niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_glmfit_sim.py

@@ -0,0 +1,537 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_GLMFIT_SIM_METADATA = Metadata(
+    id="b485cfa7c95293942f2efa8d5ccde5c8c33116e9.boutiques",
+    name="mri_glmfit-sim",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriGlmfitSimParameters = typing.TypedDict('MriGlmfitSimParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_glmfit-sim"],
+    "glmdir": str,
+    "cwp": typing.NotRequired[float | None],
+    "mczsim": typing.NotRequired[str | None],
+    "mczsim_dir": typing.NotRequired[str | None],
+    "mczsim_label": typing.NotRequired[str | None],
+    "perm": typing.NotRequired[str | None],
+    "perm_resid": bool,
+    "perm_signflip": bool,
+    "grf": typing.NotRequired[str | None],
+    "spaces_2": bool,
+    "spaces_3": bool,
+    "overwrite": bool,
+    "bg": typing.NotRequired[float | None],
+    "sleep": typing.NotRequired[float | None],
+    "a2009s": bool,
+    "annot": typing.NotRequired[str | None],
+    "log": typing.NotRequired[str | None],
+    "base": typing.NotRequired[str | None],
+    "no_sim": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[float | None],
+    "fwhm_override": typing.NotRequired[float | None],
+    "fwhm_add": typing.NotRequired[float | None],
+    "uniform": typing.NotRequired[list[float] | None],
+    "no_out_annot": bool,
+    "no_cluster_mean": bool,
+    "y_file": typing.NotRequired[InputPathType | None],
+    "centroid": bool,
+    "spatial_sum": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_glmfit-sim": mri_glmfit_sim_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 {
+        "mri_glmfit-sim": mri_glmfit_sim_outputs,
+    }.get(t)
+
+
+class MriGlmfitSimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_glmfit_sim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    sig_voxel_mgh: OutputPathType | None
+    """Sig volume corrected for voxel-wise multiple comparisons."""
+    sig_cluster_mgh: OutputPathType | None
+    """Sig volume corrected for cluster-wise multiple comparisons."""
+    sig_cluster_summary: OutputPathType | None
+    """Cluster summary table."""
+    y_ocn_dat: OutputPathType | None
+    """Summary of the input (y) over each cluster."""
+    sig_ocn_mgh: OutputPathType | None
+    """Output cluster number volume."""
+    sig_ocn_annot: OutputPathType | None
+    """Cluster annotation for surfaces."""
+    sig_masked_mgh: OutputPathType | None
+    """Original sig volume masked to show only clusters."""
+
+
+def mri_glmfit_sim_params(
+    glmdir: str,
+    cwp: float | None = None,
+    mczsim: str | None = None,
+    mczsim_dir: str | None = None,
+    mczsim_label: str | None = None,
+    perm: str | None = None,
+    perm_resid: bool = False,
+    perm_signflip: bool = False,
+    grf: str | None = None,
+    spaces_2: bool = False,
+    spaces_3: bool = False,
+    overwrite: bool = False,
+    bg: float | None = None,
+    sleep: float | None = None,
+    a2009s: bool = False,
+    annot: str | None = None,
+    log: str | None = None,
+    base: str | None = None,
+    no_sim: str | None = None,
+    seed: float | None = None,
+    fwhm_override: float | None = None,
+    fwhm_add: float | None = None,
+    uniform: list[float] | None = None,
+    no_out_annot: bool = False,
+    no_cluster_mean: bool = False,
+    y_file: InputPathType | None = None,
+    centroid: bool = False,
+    spatial_sum: bool = False,
+    help_: bool = False,
+) -> MriGlmfitSimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        glmdir: Path to GLM directory.
+        cwp: Cluster-wise p-value threshold, default is 0.05.
+        mczsim: Use pre-computed z-based Monte Carlo simulations. Requires\
+            vwthreshold and sign.
+        mczsim_dir: Directory for custom Monte Carlo simulations, default is\
+            FREESURFER_HOME/average/mult-comp-cor.
+        mczsim_label: Label for custom Monte Carlo simulations, default is\
+            cortex.
+        perm: Use permutation simulation with nsim iterations, cluster forming\
+            threshold (CFT), and sign.
+        perm_resid: Use permutation on the residual instead of raw data for\
+            non-orthogonal designs.
+        perm_signflip: Use sign flipping instead of shuffling for permutation.
+        grf: Use Gaussian Random Fields (GRF) method, with vwthreshold and\
+            sign.
+        spaces_2: Apply additional Bonferroni correction across 2 spaces.
+        spaces_3: Apply additional Bonferroni correction across 3 spaces.
+        overwrite: Delete previous CSDs.
+        bg: Divide simulation into njobs and put in background.
+        sleep: Number of seconds to sleep between background polls.
+        a2009s: Use aparc.a2009s instead of aparc for region of vertex max.
+        annot: Use specific annotation for region of vertex max.
+        log: Specify logfile, default is csdbase.mri_glmfit-sim.log.
+        base: Override csdbase name.
+        no_sim: Do not simulate, only run cluster.
+        seed: Set simulation random number generator seed.
+        fwhm_override: Override fwhm in glmdir.
+        fwhm_add: Add fwhmAdd to the estimated fwhm.
+        uniform: Use uniform PDF instead of gaussian, specify min and max.
+        no_out_annot: Do not output a cluster annotation.
+        no_cluster_mean: Do not compute means of each subject in each cluster.
+        y_file: Specify the GLM input y file.
+        centroid: Report the coordinates/annotation of the centroid instead of\
+            max.
+        spatial_sum: Compute the sum over voxels in the cluster rather than the\
+            average.
+        help_: Show the help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_glmfit-sim",
+        "glmdir": glmdir,
+        "perm_resid": perm_resid,
+        "perm_signflip": perm_signflip,
+        "spaces_2": spaces_2,
+        "spaces_3": spaces_3,
+        "overwrite": overwrite,
+        "a2009s": a2009s,
+        "no_out_annot": no_out_annot,
+        "no_cluster_mean": no_cluster_mean,
+        "centroid": centroid,
+        "spatial_sum": spatial_sum,
+        "help": help_,
+    }
+    if cwp is not None:
+        params["cwp"] = cwp
+    if mczsim is not None:
+        params["mczsim"] = mczsim
+    if mczsim_dir is not None:
+        params["mczsim_dir"] = mczsim_dir
+    if mczsim_label is not None:
+        params["mczsim_label"] = mczsim_label
+    if perm is not None:
+        params["perm"] = perm
+    if grf is not None:
+        params["grf"] = grf
+    if bg is not None:
+        params["bg"] = bg
+    if sleep is not None:
+        params["sleep"] = sleep
+    if annot is not None:
+        params["annot"] = annot
+    if log is not None:
+        params["log"] = log
+    if base is not None:
+        params["base"] = base
+    if no_sim is not None:
+        params["no_sim"] = no_sim
+    if seed is not None:
+        params["seed"] = seed
+    if fwhm_override is not None:
+        params["fwhm_override"] = fwhm_override
+    if fwhm_add is not None:
+        params["fwhm_add"] = fwhm_add
+    if uniform is not None:
+        params["uniform"] = uniform
+    if y_file is not None:
+        params["y_file"] = y_file
+    return params
+
+
+def mri_glmfit_sim_cargs(
+    params: MriGlmfitSimParameters,
+    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("mri_glmfit-sim")
+    cargs.extend([
+        "--glmdir",
+        params.get("glmdir")
+    ])
+    if params.get("cwp") is not None:
+        cargs.extend([
+            "--cwp",
+            str(params.get("cwp"))
+        ])
+    if params.get("mczsim") is not None:
+        cargs.extend([
+            "--mczsim",
+            params.get("mczsim")
+        ])
+    if params.get("mczsim_dir") is not None:
+        cargs.extend([
+            "--mczsim-dir",
+            params.get("mczsim_dir")
+        ])
+    if params.get("mczsim_label") is not None:
+        cargs.extend([
+            "--mczsim-label",
+            params.get("mczsim_label")
+        ])
+    if params.get("perm") is not None:
+        cargs.extend([
+            "--perm",
+            params.get("perm")
+        ])
+    if params.get("perm_resid"):
+        cargs.append("--perm-resid")
+    if params.get("perm_signflip"):
+        cargs.append("--perm-signflip")
+    if params.get("grf") is not None:
+        cargs.extend([
+            "--grf",
+            params.get("grf")
+        ])
+    if params.get("spaces_2"):
+        cargs.append("--2spaces")
+    if params.get("spaces_3"):
+        cargs.append("--3spaces")
+    if params.get("overwrite"):
+        cargs.append("--overwrite")
+    if params.get("bg") is not None:
+        cargs.extend([
+            "--bg",
+            str(params.get("bg"))
+        ])
+    if params.get("sleep") is not None:
+        cargs.extend([
+            "--sleep",
+            str(params.get("sleep"))
+        ])
+    if params.get("a2009s"):
+        cargs.append("--a2009s")
+    if params.get("annot") is not None:
+        cargs.extend([
+            "--annot",
+            params.get("annot")
+        ])
+    if params.get("log") is not None:
+        cargs.extend([
+            "--log",
+            params.get("log")
+        ])
+    if params.get("base") is not None:
+        cargs.extend([
+            "--base",
+            params.get("base")
+        ])
+    if params.get("no_sim") is not None:
+        cargs.extend([
+            "--no-sim",
+            params.get("no_sim")
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("seed"))
+        ])
+    if params.get("fwhm_override") is not None:
+        cargs.extend([
+            "--fwhm-override",
+            str(params.get("fwhm_override"))
+        ])
+    if params.get("fwhm_add") is not None:
+        cargs.extend([
+            "--fwhm-add",
+            str(params.get("fwhm_add"))
+        ])
+    if params.get("uniform") is not None:
+        cargs.extend([
+            "--uniform",
+            *map(str, params.get("uniform"))
+        ])
+    if params.get("no_out_annot"):
+        cargs.append("--no-out-annot")
+    if params.get("no_cluster_mean"):
+        cargs.append("--no-cluster-mean")
+    if params.get("y_file") is not None:
+        cargs.extend([
+            "--y",
+            execution.input_file(params.get("y_file"))
+        ])
+    if params.get("centroid"):
+        cargs.append("--centroid")
+    if params.get("spatial_sum"):
+        cargs.append("--spatial-sum")
+    if params.get("help"):
+        cargs.append("--help")
+    return cargs
+
+
+def mri_glmfit_sim_outputs(
+    params: MriGlmfitSimParameters,
+    execution: Execution,
+) -> MriGlmfitSimOutputs:
+    """
+    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 = MriGlmfitSimOutputs(
+        root=execution.output_file("."),
+        sig_voxel_mgh=execution.output_file(params.get("base") + ".sig.voxel.mgh") if (params.get("base") is not None) else None,
+        sig_cluster_mgh=execution.output_file(params.get("base") + ".sig.cluster.mgh") if (params.get("base") is not None) else None,
+        sig_cluster_summary=execution.output_file(params.get("base") + ".sig.cluster.summary") if (params.get("base") is not None) else None,
+        y_ocn_dat=execution.output_file(params.get("base") + ".y.ocn.dat") if (params.get("base") is not None) else None,
+        sig_ocn_mgh=execution.output_file(params.get("base") + ".sig.ocn.mgh") if (params.get("base") is not None) else None,
+        sig_ocn_annot=execution.output_file(params.get("base") + ".sig.ocn.annot") if (params.get("base") is not None) else None,
+        sig_masked_mgh=execution.output_file(params.get("base") + ".sig.masked.mgh") if (params.get("base") is not None) else None,
+    )
+    return ret
+
+
+def mri_glmfit_sim_execute(
+    params: MriGlmfitSimParameters,
+    execution: Execution,
+) -> MriGlmfitSimOutputs:
+    """
+    A tool to run corrections for multiple comparisons on volumes or surfaces, using
+    various methods including Monte Carlo simulation, permutation, and Gaussian
+    Random Fields.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriGlmfitSimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_glmfit_sim_cargs(params, execution)
+    ret = mri_glmfit_sim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_glmfit_sim(
+    glmdir: str,
+    cwp: float | None = None,
+    mczsim: str | None = None,
+    mczsim_dir: str | None = None,
+    mczsim_label: str | None = None,
+    perm: str | None = None,
+    perm_resid: bool = False,
+    perm_signflip: bool = False,
+    grf: str | None = None,
+    spaces_2: bool = False,
+    spaces_3: bool = False,
+    overwrite: bool = False,
+    bg: float | None = None,
+    sleep: float | None = None,
+    a2009s: bool = False,
+    annot: str | None = None,
+    log: str | None = None,
+    base: str | None = None,
+    no_sim: str | None = None,
+    seed: float | None = None,
+    fwhm_override: float | None = None,
+    fwhm_add: float | None = None,
+    uniform: list[float] | None = None,
+    no_out_annot: bool = False,
+    no_cluster_mean: bool = False,
+    y_file: InputPathType | None = None,
+    centroid: bool = False,
+    spatial_sum: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> MriGlmfitSimOutputs:
+    """
+    A tool to run corrections for multiple comparisons on volumes or surfaces, using
+    various methods including Monte Carlo simulation, permutation, and Gaussian
+    Random Fields.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        glmdir: Path to GLM directory.
+        cwp: Cluster-wise p-value threshold, default is 0.05.
+        mczsim: Use pre-computed z-based Monte Carlo simulations. Requires\
+            vwthreshold and sign.
+        mczsim_dir: Directory for custom Monte Carlo simulations, default is\
+            FREESURFER_HOME/average/mult-comp-cor.
+        mczsim_label: Label for custom Monte Carlo simulations, default is\
+            cortex.
+        perm: Use permutation simulation with nsim iterations, cluster forming\
+            threshold (CFT), and sign.
+        perm_resid: Use permutation on the residual instead of raw data for\
+            non-orthogonal designs.
+        perm_signflip: Use sign flipping instead of shuffling for permutation.
+        grf: Use Gaussian Random Fields (GRF) method, with vwthreshold and\
+            sign.
+        spaces_2: Apply additional Bonferroni correction across 2 spaces.
+        spaces_3: Apply additional Bonferroni correction across 3 spaces.
+        overwrite: Delete previous CSDs.
+        bg: Divide simulation into njobs and put in background.
+        sleep: Number of seconds to sleep between background polls.
+        a2009s: Use aparc.a2009s instead of aparc for region of vertex max.
+        annot: Use specific annotation for region of vertex max.
+        log: Specify logfile, default is csdbase.mri_glmfit-sim.log.
+        base: Override csdbase name.
+        no_sim: Do not simulate, only run cluster.
+        seed: Set simulation random number generator seed.
+        fwhm_override: Override fwhm in glmdir.
+        fwhm_add: Add fwhmAdd to the estimated fwhm.
+        uniform: Use uniform PDF instead of gaussian, specify min and max.
+        no_out_annot: Do not output a cluster annotation.
+        no_cluster_mean: Do not compute means of each subject in each cluster.
+        y_file: Specify the GLM input y file.
+        centroid: Report the coordinates/annotation of the centroid instead of\
+            max.
+        spatial_sum: Compute the sum over voxels in the cluster rather than the\
+            average.
+        help_: Show the help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriGlmfitSimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GLMFIT_SIM_METADATA)
+    params = mri_glmfit_sim_params(
+        glmdir=glmdir,
+        cwp=cwp,
+        mczsim=mczsim,
+        mczsim_dir=mczsim_dir,
+        mczsim_label=mczsim_label,
+        perm=perm,
+        perm_resid=perm_resid,
+        perm_signflip=perm_signflip,
+        grf=grf,
+        spaces_2=spaces_2,
+        spaces_3=spaces_3,
+        overwrite=overwrite,
+        bg=bg,
+        sleep=sleep,
+        a2009s=a2009s,
+        annot=annot,
+        log=log,
+        base=base,
+        no_sim=no_sim,
+        seed=seed,
+        fwhm_override=fwhm_override,
+        fwhm_add=fwhm_add,
+        uniform=uniform,
+        no_out_annot=no_out_annot,
+        no_cluster_mean=no_cluster_mean,
+        y_file=y_file,
+        centroid=centroid,
+        spatial_sum=spatial_sum,
+        help_=help_,
+    )
+    return mri_glmfit_sim_execute(params, execution)
+
+
+__all__ = [
+    "MRI_GLMFIT_SIM_METADATA",
+    "MriGlmfitSimOutputs",
+    "MriGlmfitSimParameters",
+    "mri_glmfit_sim",
+    "mri_glmfit_sim_params",
+]

niwrap_freesurfer/freesurfer/mri_gradient_info.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_GRADIENT_INFO_METADATA = Metadata(
+    id="31065ab477983c227eb79e13fe275d6a65852b07.boutiques",
+    name="mri_gradient_info",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriGradientInfoParameters = typing.TypedDict('MriGradientInfoParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_gradient_info"],
+    "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 {
+        "mri_gradient_info": mri_gradient_info_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 {
+        "mri_gradient_info": mri_gradient_info_outputs,
+    }.get(t)
+
+
+class MriGradientInfoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_gradient_info(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    gradient_info_output: OutputPathType
+    """Text file containing the extracted gradient information."""
+
+
+def mri_gradient_info_params(
+    input_image: InputPathType,
+) -> MriGradientInfoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Input MRI image file, typically in .mgz format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_gradient_info",
+        "input_image": input_image,
+    }
+    return params
+
+
+def mri_gradient_info_cargs(
+    params: MriGradientInfoParameters,
+    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("mri_gradient_info")
+    cargs.append(execution.input_file(params.get("input_image")))
+    return cargs
+
+
+def mri_gradient_info_outputs(
+    params: MriGradientInfoParameters,
+    execution: Execution,
+) -> MriGradientInfoOutputs:
+    """
+    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 = MriGradientInfoOutputs(
+        root=execution.output_file("."),
+        gradient_info_output=execution.output_file("gradient_info_output.txt"),
+    )
+    return ret
+
+
+def mri_gradient_info_execute(
+    params: MriGradientInfoParameters,
+    execution: Execution,
+) -> MriGradientInfoOutputs:
+    """
+    A utility to obtain gradient information from MRI images 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 `MriGradientInfoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_gradient_info_cargs(params, execution)
+    ret = mri_gradient_info_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_gradient_info(
+    input_image: InputPathType,
+    runner: Runner | None = None,
+) -> MriGradientInfoOutputs:
+    """
+    A utility to obtain gradient information from MRI images using FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_image: Input MRI image file, typically in .mgz format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriGradientInfoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GRADIENT_INFO_METADATA)
+    params = mri_gradient_info_params(
+        input_image=input_image,
+    )
+    return mri_gradient_info_execute(params, execution)
+
+
+__all__ = [
+    "MRI_GRADIENT_INFO_METADATA",
+    "MriGradientInfoOutputs",
+    "MriGradientInfoParameters",
+    "mri_gradient_info",
+    "mri_gradient_info_params",
+]