqrt = "sqrt"  # square root
+    pow = "pow"  # power operation
+    round = "round"  # round to nearest integer
+    ceil = "ceil"  # round up to nearest integer
+    floor = "floor"  # round down to nearest integer
+    not_ = "not"  # logical NOT operation
+    and_ = "and"  # logical AND operation
+    or_ = "or"  # logical OR operation
+    xor = "xor"  # logical XOR operation
+    isnan = "isnan"  # check if value is NaN
+    isinf = "isinf"  # check if value is infinity
+    finite = "finite"  # check if value is finite
+    complex = "complex"  # convert to complex number
+    polar = "polar"  # convert to polar coordinates
+    real = "real"  # get real part of complex number
+    imag = "imag"  # get imaginary part of complex number
+    phase = "phase"  # get phase angle of complex number
+    conj = "conj"  # complex conjugate
+    proj = "proj"  # projection of complex number
+    exp = "exp"  # exponential function
+    log = "log"  # natural logarithm
+    log10 = "log10"  # base-10 logarithm
+    cos = "cos"  # cosine function
+    sin = "sin"  # sine function
+    tan = "tan"  # tangent function
+    acos = "acos"  # arc cosine function
+    asin = "asin"  # arc sine function
+    atan = "atan"  # arc tangent function
+    cosh = "cosh"  # hyperbolic cosine function
+    sinh = "sinh"  # hyperbolic sine function
+    tanh = "tanh"  # hyperbolic tangent function
+    acosh = "acosh"  # inverse hyperbolic cosine function
+    asinh = "asinh"  # inverse hyperbolic sine function
+    atanh = "atanh"  # inverse hyperbolic tangent function
+
+
+def operations_formatter(
+    operations: ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]]
+):
+    return " ".join(
+        [
+            f"{' '.join([str(i) for i in operands])} -{op.value}"
+            for operands, op in operations
+        ]
+    )
+
+
+class MrCalc(specs.ShellDef["MrCalc.Outputs"]):
+    """This command will only compute per-voxel operations. Use 'mrmath' to compute
+    summary statistics across images or along image axes.
+
+        This command uses a stack-based syntax, with operators (specified using options)
+        operating on the top-most entries (i.e. images or values) in the stack. Operands
+        (values or images) are pushed onto the stack in the order they appear
+        (as arguments) on the command-line, and operators (specified as options)
+        operate on and consume the top-most entries in the stack, and push their
+        output as a new entry on the stack.
+
+        As an additional feature, this command will allow images with different
+        dimensions to be processed, provided they satisfy the following conditions:
+        for each axis, the dimensions match if they are the same size, or one of them
+        has size one. In the latter case, the entire image will be replicated along that
+        axis. This allows for example a 4D image of size [ X Y Z N ] to be added to a
+        3D image of size [ X Y Z ], as if it consisted of N copies of the 3D image along
+        the 4th axis (the missing dimension is assumed to have size 1). Another example
+        would a single-voxel 4D image of size [ 1 1 1 N ], multiplied by a 3D image of
+        size [ X Y Z ], which would allow the creation of a 4D image where each volume
+        consists of the 3D image scaled by the corresponding value for that volume in
+        the single-voxel image.
+
+
+        Example usages
+        --------------
+
+
+        Double the value stored in every voxel:
+
+            `$ mrcalc a.mif 2 -mult r.mif`
+
+            This performs the operation: r = 2*a  for every voxel a,r in images a.mif
+            and r.mif respectively.
+
+
+        A more complex example:
+
+            `$ mrcalc a.mif -neg b.mif -div -exp 9.3 -mult r.mif`
+
+            This performs the operation: r = 9.3*exp(-a/b)
+
+
+        Another complex example:
+
+            `$ mrcalc a.mif b.mif -add c.mif d.mif -mult 4.2 -add -div r.mif`
+
+            This performs: r = (a+b)/(c*d+4.2).
+
+
+        Rescale the densities in a SH l=0 image:
+
+            `$ mrcalc ODF_CSF.mif 4 pi -mult -sqrt -div ODF_CSF_scaled.mif`
+
+            This applies the spherical harmonic basis scaling factor: 1.0/sqrt(4*pi),
+            such that a single-tissue voxel containing the same intensities as the
+            response function of that tissue should contain the value 1.0.
+
+
+        References
+        ----------
+
+            Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.;
+            Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A.
+            MRtrix3: A fast, flexible and open software framework for medical image
+            processing and visualisation. NeuroImage, 2019, 202, 116137
+
+
+        MRtrix
+        ------
+
+            Version:3.0.4-691-g05465c3c-dirty, built Sep 29 2023
+
+            Author: J-Donald Tournier (jdtournier@gmail.com)
+
+            Copyright: Copyright (c) 2008-2023 the MRtrix3 contributors.
+
+    This Source Code Form is subject to the terms of the Mozilla Public
+    License, v. 2.0. If a copy of the MPL was not distributed with this
+    file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+    Covered Software is provided under this License on an "as is"
+    basis, without warranty of any kind, either expressed, implied, or
+    statutory, including, without limitation, warranties that the
+    Covered Software is free of defects, merchantable, fit for a
+    particular purpose or non-infringing.
+    See the Mozilla Public License v. 2.0 for more details.
+
+    For more details, see http://www.mrtrix.org/.
+    """
+
+    Op = Operator = MrCalcOp
+
+    executable = "mrcalc"
+
+    operations: list[tuple[list[ImageIn | float], MrCalcOp]] = shell.arg(
+        argstr="",
+        sep=" ",
+        position=0,
+        formatter=operations_formatter,
+        help=(
+            "an input image, intensity value, or the special keywords 'rand' "
+            "(random number between 0 and 1) or 'randn' (random number from unit "
+            "std.dev. normal distribution) or the mathematical constants 'e' and "
+            "'pi'."
+        ),
+    )
+
+    # Data type options Option Group
+
+    datatype: str = shell.arg(
+        argstr="-datatype",
+        help="specify output image data type.",
+        allowed_values=[
+            "float16",
+            "float16",
+            "float16le",
+            "float16be",
+            "float32",
+            "float32le",
+            "float32be",
+            "float64",
+            "float64le",
+            "float64be",
+            "int64",
+            "uint64",
+            "int64le",
+            "uint64le",
+            "int64be",
+            "uint64be",
+            "int32",
+            "uint32",
+            "int32le",
+            "uint32le",
+            "int32be",
+            "uint32be",
+            "int16",
+            "uint16",
+            "int16le",
+            "uint16le",
+            "int16be",
+            "uint16be",
+            "cfloat16",
+            "cfloat16le",
+            "cfloat16be",
+            "cfloat32",
+            "cfloat32le",
+            "cfloat32be",
+            "cfloat64",
+            "cfloat64le",
+            "cfloat64be",
+            "int8",
+            "uint8",
+            "bit",
+        ],
+    )
+
+    # Standard options
+
+    info: bool = shell.arg(
+        argstr="-info",
+        help="""display information messages.""",
+    )
+
+    quiet: bool = shell.arg(
+        argstr="-quiet",
+        help=(
+            "do not display information messages or progress status; alternatively, "
+            "this can be achieved by setting the MRTRIX_QUIET environment variable to "
+            "a non-empty string."
+        ),
+    )
+
+    debug: bool = shell.arg(
+        argstr="-debug",
+        help="""display debugging messages.""",
+    )
+
+    force: bool = shell.arg(
+        argstr="-force",
+        help=(
+            "force overwrite of output files (caution: using the same file as input and "
+            "output might cause unexpected behaviour)."
+        ),
+    )
+
+    nthreads: int = shell.arg(
+        argstr="-nthreads",
+        help=(
+            "use this number of threads in multi-threaded applications (set to 0 to "
+            "disable multi-threading)."
+        ),
+    )
+
+    config: MultiInputObj[tuple[str, str]] = shell.arg(
+        argstr="-config",
+        help="""temporarily set the value of an MRtrix config file entry.""",
+    )
+
+    help: bool = shell.arg(
+        argstr="-help",
+        help="""display this information page and exit.""",
+    )
+
+    version: bool = shell.arg(
+        argstr="-version",
+        help="""display version information and exit.""",
+    )
+
+    class Outputs(specs.ShellOutputs):
+        output: ImageOut = shell.outarg(
+            argstr="",
+            position=-1,
+            help="""the output image.""",
+            path_template="mrcalc_output.mif",
+        )
diff --git a/pydra/tasks/mrtrix3/manual/mrcalc_.py b/pydra/tasks/mrtrix3/manual/mrcalc_.py
deleted file mode 100644
index aff91a9..0000000
--- a/pydra/tasks/mrtrix3/manual/mrcalc_.py
+++ /dev/null
@@ -1,308 +0,0 @@
-import typing as ty
-from pathlib import Path  # noqa: F401
-from enum import Enum
-from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
-from pydra.engine import specs, ShellCommandTask
-
-
-class MrCalcOp(Enum):
-    abs = "abs"  # return absolute value (magnitude) of real or complex number
-    neg = "neg"  # negative value
-    add = "add"  # add values
-    subtract = "subtract"  # subtract values
-    multiply = "multiply"  # multiply values
-    divide = "divide"  # divide values
-    modulo = "modulo"  # modulo operation
-    min = "min"  # minimum value
-    max = "max"  # maximum value
-    lt = "lt"  # less than comparison
-    gt = "gt"  # greater than comparison
-    le = "le"  # less than or equal to comparison
-    ge = "ge"  # greater than or equal to comparison
-    eq = "eq"  # equal to comparison
-    neq = "neq"  # not equal to comparison
-    if_ = "if"  # if-else condition
-    replace = "replace"  # replace values
-    sqrt = "sqrt"  # square root
-    pow = "pow"  # power operation
-    round = "round"  # round to nearest integer
-    ceil = "ceil"  # round up to nearest integer
-    floor = "floor"  # round down to nearest integer
-    not_ = "not"  # logical NOT operation
-    and_ = "and"  # logical AND operation
-    or_ = "or"  # logical OR operation
-    xor = "xor"  # logical XOR operation
-    isnan = "isnan"  # check if value is NaN
-    isinf = "isinf"  # check if value is infinity
-    finite = "finite"  # check if value is finite
-    complex = "complex"  # convert to complex number
-    polar = "polar"  # convert to polar coordinates
-    real = "real"  # get real part of complex number
-    imag = "imag"  # get imaginary part of complex number
-    phase = "phase"  # get phase angle of complex number
-    conj = "conj"  # complex conjugate
-    proj = "proj"  # projection of complex number
-    exp = "exp"  # exponential function
-    log = "log"  # natural logarithm
-    log10 = "log10"  # base-10 logarithm
-    cos = "cos"  # cosine function
-    sin = "sin"  # sine function
-    tan = "tan"  # tangent function
-    acos = "acos"  # arc cosine function
-    asin = "asin"  # arc sine function
-    atan = "atan"  # arc tangent function
-    cosh = "cosh"  # hyperbolic cosine function
-    sinh = "sinh"  # hyperbolic sine function
-    tanh = "tanh"  # hyperbolic tangent function
-    acosh = "acosh"  # inverse hyperbolic cosine function
-    asinh = "asinh"  # inverse hyperbolic sine function
-    atanh = "atanh"  # inverse hyperbolic tangent function
-
-
-def operations_formatter(
-    operations: ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]]
-):
-    return " ".join(
-        [
-            f"{' '.join([str(i) for i in operands])} -{op.value}"
-            for operands, op in operations
-        ]
-    )
-
-
-input_fields = [
-    # Arguments
-    (
-        "operations",
-        ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]],
-        {
-            "argstr": "",
-            "sep": " ",
-            "position": 0,
-            "formatter": operations_formatter,
-            "help_string": """an input image, intensity value, or the special keywords 'rand' (random number between 0 and 1) or 'randn' (random number from unit std.dev. normal distribution) or the mathematical constants 'e' and 'pi'.""",
-            "mandatory": True,
-        },
-    ),
-    (
-        "output",
-        Path,
-        {
-            "argstr": "",
-            "position": -1,
-            "help_string": """the output image.""",
-            "output_file_template": "mrcalc_output.mif",
-        },
-    ),
-    # Data type options Option Group
-    (
-        "datatype",
-        str,
-        {
-            "argstr": "-datatype",
-            "help_string": "specify output image data type.",
-            "allowed_values": [
-                "float16",
-                "float16",
-                "float16le",
-                "float16be",
-                "float32",
-                "float32le",
-                "float32be",
-                "float64",
-                "float64le",
-                "float64be",
-                "int64",
-                "uint64",
-                "int64le",
-                "uint64le",
-                "int64be",
-                "uint64be",
-                "int32",
-                "uint32",
-                "int32le",
-                "uint32le",
-                "int32be",
-                "uint32be",
-                "int16",
-                "uint16",
-                "int16le",
-                "uint16le",
-                "int16be",
-                "uint16be",
-                "cfloat16",
-                "cfloat16le",
-                "cfloat16be",
-                "cfloat32",
-                "cfloat32le",
-                "cfloat32be",
-                "cfloat64",
-                "cfloat64le",
-                "cfloat64be",
-                "int8",
-                "uint8",
-                "bit",
-            ],
-        },
-    ),
-    # Standard options
-    (
-        "info",
-        bool,
-        {
-            "argstr": "-info",
-            "help_string": """display information messages.""",
-        },
-    ),
-    (
-        "quiet",
-        bool,
-        {
-            "argstr": "-quiet",
-            "help_string": """do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.""",
-        },
-    ),
-    (
-        "debug",
-        bool,
-        {
-            "argstr": "-debug",
-            "help_string": """display debugging messages.""",
-        },
-    ),
-    (
-        "force",
-        bool,
-        {
-            "argstr": "-force",
-            "help_string": """force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).""",
-        },
-    ),
-    (
-        "nthreads",
-        int,
-        {
-            "argstr": "-nthreads",
-            "help_string": """use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).""",
-        },
-    ),
-    (
-        "config",
-        specs.MultiInputObj[ty.Tuple[str, str]],
-        {
-            "argstr": "-config",
-            "help_string": """temporarily set the value of an MRtrix config file entry.""",
-        },
-    ),
-    (
-        "help",
-        bool,
-        {
-            "argstr": "-help",
-            "help_string": """display this information page and exit.""",
-        },
-    ),
-    (
-        "version",
-        bool,
-        {
-            "argstr": "-version",
-            "help_string": """display version information and exit.""",
-        },
-    ),
-]
-
-MrCalcInputSpec = specs.SpecInfo(
-    name="mrcalc_input", fields=input_fields, bases=(specs.ShellSpec,)
-)
-
-
-output_fields = [
-    (
-        "output",
-        ImageOut,
-        {
-            "help_string": """the output image.""",
-        },
-    ),
-]
-MrCalcOutputSpec = specs.SpecInfo(
-    name="mrcalc_output", fields=output_fields, bases=(specs.ShellOutSpec,)
-)
-
-
-class MrCalc(ShellCommandTask):
-    """This command will only compute per-voxel operations. Use 'mrmath' to compute summary statistics across images or along image axes.
-
-        This command uses a stack-based syntax, with operators (specified using options) operating on the top-most entries (i.e. images or values) in the stack. Operands (values or images) are pushed onto the stack in the order they appear (as arguments) on the command-line, and operators (specified as options) operate on and consume the top-most entries in the stack, and push their output as a new entry on the stack.
-
-        As an additional feature, this command will allow images with different dimensions to be processed, provided they satisfy the following conditions: for each axis, the dimensions match if they are the same size, or one of them has size one. In the latter case, the entire image will be replicated along that axis. This allows for example a 4D image of size [ X Y Z N ] to be added to a 3D image of size [ X Y Z ], as if it consisted of N copies of the 3D image along the 4th axis (the missing dimension is assumed to have size 1). Another example would a single-voxel 4D image of size [ 1 1 1 N ], multiplied by a 3D image of size [ X Y Z ], which would allow the creation of a 4D image where each volume consists of the 3D image scaled by the corresponding value for that volume in the single-voxel image.
-
-
-        Example usages
-        --------------
-
-
-        Double the value stored in every voxel:
-
-            `$ mrcalc a.mif 2 -mult r.mif`
-
-            This performs the operation: r = 2*a  for every voxel a,r in images a.mif and r.mif respectively.
-
-
-        A more complex example:
-
-            `$ mrcalc a.mif -neg b.mif -div -exp 9.3 -mult r.mif`
-
-            This performs the operation: r = 9.3*exp(-a/b)
-
-
-        Another complex example:
-
-            `$ mrcalc a.mif b.mif -add c.mif d.mif -mult 4.2 -add -div r.mif`
-
-            This performs: r = (a+b)/(c*d+4.2).
-
-
-        Rescale the densities in a SH l=0 image:
-
-            `$ mrcalc ODF_CSF.mif 4 pi -mult -sqrt -div ODF_CSF_scaled.mif`
-
-            This applies the spherical harmonic basis scaling factor: 1.0/sqrt(4*pi), such that a single-tissue voxel containing the same intensities as the response function of that tissue should contain the value 1.0.
-
-
-        References
-        ----------
-
-            Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137
-
-
-        MRtrix
-        ------
-
-            Version:3.0.4-691-g05465c3c-dirty, built Sep 29 2023
-
-            Author: J-Donald Tournier (jdtournier@gmail.com)
-
-            Copyright: Copyright (c) 2008-2023 the MRtrix3 contributors.
-
-    This Source Code Form is subject to the terms of the Mozilla Public
-    License, v. 2.0. If a copy of the MPL was not distributed with this
-    file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-    Covered Software is provided under this License on an "as is"
-    basis, without warranty of any kind, either expressed, implied, or
-    statutory, including, without limitation, warranties that the
-    Covered Software is free of defects, merchantable, fit for a
-    particular purpose or non-infringing.
-    See the Mozilla Public License v. 2.0 for more details.
-
-    For more details, see http://www.mrtrix.org/.
-    """
-
-    Op = Operator = MrCalcOp
-
-    executable = "mrcalc"
-    input_spec = MrCalcInputSpec
-    output_spec = MrCalcOutputSpec
diff --git a/pyproject.toml b/pyproject.toml
index 3aaa352..4c8109e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ requires-python = ">=3.8"
 dependencies = [
     "fileformats-medimage_mrtrix3 >=3.0.4a5",
     "numpy",
-    "pydra >=0.23",
+    "pydra >=0.25",
 ]
 license = { file = "LICENSE" }
 authors = [{ name = "Thomas G. Close", email = "tom.g.close@gmail.com" }]
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 7015c6f..1cfc522 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py
@@ -1,77 +1,47 @@
-from fileformats.core import converter
+import typing as ty
+from fileformats.core import converter, FileSet
 from fileformats.medimage.base import MedicalImage
-
 from fileformats.medimage_mrtrix3 import (
     ImageFormat as MrtrixImage,
     ImageHeader as MrtrixImageHeader,
     ImageFormatGz as MrtrixImageGz,
 )
 
-try:
-    from pydra.tasks.mrtrix3.v3_0 import MrConvert
-except ImportError:
-    from pydra.tasks.mrtrix3.latest import mrconvert as MrConvert
-
-    in_out_file_kwargs = {"in_file": "input", "out_file": "output"}
-else:
-    in_out_file_kwargs = {}
+from pydra.tasks.mrtrix3.v3_0 import MrConvert
 
 
-@converter(
-    source_format=MedicalImage,
-    target_format=MrtrixImageGz,
-    out_ext=MrtrixImageGz.ext,
-    **in_out_file_kwargs,
-)
-@converter(
-    source_format=MedicalImage,
-    target_format=MrtrixImageHeader,
-    out_ext=MrtrixImageHeader.ext,
-    **in_out_file_kwargs,
-)
-@converter(
-    source_format=MedicalImage,
-    target_format=MrtrixImage,
-    out_ext=MrtrixImage.ext,
-    **in_out_file_kwargs,
-)
-def mrconvert(name, out_ext: str, **kwargs):
-    """Initiate an MRConvert task with the output file extension set
+def out_file_template(fileformat: ty.Type[FileSet]) -> str:
+    """Return the output file name for a given file format
 
     Parameters
     ----------
-    name : str
-        name of the converter task
-    out_ext : str
-        extension of the output file, used by MRConvert to determine the desired format
+    fileformat : type
+        the file format class
 
     Returns
     -------
-    pydra.ShellCommandTask
-        the converter task
+    str
+        the output file name
     """
-    return MrConvert(name=name, out_file="out" + out_ext, **kwargs)
+    return "out" + fileformat.ext
 
 
-# @converter(
-#     source_format=MedicalImage,
-#     target_format=MrtrixImageHeader,
-#     out_ext=MrtrixImageHeader.ext,
-#     **in_out_file_kwargs,
-# )
-# def mrconvert2(name, out_ext: str, **kwargs):
-#     """Initiate an MRConvert task with the output file extension set
+# Register MrConvert as a converter for MrTrix formats
 
-#     Parameters
-#     ----------
-#     name : str
-#         name of the converter task
-#     out_ext : str
-#         extension of the output file, used by MRConvert to determine the desired format
+converter(
+    source_format=MedicalImage,
+    target_format=MrtrixImageGz,
+    out_file=out_file_template(MrtrixImageGz),
+)(MrConvert)
 
-#     Returns
-#     -------
-#     pydra.ShellCommandTask
-#         the converter task
-#     """
-#     return MrConvert(name=name, out_file="out" + out_ext, **kwargs)
+converter(
+    source_format=MedicalImage,
+    target_format=MrtrixImageHeader,
+    out_file=out_file_template(MrtrixImageHeader),
+)(MrConvert)
+
+converter(
+    source_format=MedicalImage,
+    target_format=MrtrixImage,
+    out_file=out_file_template(MrtrixImage),
+)(MrConvert)