niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_surface_stats.py

@@ -0,0 +1,346 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_SURFACE_STATS_METADATA = Metadata(
+    id="a615c38b1e647ea0789fa48d75a57ab954bd3b51.boutiques",
+    name="mris_surface_stats",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisSurfaceStatsParameters = typing.TypedDict('MrisSurfaceStatsParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_surface_stats"],
+    "nsmooth": typing.NotRequired[float | None],
+    "surf_name": InputPathType,
+    "mask_name": typing.NotRequired[InputPathType | None],
+    "out_name": str,
+    "mean": typing.NotRequired[str | None],
+    "absmean": typing.NotRequired[str | None],
+    "absstd": typing.NotRequired[str | None],
+    "zscore": typing.NotRequired[str | None],
+    "first_group_size": typing.NotRequired[float | None],
+    "src_type": typing.NotRequired[str | None],
+    "trg_type": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[float | None],
+    "data_files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_surface_stats": mris_surface_stats_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 {
+        "mris_surface_stats": mris_surface_stats_outputs,
+    }.get(t)
+
+
+class MrisSurfaceStatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_surface_stats(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    std_output: OutputPathType
+    """Standard deviation map of the input thickness difference maps"""
+    mean_output: OutputPathType | None
+    """Mean map of the input thickness difference maps"""
+    absmean_output: OutputPathType | None
+    """Absolute mean map of the input thickness difference maps"""
+    absstd_output: OutputPathType | None
+    """Standard deviation map of the absolute differences"""
+    zscore_output: OutputPathType | None
+    """Z-score map of the input thickness difference maps"""
+
+
+def mris_surface_stats_params(
+    surf_name: InputPathType,
+    out_name: str,
+    data_files: list[InputPathType],
+    nsmooth: float | None = None,
+    mask_name: InputPathType | None = None,
+    mean: str | None = None,
+    absmean: str | None = None,
+    absstd: str | None = None,
+    zscore: str | None = None,
+    first_group_size: float | None = None,
+    src_type: str | None = None,
+    trg_type: str | None = None,
+    debug: float | None = None,
+) -> MrisSurfaceStatsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surf_name: Set the surface filename.
+        out_name: Set the output filename (standard deviation of data).
+        data_files: List of input data files for computation.
+        nsmooth: Specify number of smoothing steps.
+        mask_name: Set the filename for surface mask.
+        mean: Set the output filename for mean.
+        absmean: Set the output filename for absolute mean.
+        absstd: Set the output filename for standard deviation of absolute mean.
+        zscore: Set the output filename for z-score (only if first_group_size >\
+            0).
+        first_group_size: Specify how many subjects at the beginning belong to\
+            first group.
+        src_type: Input surface data format (default = paint).
+        trg_type: Output format (default = paint).
+        debug: Specify which surface vertex number to debug.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_surface_stats",
+        "surf_name": surf_name,
+        "out_name": out_name,
+        "data_files": data_files,
+    }
+    if nsmooth is not None:
+        params["nsmooth"] = nsmooth
+    if mask_name is not None:
+        params["mask_name"] = mask_name
+    if mean is not None:
+        params["mean"] = mean
+    if absmean is not None:
+        params["absmean"] = absmean
+    if absstd is not None:
+        params["absstd"] = absstd
+    if zscore is not None:
+        params["zscore"] = zscore
+    if first_group_size is not None:
+        params["first_group_size"] = first_group_size
+    if src_type is not None:
+        params["src_type"] = src_type
+    if trg_type is not None:
+        params["trg_type"] = trg_type
+    if debug is not None:
+        params["debug"] = debug
+    return params
+
+
+def mris_surface_stats_cargs(
+    params: MrisSurfaceStatsParameters,
+    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("mris_surface_stats")
+    if params.get("nsmooth") is not None:
+        cargs.extend([
+            "-nsmooth",
+            str(params.get("nsmooth"))
+        ])
+    cargs.extend([
+        "-surf_name",
+        execution.input_file(params.get("surf_name"))
+    ])
+    if params.get("mask_name") is not None:
+        cargs.extend([
+            "-mask_name",
+            execution.input_file(params.get("mask_name"))
+        ])
+    cargs.extend([
+        "-out_name",
+        params.get("out_name")
+    ])
+    if params.get("mean") is not None:
+        cargs.extend([
+            "-mean",
+            params.get("mean")
+        ])
+    if params.get("absmean") is not None:
+        cargs.extend([
+            "-absmean",
+            params.get("absmean")
+        ])
+    if params.get("absstd") is not None:
+        cargs.extend([
+            "-absstd",
+            params.get("absstd")
+        ])
+    if params.get("zscore") is not None:
+        cargs.extend([
+            "-zscore",
+            params.get("zscore")
+        ])
+    if params.get("first_group_size") is not None:
+        cargs.extend([
+            "-first_group_size",
+            str(params.get("first_group_size"))
+        ])
+    if params.get("src_type") is not None:
+        cargs.extend([
+            "-src_type",
+            params.get("src_type")
+        ])
+    if params.get("trg_type") is not None:
+        cargs.extend([
+            "-trg_type",
+            params.get("trg_type")
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("data_files")])
+    return cargs
+
+
+def mris_surface_stats_outputs(
+    params: MrisSurfaceStatsParameters,
+    execution: Execution,
+) -> MrisSurfaceStatsOutputs:
+    """
+    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 = MrisSurfaceStatsOutputs(
+        root=execution.output_file("."),
+        std_output=execution.output_file(params.get("out_name")),
+        mean_output=execution.output_file(params.get("mean")) if (params.get("mean") is not None) else None,
+        absmean_output=execution.output_file(params.get("absmean")) if (params.get("absmean") is not None) else None,
+        absstd_output=execution.output_file(params.get("absstd")) if (params.get("absstd") is not None) else None,
+        zscore_output=execution.output_file(params.get("zscore")) if (params.get("zscore") is not None) else None,
+    )
+    return ret
+
+
+def mris_surface_stats_execute(
+    params: MrisSurfaceStatsParameters,
+    execution: Execution,
+) -> MrisSurfaceStatsOutputs:
+    """
+    Computes the group-wise mean and standard deviation of thickness differences at
+    every vertex of the template surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisSurfaceStatsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_surface_stats_cargs(params, execution)
+    ret = mris_surface_stats_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_surface_stats(
+    surf_name: InputPathType,
+    out_name: str,
+    data_files: list[InputPathType],
+    nsmooth: float | None = None,
+    mask_name: InputPathType | None = None,
+    mean: str | None = None,
+    absmean: str | None = None,
+    absstd: str | None = None,
+    zscore: str | None = None,
+    first_group_size: float | None = None,
+    src_type: str | None = None,
+    trg_type: str | None = None,
+    debug: float | None = None,
+    runner: Runner | None = None,
+) -> MrisSurfaceStatsOutputs:
+    """
+    Computes the group-wise mean and standard deviation of thickness differences at
+    every vertex of the template surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        surf_name: Set the surface filename.
+        out_name: Set the output filename (standard deviation of data).
+        data_files: List of input data files for computation.
+        nsmooth: Specify number of smoothing steps.
+        mask_name: Set the filename for surface mask.
+        mean: Set the output filename for mean.
+        absmean: Set the output filename for absolute mean.
+        absstd: Set the output filename for standard deviation of absolute mean.
+        zscore: Set the output filename for z-score (only if first_group_size >\
+            0).
+        first_group_size: Specify how many subjects at the beginning belong to\
+            first group.
+        src_type: Input surface data format (default = paint).
+        trg_type: Output format (default = paint).
+        debug: Specify which surface vertex number to debug.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisSurfaceStatsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SURFACE_STATS_METADATA)
+    params = mris_surface_stats_params(
+        nsmooth=nsmooth,
+        surf_name=surf_name,
+        mask_name=mask_name,
+        out_name=out_name,
+        mean=mean,
+        absmean=absmean,
+        absstd=absstd,
+        zscore=zscore,
+        first_group_size=first_group_size,
+        src_type=src_type,
+        trg_type=trg_type,
+        debug=debug,
+        data_files=data_files,
+    )
+    return mris_surface_stats_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_SURFACE_STATS_METADATA",
+    "MrisSurfaceStatsOutputs",
+    "MrisSurfaceStatsParameters",
+    "mris_surface_stats",
+    "mris_surface_stats_params",
+]

niwrap_freesurfer/freesurfer/mris_surface_to_vol_distances.py

@@ -0,0 +1,200 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_SURFACE_TO_VOL_DISTANCES_METADATA = Metadata(
+    id="b436cdee4792f571a6fb7c9b7311696958c3dc2d.boutiques",
+    name="mris_surface_to_vol_distances",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisSurfaceToVolDistancesParameters = typing.TypedDict('MrisSurfaceToVolDistancesParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_surface_to_vol_distances"],
+    "average_subject": str,
+    "hemisphere": str,
+    "subjects": list[str],
+    "output_prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_surface_to_vol_distances": mris_surface_to_vol_distances_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 {
+        "mris_surface_to_vol_distances": mris_surface_to_vol_distances_outputs,
+    }.get(t)
+
+
+class MrisSurfaceToVolDistancesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_surface_to_vol_distances(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_distances: OutputPathType
+    """Output file containing surface-to-volume distances."""
+
+
+def mris_surface_to_vol_distances_params(
+    average_subject: str,
+    hemisphere: str,
+    subjects: list[str],
+    output_prefix: str,
+) -> MrisSurfaceToVolDistancesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        average_subject: The average subject.
+        hemisphere: Hemisphere identifier (e.g., lh or rh).
+        subjects: List of subjects for distance calculation.
+        output_prefix: Prefix for output files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_surface_to_vol_distances",
+        "average_subject": average_subject,
+        "hemisphere": hemisphere,
+        "subjects": subjects,
+        "output_prefix": output_prefix,
+    }
+    return params
+
+
+def mris_surface_to_vol_distances_cargs(
+    params: MrisSurfaceToVolDistancesParameters,
+    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("mris_surface_to_vol_distances")
+    cargs.append(params.get("average_subject"))
+    cargs.append(params.get("hemisphere"))
+    cargs.extend(params.get("subjects"))
+    cargs.append(params.get("output_prefix"))
+    return cargs
+
+
+def mris_surface_to_vol_distances_outputs(
+    params: MrisSurfaceToVolDistancesParameters,
+    execution: Execution,
+) -> MrisSurfaceToVolDistancesOutputs:
+    """
+    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 = MrisSurfaceToVolDistancesOutputs(
+        root=execution.output_file("."),
+        output_distances=execution.output_file(params.get("output_prefix") + "_distances.txt"),
+    )
+    return ret
+
+
+def mris_surface_to_vol_distances_execute(
+    params: MrisSurfaceToVolDistancesParameters,
+    execution: Execution,
+) -> MrisSurfaceToVolDistancesOutputs:
+    """
+    Tool from FreeSurfer to calculate surface-to-volume distances.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisSurfaceToVolDistancesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_surface_to_vol_distances_cargs(params, execution)
+    ret = mris_surface_to_vol_distances_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_surface_to_vol_distances(
+    average_subject: str,
+    hemisphere: str,
+    subjects: list[str],
+    output_prefix: str,
+    runner: Runner | None = None,
+) -> MrisSurfaceToVolDistancesOutputs:
+    """
+    Tool from FreeSurfer to calculate surface-to-volume distances.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        average_subject: The average subject.
+        hemisphere: Hemisphere identifier (e.g., lh or rh).
+        subjects: List of subjects for distance calculation.
+        output_prefix: Prefix for output files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisSurfaceToVolDistancesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SURFACE_TO_VOL_DISTANCES_METADATA)
+    params = mris_surface_to_vol_distances_params(
+        average_subject=average_subject,
+        hemisphere=hemisphere,
+        subjects=subjects,
+        output_prefix=output_prefix,
+    )
+    return mris_surface_to_vol_distances_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_SURFACE_TO_VOL_DISTANCES_METADATA",
+    "MrisSurfaceToVolDistancesOutputs",
+    "MrisSurfaceToVolDistancesParameters",
+    "mris_surface_to_vol_distances",
+    "mris_surface_to_vol_distances_params",
+]

niwrap_freesurfer/freesurfer/mris_talairach.py

@@ -0,0 +1,172 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRIS_TALAIRACH_METADATA = Metadata(
+    id="2a27ec50232d56f8e8e079035c459f747d644292.boutiques",
+    name="mris_talairach",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MrisTalairachParameters = typing.TypedDict('MrisTalairachParameters', {
+    "__STYX_TYPE__": typing.Literal["mris_talairach"],
+    "input_image": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mris_talairach": mris_talairach_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 MrisTalairachOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mris_talairach(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def mris_talairach_params(
+    input_image: InputPathType,
+) -> MrisTalairachParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Input image file to be transformed into Talairach space.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mris_talairach",
+        "input_image": input_image,
+    }
+    return params
+
+
+def mris_talairach_cargs(
+    params: MrisTalairachParameters,
+    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("mris_talairach")
+    cargs.append(execution.input_file(params.get("input_image")))
+    return cargs
+
+
+def mris_talairach_outputs(
+    params: MrisTalairachParameters,
+    execution: Execution,
+) -> MrisTalairachOutputs:
+    """
+    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 = MrisTalairachOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def mris_talairach_execute(
+    params: MrisTalairachParameters,
+    execution: Execution,
+) -> MrisTalairachOutputs:
+    """
+    Transforms an MRI surface into Talairach space.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrisTalairachOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mris_talairach_cargs(params, execution)
+    ret = mris_talairach_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mris_talairach(
+    input_image: InputPathType,
+    runner: Runner | None = None,
+) -> MrisTalairachOutputs:
+    """
+    Transforms an MRI surface into Talairach space.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_image: Input image file to be transformed into Talairach space.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrisTalairachOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_TALAIRACH_METADATA)
+    params = mris_talairach_params(
+        input_image=input_image,
+    )
+    return mris_talairach_execute(params, execution)
+
+
+__all__ = [
+    "MRIS_TALAIRACH_METADATA",
+    "MrisTalairachOutputs",
+    "MrisTalairachParameters",
+    "mris_talairach",
+    "mris_talairach_params",
+]