niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/morph_only_subject_rh.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MORPH_ONLY_SUBJECT_RH_METADATA = Metadata(
+    id="cf178313d144b58ca109c79e9c3499855a731ab6.boutiques",
+    name="morph_only_subject-rh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MorphOnlySubjectRhParameters = typing.TypedDict('MorphOnlySubjectRhParameters', {
+    "__STYX_TYPE__": typing.Literal["morph_only_subject-rh"],
+    "subject_dir": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "morph_only_subject-rh": morph_only_subject_rh_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "morph_only_subject-rh": morph_only_subject_rh_outputs,
+    }.get(t)
+
+
+class MorphOnlySubjectRhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `morph_only_subject_rh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """The output morphing files for the right hemisphere generated by the
+    process."""
+
+
+def morph_only_subject_rh_params(
+    subject_dir: InputPathType,
+) -> MorphOnlySubjectRhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_dir: Path to the subject's directory containing the necessary\
+            input files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "morph_only_subject-rh",
+        "subject_dir": subject_dir,
+    }
+    return params
+
+
+def morph_only_subject_rh_cargs(
+    params: MorphOnlySubjectRhParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.extend([
+        "-rh",
+        "morph_only_subject" + execution.input_file(params.get("subject_dir"))
+    ])
+    return cargs
+
+
+def morph_only_subject_rh_outputs(
+    params: MorphOnlySubjectRhParameters,
+    execution: Execution,
+) -> MorphOnlySubjectRhOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MorphOnlySubjectRhOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file("/usr/local/freesurfer/subjects/" + pathlib.Path(params.get("subject_dir")).name + "/rh.morph"),
+    )
+    return ret
+
+
+def morph_only_subject_rh_execute(
+    params: MorphOnlySubjectRhParameters,
+    execution: Execution,
+) -> MorphOnlySubjectRhOutputs:
+    """
+    This tool processes morph-specific operations for the right hemisphere of the
+    brain using Freesurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MorphOnlySubjectRhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = morph_only_subject_rh_cargs(params, execution)
+    ret = morph_only_subject_rh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def morph_only_subject_rh(
+    subject_dir: InputPathType,
+    runner: Runner | None = None,
+) -> MorphOnlySubjectRhOutputs:
+    """
+    This tool processes morph-specific operations for the right hemisphere of the
+    brain using Freesurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_dir: Path to the subject's directory containing the necessary\
+            input files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MorphOnlySubjectRhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_ONLY_SUBJECT_RH_METADATA)
+    params = morph_only_subject_rh_params(
+        subject_dir=subject_dir,
+    )
+    return morph_only_subject_rh_execute(params, execution)
+
+
+__all__ = [
+    "MORPH_ONLY_SUBJECT_RH_METADATA",
+    "MorphOnlySubjectRhOutputs",
+    "MorphOnlySubjectRhParameters",
+    "morph_only_subject_rh",
+    "morph_only_subject_rh_params",
+]

niwrap_freesurfer/freesurfer/morph_rgb_lh.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MORPH_RGB_LH_METADATA = Metadata(
+    id="8a27176b135c7e00506bbb223dc33d4f8b5c331f.boutiques",
+    name="morph_rgb-lh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MorphRgbLhParameters = typing.TypedDict('MorphRgbLhParameters', {
+    "__STYX_TYPE__": typing.Literal["morph_rgb-lh"],
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "morph_rgb-lh": morph_rgb_lh_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class MorphRgbLhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `morph_rgb_lh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def morph_rgb_lh_params(
+    subject_id: str,
+) -> MorphRgbLhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: The subject ID to process. This refers to the sub-directory\
+            within $SUBJECTS_DIR containing the FreeSurfer processed data for the\
+            subject.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "morph_rgb-lh",
+        "subject_id": subject_id,
+    }
+    return params
+
+
+def morph_rgb_lh_cargs(
+    params: MorphRgbLhParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.extend([
+        "-lh",
+        "morph_rgb" + params.get("subject_id")
+    ])
+    return cargs
+
+
+def morph_rgb_lh_outputs(
+    params: MorphRgbLhParameters,
+    execution: Execution,
+) -> MorphRgbLhOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MorphRgbLhOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def morph_rgb_lh_execute(
+    params: MorphRgbLhParameters,
+    execution: Execution,
+) -> MorphRgbLhOutputs:
+    """
+    Tool for working with and generating RGB images of morphometric data for the
+    left hemisphere in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MorphRgbLhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = morph_rgb_lh_cargs(params, execution)
+    ret = morph_rgb_lh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def morph_rgb_lh(
+    subject_id: str,
+    runner: Runner | None = None,
+) -> MorphRgbLhOutputs:
+    """
+    Tool for working with and generating RGB images of morphometric data for the
+    left hemisphere in FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_id: The subject ID to process. This refers to the sub-directory\
+            within $SUBJECTS_DIR containing the FreeSurfer processed data for the\
+            subject.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MorphRgbLhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_RGB_LH_METADATA)
+    params = morph_rgb_lh_params(
+        subject_id=subject_id,
+    )
+    return morph_rgb_lh_execute(params, execution)
+
+
+__all__ = [
+    "MORPH_RGB_LH_METADATA",
+    "MorphRgbLhOutputs",
+    "MorphRgbLhParameters",
+    "morph_rgb_lh",
+    "morph_rgb_lh_params",
+]

niwrap_freesurfer/freesurfer/morph_rgb_rh.py

@@ -0,0 +1,174 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MORPH_RGB_RH_METADATA = Metadata(
+    id="d9ff451dc5d9779a26edbf9b5422cc9aac7df58e.boutiques",
+    name="morph_rgb-rh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MorphRgbRhParameters = typing.TypedDict('MorphRgbRhParameters', {
+    "__STYX_TYPE__": typing.Literal["morph_rgb-rh"],
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "morph_rgb-rh": morph_rgb_rh_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class MorphRgbRhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `morph_rgb_rh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def morph_rgb_rh_params(
+    subject_id: str,
+) -> MorphRgbRhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Subject ID for which the RGB morphing should be performed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "morph_rgb-rh",
+        "subject_id": subject_id,
+    }
+    return params
+
+
+def morph_rgb_rh_cargs(
+    params: MorphRgbRhParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.extend([
+        "-rh",
+        "morph_rgb" + params.get("subject_id")
+    ])
+    return cargs
+
+
+def morph_rgb_rh_outputs(
+    params: MorphRgbRhParameters,
+    execution: Execution,
+) -> MorphRgbRhOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MorphRgbRhOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def morph_rgb_rh_execute(
+    params: MorphRgbRhParameters,
+    execution: Execution,
+) -> MorphRgbRhOutputs:
+    """
+    Morphs RGB values onto a FreeSurfer right hemisphere surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MorphRgbRhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = morph_rgb_rh_cargs(params, execution)
+    ret = morph_rgb_rh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def morph_rgb_rh(
+    subject_id: str,
+    runner: Runner | None = None,
+) -> MorphRgbRhOutputs:
+    """
+    Morphs RGB values onto a FreeSurfer right hemisphere surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_id: Subject ID for which the RGB morphing should be performed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MorphRgbRhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_RGB_RH_METADATA)
+    params = morph_rgb_rh_params(
+        subject_id=subject_id,
+    )
+    return morph_rgb_rh_execute(params, execution)
+
+
+__all__ = [
+    "MORPH_RGB_RH_METADATA",
+    "MorphRgbRhOutputs",
+    "MorphRgbRhParameters",
+    "morph_rgb_rh",
+    "morph_rgb_rh_params",
+]

niwrap_freesurfer/freesurfer/morph_subject.py

@@ -0,0 +1,174 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MORPH_SUBJECT_METADATA = Metadata(
+    id="685f97530d830d12a67cb8468c38864b69d1e65c.boutiques",
+    name="morph_subject",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MorphSubjectParameters = typing.TypedDict('MorphSubjectParameters', {
+    "__STYX_TYPE__": typing.Literal["morph_subject"],
+    "subjid": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "morph_subject": morph_subject_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class MorphSubjectOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `morph_subject(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def morph_subject_params(
+    subjid: str,
+) -> MorphSubjectParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subjid: Subject ID for processing.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "morph_subject",
+        "subjid": subjid,
+    }
+    return params
+
+
+def morph_subject_cargs(
+    params: MorphSubjectParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("morph_subject")
+    cargs.append(params.get("subjid"))
+    return cargs
+
+
+def morph_subject_outputs(
+    params: MorphSubjectParameters,
+    execution: Execution,
+) -> MorphSubjectOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MorphSubjectOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def morph_subject_execute(
+    params: MorphSubjectParameters,
+    execution: Execution,
+) -> MorphSubjectOutputs:
+    """
+    A morphological processing tool for Freesurfer subjects. The specific operations
+    and options are not documented in the available help text.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MorphSubjectOutputs`).
+    """
+    params = execution.params(params)
+    cargs = morph_subject_cargs(params, execution)
+    ret = morph_subject_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def morph_subject(
+    subjid: str,
+    runner: Runner | None = None,
+) -> MorphSubjectOutputs:
+    """
+    A morphological processing tool for Freesurfer subjects. The specific operations
+    and options are not documented in the available help text.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subjid: Subject ID for processing.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MorphSubjectOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_SUBJECT_METADATA)
+    params = morph_subject_params(
+        subjid=subjid,
+    )
+    return morph_subject_execute(params, execution)
+
+
+__all__ = [
+    "MORPH_SUBJECT_METADATA",
+    "MorphSubjectOutputs",
+    "MorphSubjectParameters",
+    "morph_subject",
+    "morph_subject_params",
+]