niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_glmfit.py

@@ -0,0 +1,1023 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_GLMFIT_METADATA = Metadata(
+    id="79f830582903b4c568e10c98abbe12709997f2f4.boutiques",
+    name="mri_glmfit",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriGlmfitParameters = typing.TypedDict('MriGlmfitParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_glmfit"],
+    "glmdir": typing.NotRequired[str | None],
+    "y_input": InputPathType,
+    "table_input": typing.NotRequired[InputPathType | None],
+    "fsgd": typing.NotRequired[InputPathType | None],
+    "design_matrix": typing.NotRequired[InputPathType | None],
+    "contrast_matrix": typing.NotRequired[list[InputPathType] | None],
+    "osgm_flag": bool,
+    "no_contrasts_ok_flag": bool,
+    "dti_params": typing.NotRequired[list[str] | None],
+    "dti_matrix": typing.NotRequired[InputPathType | None],
+    "pvr": typing.NotRequired[list[InputPathType] | None],
+    "selfreg": typing.NotRequired[list[float] | None],
+    "wls": typing.NotRequired[str | None],
+    "yffxvar": typing.NotRequired[InputPathType | None],
+    "ffxdof": typing.NotRequired[float | None],
+    "ffxdofdat": typing.NotRequired[InputPathType | None],
+    "weight": typing.NotRequired[InputPathType | None],
+    "weight_inv_flag": bool,
+    "weight_sqrt_flag": bool,
+    "fwhm": typing.NotRequired[float | None],
+    "var_fwhm": typing.NotRequired[float | None],
+    "no_mask_smooth_flag": bool,
+    "no_est_fwhm_flag": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "label": typing.NotRequired[InputPathType | None],
+    "no_mask_flag": bool,
+    "no_cortex_flag": bool,
+    "mask_inv_flag": bool,
+    "prune_flag": bool,
+    "no_prune_flag": bool,
+    "logy_flag": bool,
+    "no_logy_flag": bool,
+    "rm_spatial_mean_flag": bool,
+    "yhat_save_flag": bool,
+    "eres_save_flag": bool,
+    "eres_scm_flag": bool,
+    "save_fwhm_map_flag": bool,
+    "y_out": typing.NotRequired[InputPathType | None],
+    "surface": typing.NotRequired[str | None],
+    "skew_flag": bool,
+    "kurtosis_flag": bool,
+    "sim_params": typing.NotRequired[list[str] | None],
+    "sim_sign": typing.NotRequired[str | None],
+    "uniform_params": typing.NotRequired[list[str] | None],
+    "permute_input_flag": bool,
+    "pca_flag": bool,
+    "tar1_flag": bool,
+    "save_yhat_flag": bool,
+    "save_cond_flag": bool,
+    "voxdump": typing.NotRequired[list[float] | None],
+    "seed": typing.NotRequired[float | None],
+    "synth_flag": bool,
+    "resynthtest_it": typing.NotRequired[float | None],
+    "profile_it": typing.NotRequired[float | None],
+    "mrtm1_params": typing.NotRequired[list[str] | None],
+    "mrtm2_params": typing.NotRequired[list[str] | None],
+    "logan_params": typing.NotRequired[list[str] | None],
+    "bp_clip_neg_flag": bool,
+    "bp_clip_max": typing.NotRequired[float | None],
+    "perm_force_flag": bool,
+    "diag_level": typing.NotRequired[float | None],
+    "diag_cluster_flag": bool,
+    "debug_flag": bool,
+    "checkopts_flag": bool,
+    "help_flag": bool,
+    "version_flag": bool,
+    "no_fix_vertex_area_flag": bool,
+    "allowsubjrep_flag": bool,
+    "allow_zero_dof_flag": bool,
+    "illcond_flag": bool,
+    "sim_done_file": typing.NotRequired[InputPathType | None],
+    "no_sig_double_flag": 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": mri_glmfit_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": mri_glmfit_outputs,
+    }.get(t)
+
+
+class MriGlmfitOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_glmfit(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    regression_coefs: OutputPathType
+    """All regression coefficients (B)."""
+    residual_error: OutputPathType
+    """Residual error."""
+    residual_variance: OutputPathType
+    """Residual error variance."""
+    residual_stddev: OutputPathType
+    """Residual error standard deviation."""
+    fsgd_output: OutputPathType
+    """FSGD file if one was input."""
+    normalized_weights: OutputPathType
+    """Normalized weights with --w or --wls."""
+    signal_estimate: OutputPathType
+    """Signal estimate with --save-yhat."""
+    final_mask: OutputPathType
+    """Final mask when a mask is used."""
+    design_condition: OutputPathType
+    """Design matrix condition at each voxel with --save-cond."""
+    contrast_output_dir: OutputPathType
+    """Directory for each contrast output files."""
+
+
+def mri_glmfit_params(
+    y_input: InputPathType,
+    glmdir: str | None = None,
+    table_input: InputPathType | None = None,
+    fsgd: InputPathType | None = None,
+    design_matrix: InputPathType | None = None,
+    contrast_matrix: list[InputPathType] | None = None,
+    osgm_flag: bool = False,
+    no_contrasts_ok_flag: bool = False,
+    dti_params: list[str] | None = None,
+    dti_matrix: InputPathType | None = None,
+    pvr: list[InputPathType] | None = None,
+    selfreg: list[float] | None = None,
+    wls: str | None = None,
+    yffxvar: InputPathType | None = None,
+    ffxdof: float | None = None,
+    ffxdofdat: InputPathType | None = None,
+    weight: InputPathType | None = None,
+    weight_inv_flag: bool = False,
+    weight_sqrt_flag: bool = False,
+    fwhm: float | None = None,
+    var_fwhm: float | None = None,
+    no_mask_smooth_flag: bool = False,
+    no_est_fwhm_flag: bool = False,
+    mask: InputPathType | None = None,
+    label: InputPathType | None = None,
+    no_mask_flag: bool = False,
+    no_cortex_flag: bool = False,
+    mask_inv_flag: bool = False,
+    prune_flag: bool = False,
+    no_prune_flag: bool = False,
+    logy_flag: bool = False,
+    no_logy_flag: bool = False,
+    rm_spatial_mean_flag: bool = False,
+    yhat_save_flag: bool = False,
+    eres_save_flag: bool = False,
+    eres_scm_flag: bool = False,
+    save_fwhm_map_flag: bool = False,
+    y_out: InputPathType | None = None,
+    surface: str | None = None,
+    skew_flag: bool = False,
+    kurtosis_flag: bool = False,
+    sim_params: list[str] | None = None,
+    sim_sign: str | None = None,
+    uniform_params: list[str] | None = None,
+    permute_input_flag: bool = False,
+    pca_flag: bool = False,
+    tar1_flag: bool = False,
+    save_yhat_flag: bool = False,
+    save_cond_flag: bool = False,
+    voxdump: list[float] | None = None,
+    seed: float | None = None,
+    synth_flag: bool = False,
+    resynthtest_it: float | None = None,
+    profile_it: float | None = None,
+    mrtm1_params: list[str] | None = None,
+    mrtm2_params: list[str] | None = None,
+    logan_params: list[str] | None = None,
+    bp_clip_neg_flag: bool = False,
+    bp_clip_max: float | None = None,
+    perm_force_flag: bool = False,
+    diag_level: float | None = None,
+    diag_cluster_flag: bool = False,
+    debug_flag: bool = False,
+    checkopts_flag: bool = False,
+    help_flag: bool = False,
+    version_flag: bool = False,
+    no_fix_vertex_area_flag: bool = False,
+    allowsubjrep_flag: bool = False,
+    allow_zero_dof_flag: bool = False,
+    illcond_flag: bool = False,
+    sim_done_file: InputPathType | None = None,
+    no_sig_double_flag: bool = False,
+) -> MriGlmfitParameters:
+    """
+    Build parameters.
+    
+    Args:
+        y_input: Path to input file where each frame is a separate input.\
+            Accepts volume or surface-based formats.
+        glmdir: Directory where output will be saved.
+        table_input: Use text table as input instead of --y. Table should be of\
+            form produced by asegstats2table or aparcstats2table.
+        fsgd: Specify the global design matrix with a FreeSurfer Group\
+            Descriptor File (FSGDF).
+        design_matrix: Explicitly specify the design matrix. Can be in simple\
+            text or in matlab4 format.
+        contrast_matrix: Specify one or more contrasts to test. File should be\
+            ASCII text with the contrast matrix.
+        osgm_flag: Construct X and C as a one-sample group mean.
+        no_contrasts_ok_flag: Do not fail if no contrasts are specified.
+        dti_params: Do DTI analysis using bvals and bvecs.
+        dti_matrix: Do DTI analysis using provided matrix.
+        pvr: Per-voxel (or vertex) regressors.
+        selfreg: Create a 'self-regressor' from the input data based on the\
+            waveform at index col row slice.
+        wls: Perform weighted least squares (WLS) random effects analysis\
+            instead of ordinary least squares (OLS) using yffxvar.
+        yffxvar: For fixed effects analysis.
+        ffxdof: Degrees of Freedom (DOF) for fixed effects analysis.
+        ffxdofdat: Text file with DOF for fixed effects analysis.
+        weight: Perform weighted LMS using per-voxel weights from the\
+            weightfile.
+        weight_inv_flag: Invert weights.
+        weight_sqrt_flag: Square root of (inverted) weights.
+        fwhm: Smooth input with a Gaussian kernel, specified in mm.
+        var_fwhm: Smooth residual variance map with a Gaussian kernel,\
+            specified in mm.
+        no_mask_smooth_flag: Do not mask when smoothing.
+        no_est_fwhm_flag: Turn off FWHM output estimation.
+        mask: Binary mask file for analysis.
+        label: Use label as mask for surface data.
+        no_mask_flag: Do NOT use a mask, same as --no-cortex.
+        no_cortex_flag: Do NOT use subjects ?h.cortex.label as --label.
+        mask_inv_flag: Invert mask for analysis.
+        prune_flag: Remove voxels that do not have a non-zero value at each\
+            frame.
+        no_prune_flag: Do not prune zero-value voxels.
+        logy_flag: Compute natural log of y prior to analysis.
+        no_logy_flag: Do not compute natural log of y prior to analysis.
+        rm_spatial_mean_flag: Subtract the (masked) mean from each frame.
+        yhat_save_flag: Save signal estimate (yhat).
+        eres_save_flag: Save residual error (eres).
+        eres_scm_flag: Save residual error spatial correlation matrix\
+            (eres.scm).
+        save_fwhm_map_flag: Save voxel-wise map of FWHM estimates.
+        y_out: Save input after any pre-processing.
+        surface: Specify that the input has a surface geometry from the\
+            hemisphere of the given FreeSurfer subject. Required for surface data\
+            operations.
+        skew_flag: Compute skew and p-value for skew.
+        kurtosis_flag: Compute kurtosis and p-value for kurtosis.
+        sim_params: Simulate data for statistical testing. Specify nulltype,\
+            number of simulations, threshold and csd basename.
+        sim_sign: Specify sign for simulation: abs, pos, or neg.
+        uniform_params: Use uniform distribution for mc-full, specify min and\
+            max.
+        permute_input_flag: Permute input for testing purposes (not related to\
+            simulation).
+        pca_flag: Perform PCA/SVD analysis on the residual.
+        tar1_flag: Compute and save temporal AR1 of residual.
+        save_yhat_flag: Flag to save the signal estimate.
+        save_cond_flag: Flag to save design matrix condition at each voxel.
+        voxdump: Save GLM data for a single voxel at the specified col, row,\
+            slice.
+        seed: Use seed for random number generation.
+        synth_flag: Replace input data with Gaussian noise for testing.
+        resynthtest_it: Test GLM by resynthsis with the number of iterations\
+            specified.
+        profile_it: Test speed with specified number of iterations.
+        mrtm1_params: Perform MRTM1 kinetic modeling with specified reference\
+            tissue activity and time in seconds.
+        mrtm2_params: Perform MRTM2 kinetic modeling with specified parameters.
+        logan_params: Perform Logan kinetic modeling with specified parameters.
+        bp_clip_neg_flag: Set negative BP voxels to 0.
+        bp_clip_max: Set BP voxels above max to max.
+        perm_force_flag: Force permutation test, even when design matrix is not\
+            orthogonal.
+        diag_level: Set diagnostic level.
+        diag_cluster_flag: Save significant volume and exit from first\
+            simulation loop.
+        debug_flag: Turn on debugging mode.
+        checkopts_flag: Check options and exit without executing.
+        help_flag: Display help information.
+        version_flag: Print out version and exit.
+        no_fix_vertex_area_flag: Turn off fixing of vertex area (backward\
+            compatibility).
+        allowsubjrep_flag: Allow subject names to repeat in the fsgd file.
+        allow_zero_dof_flag: Allow analyses with zero degrees of freedom.
+        illcond_flag: Allow ill-conditioned design matrices.
+        sim_done_file: Create done file when simulation finishes.
+        no_sig_double_flag: Compute sig = -log10(p) from float p value, not\
+            double.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_glmfit",
+        "y_input": y_input,
+        "osgm_flag": osgm_flag,
+        "no_contrasts_ok_flag": no_contrasts_ok_flag,
+        "weight_inv_flag": weight_inv_flag,
+        "weight_sqrt_flag": weight_sqrt_flag,
+        "no_mask_smooth_flag": no_mask_smooth_flag,
+        "no_est_fwhm_flag": no_est_fwhm_flag,
+        "no_mask_flag": no_mask_flag,
+        "no_cortex_flag": no_cortex_flag,
+        "mask_inv_flag": mask_inv_flag,
+        "prune_flag": prune_flag,
+        "no_prune_flag": no_prune_flag,
+        "logy_flag": logy_flag,
+        "no_logy_flag": no_logy_flag,
+        "rm_spatial_mean_flag": rm_spatial_mean_flag,
+        "yhat_save_flag": yhat_save_flag,
+        "eres_save_flag": eres_save_flag,
+        "eres_scm_flag": eres_scm_flag,
+        "save_fwhm_map_flag": save_fwhm_map_flag,
+        "skew_flag": skew_flag,
+        "kurtosis_flag": kurtosis_flag,
+        "permute_input_flag": permute_input_flag,
+        "pca_flag": pca_flag,
+        "tar1_flag": tar1_flag,
+        "save_yhat_flag": save_yhat_flag,
+        "save_cond_flag": save_cond_flag,
+        "synth_flag": synth_flag,
+        "bp_clip_neg_flag": bp_clip_neg_flag,
+        "perm_force_flag": perm_force_flag,
+        "diag_cluster_flag": diag_cluster_flag,
+        "debug_flag": debug_flag,
+        "checkopts_flag": checkopts_flag,
+        "help_flag": help_flag,
+        "version_flag": version_flag,
+        "no_fix_vertex_area_flag": no_fix_vertex_area_flag,
+        "allowsubjrep_flag": allowsubjrep_flag,
+        "allow_zero_dof_flag": allow_zero_dof_flag,
+        "illcond_flag": illcond_flag,
+        "no_sig_double_flag": no_sig_double_flag,
+    }
+    if glmdir is not None:
+        params["glmdir"] = glmdir
+    if table_input is not None:
+        params["table_input"] = table_input
+    if fsgd is not None:
+        params["fsgd"] = fsgd
+    if design_matrix is not None:
+        params["design_matrix"] = design_matrix
+    if contrast_matrix is not None:
+        params["contrast_matrix"] = contrast_matrix
+    if dti_params is not None:
+        params["dti_params"] = dti_params
+    if dti_matrix is not None:
+        params["dti_matrix"] = dti_matrix
+    if pvr is not None:
+        params["pvr"] = pvr
+    if selfreg is not None:
+        params["selfreg"] = selfreg
+    if wls is not None:
+        params["wls"] = wls
+    if yffxvar is not None:
+        params["yffxvar"] = yffxvar
+    if ffxdof is not None:
+        params["ffxdof"] = ffxdof
+    if ffxdofdat is not None:
+        params["ffxdofdat"] = ffxdofdat
+    if weight is not None:
+        params["weight"] = weight
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if var_fwhm is not None:
+        params["var_fwhm"] = var_fwhm
+    if mask is not None:
+        params["mask"] = mask
+    if label is not None:
+        params["label"] = label
+    if y_out is not None:
+        params["y_out"] = y_out
+    if surface is not None:
+        params["surface"] = surface
+    if sim_params is not None:
+        params["sim_params"] = sim_params
+    if sim_sign is not None:
+        params["sim_sign"] = sim_sign
+    if uniform_params is not None:
+        params["uniform_params"] = uniform_params
+    if voxdump is not None:
+        params["voxdump"] = voxdump
+    if seed is not None:
+        params["seed"] = seed
+    if resynthtest_it is not None:
+        params["resynthtest_it"] = resynthtest_it
+    if profile_it is not None:
+        params["profile_it"] = profile_it
+    if mrtm1_params is not None:
+        params["mrtm1_params"] = mrtm1_params
+    if mrtm2_params is not None:
+        params["mrtm2_params"] = mrtm2_params
+    if logan_params is not None:
+        params["logan_params"] = logan_params
+    if bp_clip_max is not None:
+        params["bp_clip_max"] = bp_clip_max
+    if diag_level is not None:
+        params["diag_level"] = diag_level
+    if sim_done_file is not None:
+        params["sim_done_file"] = sim_done_file
+    return params
+
+
+def mri_glmfit_cargs(
+    params: MriGlmfitParameters,
+    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")
+    if params.get("glmdir") is not None:
+        cargs.extend([
+            "--glmdir",
+            params.get("glmdir")
+        ])
+    cargs.extend([
+        "--y",
+        execution.input_file(params.get("y_input"))
+    ])
+    if params.get("table_input") is not None:
+        cargs.extend([
+            "--table",
+            execution.input_file(params.get("table_input"))
+        ])
+    if params.get("fsgd") is not None:
+        cargs.extend([
+            "--fsgd",
+            execution.input_file(params.get("fsgd"))
+        ])
+    if params.get("design_matrix") is not None:
+        cargs.extend([
+            "--X",
+            execution.input_file(params.get("design_matrix"))
+        ])
+    if params.get("contrast_matrix") is not None:
+        cargs.extend([
+            "--C",
+            *[execution.input_file(f) for f in params.get("contrast_matrix")]
+        ])
+    if params.get("osgm_flag"):
+        cargs.append("--osgm")
+    if params.get("no_contrasts_ok_flag"):
+        cargs.append("--no-contrasts-ok")
+    if params.get("dti_params") is not None:
+        cargs.extend([
+            "--dti",
+            *params.get("dti_params")
+        ])
+    if params.get("dti_matrix") is not None:
+        cargs.extend([
+            "--dti-X",
+            execution.input_file(params.get("dti_matrix"))
+        ])
+    if params.get("pvr") is not None:
+        cargs.extend([
+            "--pvr",
+            *[execution.input_file(f) for f in params.get("pvr")]
+        ])
+    if params.get("selfreg") is not None:
+        cargs.extend([
+            "--selfreg",
+            *map(str, params.get("selfreg"))
+        ])
+    if params.get("wls") is not None:
+        cargs.extend([
+            "--wls",
+            params.get("wls")
+        ])
+    if params.get("yffxvar") is not None:
+        cargs.extend([
+            "--yffxvar",
+            execution.input_file(params.get("yffxvar"))
+        ])
+    if params.get("ffxdof") is not None:
+        cargs.extend([
+            "--ffxdof",
+            str(params.get("ffxdof"))
+        ])
+    if params.get("ffxdofdat") is not None:
+        cargs.extend([
+            "--ffxdofdat",
+            execution.input_file(params.get("ffxdofdat"))
+        ])
+    if params.get("weight") is not None:
+        cargs.extend([
+            "--w",
+            execution.input_file(params.get("weight"))
+        ])
+    if params.get("weight_inv_flag"):
+        cargs.append("--w-inv")
+    if params.get("weight_sqrt_flag"):
+        cargs.append("--w-sqrt")
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("var_fwhm") is not None:
+        cargs.extend([
+            "--var-fwhm",
+            str(params.get("var_fwhm"))
+        ])
+    if params.get("no_mask_smooth_flag"):
+        cargs.append("--no-mask-smooth")
+    if params.get("no_est_fwhm_flag"):
+        cargs.append("--no-est-fwhm")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "--mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("label") is not None:
+        cargs.extend([
+            "--label",
+            execution.input_file(params.get("label"))
+        ])
+    if params.get("no_mask_flag"):
+        cargs.append("--no-mask")
+    if params.get("no_cortex_flag"):
+        cargs.append("--no-cortex")
+    if params.get("mask_inv_flag"):
+        cargs.append("--mask-inv")
+    if params.get("prune_flag"):
+        cargs.append("--prune")
+    if params.get("no_prune_flag"):
+        cargs.append("--no-prune")
+    if params.get("logy_flag"):
+        cargs.append("--logy")
+    if params.get("no_logy_flag"):
+        cargs.append("--no-logy")
+    if params.get("rm_spatial_mean_flag"):
+        cargs.append("--rm-spatial-mean")
+    if params.get("yhat_save_flag"):
+        cargs.append("--yhat-save")
+    if params.get("eres_save_flag"):
+        cargs.append("--eres-save")
+    if params.get("eres_scm_flag"):
+        cargs.append("--eres-scm")
+    if params.get("save_fwhm_map_flag"):
+        cargs.append("--save-fwhm-map")
+    if params.get("y_out") is not None:
+        cargs.extend([
+            "--y-out",
+            execution.input_file(params.get("y_out"))
+        ])
+    if params.get("surface") is not None:
+        cargs.extend([
+            "--surf",
+            params.get("surface")
+        ])
+    if params.get("skew_flag"):
+        cargs.append("--skew")
+    if params.get("kurtosis_flag"):
+        cargs.append("--kurtosis")
+    if params.get("sim_params") is not None:
+        cargs.extend([
+            "--sim",
+            *params.get("sim_params")
+        ])
+    if params.get("sim_sign") is not None:
+        cargs.extend([
+            "--sim-sign",
+            params.get("sim_sign")
+        ])
+    if params.get("uniform_params") is not None:
+        cargs.extend([
+            "--uniform",
+            *params.get("uniform_params")
+        ])
+    if params.get("permute_input_flag"):
+        cargs.append("--permute-input")
+    if params.get("pca_flag"):
+        cargs.append("--pca")
+    if params.get("tar1_flag"):
+        cargs.append("--tar1")
+    if params.get("save_yhat_flag"):
+        cargs.append("--save-yhat")
+    if params.get("save_cond_flag"):
+        cargs.append("--save-cond")
+    if params.get("voxdump") is not None:
+        cargs.extend([
+            "--voxdump",
+            *map(str, params.get("voxdump"))
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "--seed",
+            str(params.get("seed"))
+        ])
+    if params.get("synth_flag"):
+        cargs.append("--synth")
+    if params.get("resynthtest_it") is not None:
+        cargs.extend([
+            "--resynthtest",
+            str(params.get("resynthtest_it"))
+        ])
+    if params.get("profile_it") is not None:
+        cargs.extend([
+            "--profile",
+            str(params.get("profile_it"))
+        ])
+    if params.get("mrtm1_params") is not None:
+        cargs.extend([
+            "--mrtm1",
+            *params.get("mrtm1_params")
+        ])
+    if params.get("mrtm2_params") is not None:
+        cargs.extend([
+            "--mrtm2",
+            *params.get("mrtm2_params")
+        ])
+    if params.get("logan_params") is not None:
+        cargs.extend([
+            "--logan",
+            *params.get("logan_params")
+        ])
+    if params.get("bp_clip_neg_flag"):
+        cargs.append("--bp-clip-neg")
+    if params.get("bp_clip_max") is not None:
+        cargs.extend([
+            "--bp-clip-max",
+            str(params.get("bp_clip_max"))
+        ])
+    if params.get("perm_force_flag"):
+        cargs.append("--perm-force")
+    if params.get("diag_level") is not None:
+        cargs.extend([
+            "--diag",
+            str(params.get("diag_level"))
+        ])
+    if params.get("diag_cluster_flag"):
+        cargs.append("--diag-cluster")
+    if params.get("debug_flag"):
+        cargs.append("--debug")
+    if params.get("checkopts_flag"):
+        cargs.append("--checkopts")
+    if params.get("help_flag"):
+        cargs.append("--help")
+    if params.get("version_flag"):
+        cargs.append("--version")
+    if params.get("no_fix_vertex_area_flag"):
+        cargs.append("--no-fix-vertex-area")
+    if params.get("allowsubjrep_flag"):
+        cargs.append("--allowsubjrep")
+    if params.get("allow_zero_dof_flag"):
+        cargs.append("--allow-zero-dof")
+    if params.get("illcond_flag"):
+        cargs.append("--illcond")
+    if params.get("sim_done_file") is not None:
+        cargs.extend([
+            "--sim-done",
+            execution.input_file(params.get("sim_done_file"))
+        ])
+    if params.get("no_sig_double_flag"):
+        cargs.append("--no-sig-double")
+    return cargs
+
+
+def mri_glmfit_outputs(
+    params: MriGlmfitParameters,
+    execution: Execution,
+) -> MriGlmfitOutputs:
+    """
+    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 = MriGlmfitOutputs(
+        root=execution.output_file("."),
+        regression_coefs=execution.output_file("beta.mgh"),
+        residual_error=execution.output_file("eres.mgh"),
+        residual_variance=execution.output_file("rvar.mgh"),
+        residual_stddev=execution.output_file("rstd.mgh"),
+        fsgd_output=execution.output_file("y.fsgd"),
+        normalized_weights=execution.output_file("wn.mgh"),
+        signal_estimate=execution.output_file("yhat.mgh"),
+        final_mask=execution.output_file("mask.mgh"),
+        design_condition=execution.output_file("cond.mgh"),
+        contrast_output_dir=execution.output_file("contrast1name"),
+    )
+    return ret
+
+
+def mri_glmfit_execute(
+    params: MriGlmfitParameters,
+    execution: Execution,
+) -> MriGlmfitOutputs:
+    """
+    Performs general linear model (GLM) analysis in the volume or the surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriGlmfitOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_glmfit_cargs(params, execution)
+    ret = mri_glmfit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_glmfit(
+    y_input: InputPathType,
+    glmdir: str | None = None,
+    table_input: InputPathType | None = None,
+    fsgd: InputPathType | None = None,
+    design_matrix: InputPathType | None = None,
+    contrast_matrix: list[InputPathType] | None = None,
+    osgm_flag: bool = False,
+    no_contrasts_ok_flag: bool = False,
+    dti_params: list[str] | None = None,
+    dti_matrix: InputPathType | None = None,
+    pvr: list[InputPathType] | None = None,
+    selfreg: list[float] | None = None,
+    wls: str | None = None,
+    yffxvar: InputPathType | None = None,
+    ffxdof: float | None = None,
+    ffxdofdat: InputPathType | None = None,
+    weight: InputPathType | None = None,
+    weight_inv_flag: bool = False,
+    weight_sqrt_flag: bool = False,
+    fwhm: float | None = None,
+    var_fwhm: float | None = None,
+    no_mask_smooth_flag: bool = False,
+    no_est_fwhm_flag: bool = False,
+    mask: InputPathType | None = None,
+    label: InputPathType | None = None,
+    no_mask_flag: bool = False,
+    no_cortex_flag: bool = False,
+    mask_inv_flag: bool = False,
+    prune_flag: bool = False,
+    no_prune_flag: bool = False,
+    logy_flag: bool = False,
+    no_logy_flag: bool = False,
+    rm_spatial_mean_flag: bool = False,
+    yhat_save_flag: bool = False,
+    eres_save_flag: bool = False,
+    eres_scm_flag: bool = False,
+    save_fwhm_map_flag: bool = False,
+    y_out: InputPathType | None = None,
+    surface: str | None = None,
+    skew_flag: bool = False,
+    kurtosis_flag: bool = False,
+    sim_params: list[str] | None = None,
+    sim_sign: str | None = None,
+    uniform_params: list[str] | None = None,
+    permute_input_flag: bool = False,
+    pca_flag: bool = False,
+    tar1_flag: bool = False,
+    save_yhat_flag: bool = False,
+    save_cond_flag: bool = False,
+    voxdump: list[float] | None = None,
+    seed: float | None = None,
+    synth_flag: bool = False,
+    resynthtest_it: float | None = None,
+    profile_it: float | None = None,
+    mrtm1_params: list[str] | None = None,
+    mrtm2_params: list[str] | None = None,
+    logan_params: list[str] | None = None,
+    bp_clip_neg_flag: bool = False,
+    bp_clip_max: float | None = None,
+    perm_force_flag: bool = False,
+    diag_level: float | None = None,
+    diag_cluster_flag: bool = False,
+    debug_flag: bool = False,
+    checkopts_flag: bool = False,
+    help_flag: bool = False,
+    version_flag: bool = False,
+    no_fix_vertex_area_flag: bool = False,
+    allowsubjrep_flag: bool = False,
+    allow_zero_dof_flag: bool = False,
+    illcond_flag: bool = False,
+    sim_done_file: InputPathType | None = None,
+    no_sig_double_flag: bool = False,
+    runner: Runner | None = None,
+) -> MriGlmfitOutputs:
+    """
+    Performs general linear model (GLM) analysis in the volume or the surface.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        y_input: Path to input file where each frame is a separate input.\
+            Accepts volume or surface-based formats.
+        glmdir: Directory where output will be saved.
+        table_input: Use text table as input instead of --y. Table should be of\
+            form produced by asegstats2table or aparcstats2table.
+        fsgd: Specify the global design matrix with a FreeSurfer Group\
+            Descriptor File (FSGDF).
+        design_matrix: Explicitly specify the design matrix. Can be in simple\
+            text or in matlab4 format.
+        contrast_matrix: Specify one or more contrasts to test. File should be\
+            ASCII text with the contrast matrix.
+        osgm_flag: Construct X and C as a one-sample group mean.
+        no_contrasts_ok_flag: Do not fail if no contrasts are specified.
+        dti_params: Do DTI analysis using bvals and bvecs.
+        dti_matrix: Do DTI analysis using provided matrix.
+        pvr: Per-voxel (or vertex) regressors.
+        selfreg: Create a 'self-regressor' from the input data based on the\
+            waveform at index col row slice.
+        wls: Perform weighted least squares (WLS) random effects analysis\
+            instead of ordinary least squares (OLS) using yffxvar.
+        yffxvar: For fixed effects analysis.
+        ffxdof: Degrees of Freedom (DOF) for fixed effects analysis.
+        ffxdofdat: Text file with DOF for fixed effects analysis.
+        weight: Perform weighted LMS using per-voxel weights from the\
+            weightfile.
+        weight_inv_flag: Invert weights.
+        weight_sqrt_flag: Square root of (inverted) weights.
+        fwhm: Smooth input with a Gaussian kernel, specified in mm.
+        var_fwhm: Smooth residual variance map with a Gaussian kernel,\
+            specified in mm.
+        no_mask_smooth_flag: Do not mask when smoothing.
+        no_est_fwhm_flag: Turn off FWHM output estimation.
+        mask: Binary mask file for analysis.
+        label: Use label as mask for surface data.
+        no_mask_flag: Do NOT use a mask, same as --no-cortex.
+        no_cortex_flag: Do NOT use subjects ?h.cortex.label as --label.
+        mask_inv_flag: Invert mask for analysis.
+        prune_flag: Remove voxels that do not have a non-zero value at each\
+            frame.
+        no_prune_flag: Do not prune zero-value voxels.
+        logy_flag: Compute natural log of y prior to analysis.
+        no_logy_flag: Do not compute natural log of y prior to analysis.
+        rm_spatial_mean_flag: Subtract the (masked) mean from each frame.
+        yhat_save_flag: Save signal estimate (yhat).
+        eres_save_flag: Save residual error (eres).
+        eres_scm_flag: Save residual error spatial correlation matrix\
+            (eres.scm).
+        save_fwhm_map_flag: Save voxel-wise map of FWHM estimates.
+        y_out: Save input after any pre-processing.
+        surface: Specify that the input has a surface geometry from the\
+            hemisphere of the given FreeSurfer subject. Required for surface data\
+            operations.
+        skew_flag: Compute skew and p-value for skew.
+        kurtosis_flag: Compute kurtosis and p-value for kurtosis.
+        sim_params: Simulate data for statistical testing. Specify nulltype,\
+            number of simulations, threshold and csd basename.
+        sim_sign: Specify sign for simulation: abs, pos, or neg.
+        uniform_params: Use uniform distribution for mc-full, specify min and\
+            max.
+        permute_input_flag: Permute input for testing purposes (not related to\
+            simulation).
+        pca_flag: Perform PCA/SVD analysis on the residual.
+        tar1_flag: Compute and save temporal AR1 of residual.
+        save_yhat_flag: Flag to save the signal estimate.
+        save_cond_flag: Flag to save design matrix condition at each voxel.
+        voxdump: Save GLM data for a single voxel at the specified col, row,\
+            slice.
+        seed: Use seed for random number generation.
+        synth_flag: Replace input data with Gaussian noise for testing.
+        resynthtest_it: Test GLM by resynthsis with the number of iterations\
+            specified.
+        profile_it: Test speed with specified number of iterations.
+        mrtm1_params: Perform MRTM1 kinetic modeling with specified reference\
+            tissue activity and time in seconds.
+        mrtm2_params: Perform MRTM2 kinetic modeling with specified parameters.
+        logan_params: Perform Logan kinetic modeling with specified parameters.
+        bp_clip_neg_flag: Set negative BP voxels to 0.
+        bp_clip_max: Set BP voxels above max to max.
+        perm_force_flag: Force permutation test, even when design matrix is not\
+            orthogonal.
+        diag_level: Set diagnostic level.
+        diag_cluster_flag: Save significant volume and exit from first\
+            simulation loop.
+        debug_flag: Turn on debugging mode.
+        checkopts_flag: Check options and exit without executing.
+        help_flag: Display help information.
+        version_flag: Print out version and exit.
+        no_fix_vertex_area_flag: Turn off fixing of vertex area (backward\
+            compatibility).
+        allowsubjrep_flag: Allow subject names to repeat in the fsgd file.
+        allow_zero_dof_flag: Allow analyses with zero degrees of freedom.
+        illcond_flag: Allow ill-conditioned design matrices.
+        sim_done_file: Create done file when simulation finishes.
+        no_sig_double_flag: Compute sig = -log10(p) from float p value, not\
+            double.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriGlmfitOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GLMFIT_METADATA)
+    params = mri_glmfit_params(
+        glmdir=glmdir,
+        y_input=y_input,
+        table_input=table_input,
+        fsgd=fsgd,
+        design_matrix=design_matrix,
+        contrast_matrix=contrast_matrix,
+        osgm_flag=osgm_flag,
+        no_contrasts_ok_flag=no_contrasts_ok_flag,
+        dti_params=dti_params,
+        dti_matrix=dti_matrix,
+        pvr=pvr,
+        selfreg=selfreg,
+        wls=wls,
+        yffxvar=yffxvar,
+        ffxdof=ffxdof,
+        ffxdofdat=ffxdofdat,
+        weight=weight,
+        weight_inv_flag=weight_inv_flag,
+        weight_sqrt_flag=weight_sqrt_flag,
+        fwhm=fwhm,
+        var_fwhm=var_fwhm,
+        no_mask_smooth_flag=no_mask_smooth_flag,
+        no_est_fwhm_flag=no_est_fwhm_flag,
+        mask=mask,
+        label=label,
+        no_mask_flag=no_mask_flag,
+        no_cortex_flag=no_cortex_flag,
+        mask_inv_flag=mask_inv_flag,
+        prune_flag=prune_flag,
+        no_prune_flag=no_prune_flag,
+        logy_flag=logy_flag,
+        no_logy_flag=no_logy_flag,
+        rm_spatial_mean_flag=rm_spatial_mean_flag,
+        yhat_save_flag=yhat_save_flag,
+        eres_save_flag=eres_save_flag,
+        eres_scm_flag=eres_scm_flag,
+        save_fwhm_map_flag=save_fwhm_map_flag,
+        y_out=y_out,
+        surface=surface,
+        skew_flag=skew_flag,
+        kurtosis_flag=kurtosis_flag,
+        sim_params=sim_params,
+        sim_sign=sim_sign,
+        uniform_params=uniform_params,
+        permute_input_flag=permute_input_flag,
+        pca_flag=pca_flag,
+        tar1_flag=tar1_flag,
+        save_yhat_flag=save_yhat_flag,
+        save_cond_flag=save_cond_flag,
+        voxdump=voxdump,
+        seed=seed,
+        synth_flag=synth_flag,
+        resynthtest_it=resynthtest_it,
+        profile_it=profile_it,
+        mrtm1_params=mrtm1_params,
+        mrtm2_params=mrtm2_params,
+        logan_params=logan_params,
+        bp_clip_neg_flag=bp_clip_neg_flag,
+        bp_clip_max=bp_clip_max,
+        perm_force_flag=perm_force_flag,
+        diag_level=diag_level,
+        diag_cluster_flag=diag_cluster_flag,
+        debug_flag=debug_flag,
+        checkopts_flag=checkopts_flag,
+        help_flag=help_flag,
+        version_flag=version_flag,
+        no_fix_vertex_area_flag=no_fix_vertex_area_flag,
+        allowsubjrep_flag=allowsubjrep_flag,
+        allow_zero_dof_flag=allow_zero_dof_flag,
+        illcond_flag=illcond_flag,
+        sim_done_file=sim_done_file,
+        no_sig_double_flag=no_sig_double_flag,
+    )
+    return mri_glmfit_execute(params, execution)
+
+
+__all__ = [
+    "MRI_GLMFIT_METADATA",
+    "MriGlmfitOutputs",
+    "MriGlmfitParameters",
+    "mri_glmfit",
+    "mri_glmfit_params",
+]