updated generated code from latest dev branch

Author: tclose

pydra/tasks/mrtrix3/v3_1/afdconnectivity.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -20,7 +20,7 @@ class AfdConnectivity(shell.Task["AfdConnectivity.Outputs"]):
 
         Note that the sum of the AFD is normalised by streamline length to account for subject differences in fibre bundle length. This normalisation results in a measure that is more related to the cross-sectional volume of the tract (and therefore 'connectivity'). Note that SIFT-ed tract count is a superior measure because it is unaffected by tangential yet unrelated fibres. However, AFD connectivity may be used as a substitute when Anatomically Constrained Tractography is not possible due to uncorrectable EPI distortions, and SIFT may therefore not be as effective.
 
-        Longer discussion regarding this command can additionally be found at: https://mrtrix.readthedocs.io/en/3.0.4/concepts/afd_connectivity.html (as well as in the relevant reference).
+        Longer discussion regarding this command can additionally be found at: https://mrtrix.readthedocs.io/en/3.0.7/concepts/afd_connectivity.html (as well as in the relevant reference).
 
 
         References
@@ -34,7 +34,7 @@ class AfdConnectivity(shell.Task["AfdConnectivity.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: David Raffelt (david.raffelt@florey.edu.au) and Robert E. Smith (robert.smith@florey.edu.au)
 

pydra/tasks/mrtrix3/v3_1/amp2response.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -26,7 +26,7 @@ class Amp2Response(shell.Task["Amp2Response.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: Robert E. Smith (robert.smith@florey.edu.au) and J-Donald Tournier (jdtournier@gmail.com)
 
@@ -59,7 +59,7 @@ class Amp2Response(shell.Task["Amp2Response.Outputs"]):
         position=2,
         help="""the mask containing the voxels from which to estimate the response function""",
     )
-    directions_image: ImageIn = shell.arg(
+    fibre_directions: ImageIn = shell.arg(
         argstr="",
         position=3,
         help="""a 4D image containing the estimated fibre directions""",

pydra/tasks/mrtrix3/v3_1/amp2sh.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -12,10 +12,10 @@
 class Amp2Sh(shell.Task["Amp2Sh.Outputs"]):
     """The spherical harmonic decomposition is calculated by least-squares linear fitting to the amplitude data.
 
-        The directions can be defined either as a DW gradient scheme (for example to compute the SH representation of the DW signal), a set of [az el] pairs as output by the dirgen command, or a set of [ x y z ] directions in Cartesian coordinates. The DW gradient scheme or direction set can be supplied within the input image header or using the -gradient or -directions option. Note that if a direction set and DW gradient scheme can be found, the direction set will be used by default.
+        The directions can be defined either as a DW gradient scheme (for example to compute the SH representation of the DW signal), a set of [az in] pairs as output by the dirgen command, or a set of [ x y z ] directions in Cartesian coordinates. The DW gradient scheme or direction set can be supplied within the input image header or using the -gradient or -directions option. Note that if a direction set and DW gradient scheme can be found, the direction set will be used by default.
 
         The spherical harmonic coefficients are stored according to the conventions described in the main documentation, which can be found at the following link:
-    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    https://mrtrix.readthedocs.io/en/3.0.7/concepts/spherical_harmonics.html
 
 
         References
@@ -27,7 +27,7 @@ class Amp2Sh(shell.Task["Amp2Sh.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: J-Donald Tournier (jdtournier@gmail.com)
 
@@ -70,7 +70,7 @@ class Amp2Sh(shell.Task["Amp2Sh.Outputs"]):
     directions: File | None = shell.arg(
         default=None,
         argstr="-directions",
-        help="""the directions corresponding to the input amplitude image used to sample AFD. By default this option is not required providing the direction set is supplied in the amplitude image. This should be supplied as a list of directions [az el], as generated using the dirgen command, or as a list of [ x y z ] Cartesian coordinates.""",
+        help="""the directions corresponding to the input amplitude image used to sample AFD. By default this option is not required providing the direction set is supplied in the amplitude image. This should be supplied as a list of directions [az in], as generated using the dirgen command, or as a list of [ x y z ] Cartesian coordinates.""",
     )
     rician: ImageIn | None = shell.arg(
         default=None,
@@ -101,10 +101,11 @@ class Amp2Sh(shell.Task["Amp2Sh.Outputs"]):
     )
 
     # Stride options:
-    strides: ty.Any = shell.arg(
+    strides: ImageIn | list[int] | None = shell.arg(
         default=None,
         argstr="-strides",
         help="""specify the strides of the output data in memory; either as a comma-separated list of (signed) integers, or as a template image from which the strides shall be extracted and used. The actual strides produced will depend on whether the output image format can support it.""",
+        sep=",",
     )
 
     # Standard options

pydra/tasks/mrtrix3/v3_1/connectome2tck.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -68,7 +68,7 @@ class Connectome2Tck(shell.Task["Connectome2Tck.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: Robert E. Smith (robert.smith@florey.edu.au)
 

pydra/tasks/mrtrix3/v3_1/connectomeedit.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -20,7 +20,7 @@ class ConnectomeEdit(shell.Task["ConnectomeEdit.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: Matteo Frigo (matteo.frigo@inria.fr)
 
@@ -43,7 +43,7 @@ class ConnectomeEdit(shell.Task["ConnectomeEdit.Outputs"]):
     executable = "connectomeedit"
 
     # Arguments
-    input: str = shell.arg(
+    in_file: File = shell.arg(
         argstr="",
         position=1,
         help="""the input connectome.""",
@@ -60,11 +60,6 @@ class ConnectomeEdit(shell.Task["ConnectomeEdit.Outputs"]):
             "zero_diagonal",
         ],
     )
-    output: str = shell.arg(
-        argstr="",
-        position=3,
-        help="""the output connectome.""",
-    )
 
     # Options
 
@@ -102,4 +97,9 @@ class ConnectomeEdit(shell.Task["ConnectomeEdit.Outputs"]):
     )
 
     class Outputs(shell.Outputs):
-        pass
+        out_file: File = shell.outarg(
+            argstr="",
+            position=3,
+            path_template="out_file.txt",
+            help="""the output connectome.""",
+        )

pydra/tasks/mrtrix3/v3_1/connectomestats.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -37,7 +37,7 @@ class ConnectomeStats(shell.Task["ConnectomeStats.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: Robert E. Smith (robert.smith@florey.edu.au)
 

pydra/tasks/mrtrix3/v3_1/dcmedit.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -29,7 +29,7 @@ class DcmEdit(shell.Task["DcmEdit.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: J-Donald Tournier (jdtournier@gmail.com)
 
@@ -69,7 +69,7 @@ class DcmEdit(shell.Task["DcmEdit.Outputs"]):
         argstr="-id",
         help="""replace all ID tags with string supplied. This consists of tags (0010, 0020) PatientID and (0010, 1000) OtherPatientIDs""",
     )
-    tag: MultiInputObj[tuple[ty.Any, ty.Any, ty.Any]] | None = shell.arg(
+    tag: MultiInputObj[tuple[Any, Any, Any]] | None = shell.arg(
         default=None,
         argstr="-tag",
         help="""replace specific tag.""",

pydra/tasks/mrtrix3/v3_1/dcminfo.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -20,7 +20,7 @@ class DcmInfo(shell.Task["DcmInfo.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: J-Donald Tournier (jdtournier@gmail.com)
 

pydra/tasks/mrtrix3/v3_1/dirflip.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -22,7 +22,7 @@ class DirFlip(shell.Task["DirFlip.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: J-Donald Tournier (jdtournier@gmail.com)
 
@@ -57,10 +57,15 @@ class DirFlip(shell.Task["DirFlip.Outputs"]):
         argstr="-number",
         help="""number of shuffles to try (default: 100000000)""",
     )
+    preserve: int | None = shell.arg(
+        default=None,
+        argstr="-preserve",
+        help="""preserve the sign of some number of directions at the start of the set""",
+    )
     cartesian: bool = shell.arg(
         default=False,
         argstr="-cartesian",
-        help="""Output the directions in Cartesian coordinates [x y z] instead of [az el].""",
+        help="""Output directions in Cartesian coordinates [x y z] instead of spherical angles [az in].""",
     )
 
     # Standard options

pydra/tasks/mrtrix3/v3_1/dirgen.py

@@ -1,6 +1,6 @@
 # Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
 
-import typing as ty
+from typing import Any
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
@@ -26,7 +26,7 @@ class DirGen(shell.Task["DirGen.Outputs"]):
         MRtrix
         ------
 
-        Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
+        Version:3.0.7-1578-g23fff5b8-dirty, built Nov 28 2025
 
         Author: J-Donald Tournier (jdtournier@gmail.com)
 
@@ -71,6 +71,12 @@ class DirGen(shell.Task["DirGen.Outputs"]):
         argstr="-restarts",
         help="""specify the number of restarts to perform (default: 10).""",
     )
+    fixed: MultiInputObj[list[float]] | None = shell.arg(
+        default=None,
+        argstr="-fixed",
+        help="""specify a fixed direction (comm-separateed floats) that will always be included at the start of the scheme""",
+        sep=",",
+    )
     unipolar: bool = shell.arg(
         default=False,
         argstr="-unipolar",
@@ -79,7 +85,7 @@ class DirGen(shell.Task["DirGen.Outputs"]):
     cartesian: bool = shell.arg(
         default=False,
         argstr="-cartesian",
-        help="""Output the directions in Cartesian coordinates [x y z] instead of [az el].""",
+        help="""Output directions in Cartesian coordinates [x y z] instead of spherical angles [az in].""",
     )
 
     # Standard options
@@ -120,5 +126,5 @@ class Outputs(shell.Outputs):
             argstr="",
             position=2,
             path_template="dirs.txt",
-            help="""the text file to write the directions to, as [ az el ] pairs.""",
+            help="""the text file to write the directions to, as [ az in ] pairs.""",
         )