niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/long_mris_slopes.py

@@ -0,0 +1,574 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+LONG_MRIS_SLOPES_METADATA = Metadata(
+    id="5ba2dca61a52a3d9141cc6cd000056f304bcba66.boutiques",
+    name="long_mris_slopes",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+LongMrisSlopesParameters = typing.TypedDict('LongMrisSlopesParameters', {
+    "__STYX_TYPE__": typing.Literal["long_mris_slopes"],
+    "qdec": InputPathType,
+    "meas": str,
+    "hemi": str,
+    "sd": str,
+    "do_avg": bool,
+    "do_rate": bool,
+    "do_pc1fit": bool,
+    "do_pc1": bool,
+    "do_spc": bool,
+    "do_stack": bool,
+    "do_label": bool,
+    "qcache": typing.NotRequired[str | None],
+    "resid": typing.NotRequired[str | None],
+    "fwhm": typing.NotRequired[str | None],
+    "nosmooth": bool,
+    "time": typing.NotRequired[str | None],
+    "generic_time": bool,
+    "in_label": typing.NotRequired[str | None],
+    "jac": bool,
+    "name_avg": typing.NotRequired[str | None],
+    "name_rate": typing.NotRequired[str | None],
+    "name_pc1fit": typing.NotRequired[str | None],
+    "name_pc1": typing.NotRequired[str | None],
+    "name_spc": typing.NotRequired[str | None],
+    "name_resid": typing.NotRequired[str | None],
+    "out_stack": typing.NotRequired[str | None],
+    "out_label": typing.NotRequired[str | None],
+    "isec_labels": typing.NotRequired[str | None],
+    "stack_avg": typing.NotRequired[str | None],
+    "stack_rate": typing.NotRequired[str | None],
+    "stack_pc1fit": typing.NotRequired[str | None],
+    "stack_pc1": typing.NotRequired[str | None],
+    "stack_spc": typing.NotRequired[str | None],
+    "stack_resid": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "long_mris_slopes": long_mris_slopes_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 LongMrisSlopesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `long_mris_slopes(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def long_mris_slopes_params(
+    qdec: InputPathType,
+    meas: str,
+    hemi: str,
+    sd: str,
+    do_avg: bool = False,
+    do_rate: bool = False,
+    do_pc1fit: bool = False,
+    do_pc1: bool = False,
+    do_spc: bool = False,
+    do_stack: bool = False,
+    do_label: bool = False,
+    qcache: str | None = None,
+    resid: str | None = None,
+    fwhm: str | None = None,
+    nosmooth: bool = False,
+    time_: str | None = None,
+    generic_time: bool = False,
+    in_label: str | None = None,
+    jac: bool = False,
+    name_avg: str | None = None,
+    name_rate: str | None = None,
+    name_pc1fit: str | None = None,
+    name_pc1: str | None = None,
+    name_spc: str | None = None,
+    name_resid: str | None = None,
+    out_stack: str | None = None,
+    out_label: str | None = None,
+    isec_labels: str | None = None,
+    stack_avg: str | None = None,
+    stack_rate: str | None = None,
+    stack_pc1fit: str | None = None,
+    stack_pc1: str | None = None,
+    stack_spc: str | None = None,
+    stack_resid: str | None = None,
+) -> LongMrisSlopesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        qdec: (REQUIRED) QDEC table file specifying the subjects and time\
+            points.
+        meas: (REQUIRED) The surface input measure (e.g. thickness).
+        hemi: (REQUIRED) Run one hemisphere: lh or rh or both.
+        sd: (REQUIRED) Full path to FreeSurfer subjects directory.
+        do_avg: Compute and output the temporal average.
+        do_rate: Compute and output the rate.
+        do_pc1fit: Compute and output the percent change (w.r.t. tp1 from\
+            linear fit).
+        do_pc1: Compute and output the percent change (w.r.t. tp1).
+        do_spc: Compute and output the symmetrized percent change (w.r.t.\
+            temporal average).
+        do_stack: Save the stacked within subject file (time series).
+        do_label: Compute and output intersected cortex label.
+        qcache: Create cache for QDEC (resample to subject <QCACHE>, e.g.\
+            fsaverage).
+        resid: Residual time point (pass 1 for tp1 etc., pass 0 for average) to\
+            export.
+        fwhm: Smoothing at specific FWHM (required for percent change).
+        nosmooth: Do not smooth the data.
+        time_: Variable name for time column variable (e.g. age) in QDEC table.
+        generic_time: Time points are ordered in QDEC file, assume\
+            time=1,2,3...
+        in_label: Use pre-existing label for smoothing and to mask the output.
+        jac: Use this flag when mapping area or volume maps to correct Jacobian.
+        name_avg: Filename (without hemi ?h) to store temporal average.
+        name_rate: Filename (without hemi ?h) to store rate.
+        name_pc1fit: Filename (without hemi ?h) to store percent change fit.
+        name_pc1: Filename (without hemi ?h) to store percent change.
+        name_spc: Filename (without hemi ?h) to store symmetrized percent\
+            change.
+        name_resid: Filename (without hemi ?h) to store residual.
+        out_stack: Filename to store stacked measure file.
+        out_label: Filename to store within-subject intersected cortex labels.
+        isec_labels: Intersect labels on <qtarget> (usually cortex labels).
+        stack_avg: Output stacked avg maps on <qtarget>.
+        stack_rate: Output stacked rate maps on <qtarget>.
+        stack_pc1fit: Output stacked PC1FIT maps on <qtarget>.
+        stack_pc1: Output stacked PC1 maps on <qtarget>.
+        stack_spc: Output stacked SPC maps on <qtarget>.
+        stack_resid: Output stacked residual maps on <qtarget>.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "long_mris_slopes",
+        "qdec": qdec,
+        "meas": meas,
+        "hemi": hemi,
+        "sd": sd,
+        "do_avg": do_avg,
+        "do_rate": do_rate,
+        "do_pc1fit": do_pc1fit,
+        "do_pc1": do_pc1,
+        "do_spc": do_spc,
+        "do_stack": do_stack,
+        "do_label": do_label,
+        "nosmooth": nosmooth,
+        "generic_time": generic_time,
+        "jac": jac,
+    }
+    if qcache is not None:
+        params["qcache"] = qcache
+    if resid is not None:
+        params["resid"] = resid
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if time_ is not None:
+        params["time"] = time_
+    if in_label is not None:
+        params["in_label"] = in_label
+    if name_avg is not None:
+        params["name_avg"] = name_avg
+    if name_rate is not None:
+        params["name_rate"] = name_rate
+    if name_pc1fit is not None:
+        params["name_pc1fit"] = name_pc1fit
+    if name_pc1 is not None:
+        params["name_pc1"] = name_pc1
+    if name_spc is not None:
+        params["name_spc"] = name_spc
+    if name_resid is not None:
+        params["name_resid"] = name_resid
+    if out_stack is not None:
+        params["out_stack"] = out_stack
+    if out_label is not None:
+        params["out_label"] = out_label
+    if isec_labels is not None:
+        params["isec_labels"] = isec_labels
+    if stack_avg is not None:
+        params["stack_avg"] = stack_avg
+    if stack_rate is not None:
+        params["stack_rate"] = stack_rate
+    if stack_pc1fit is not None:
+        params["stack_pc1fit"] = stack_pc1fit
+    if stack_pc1 is not None:
+        params["stack_pc1"] = stack_pc1
+    if stack_spc is not None:
+        params["stack_spc"] = stack_spc
+    if stack_resid is not None:
+        params["stack_resid"] = stack_resid
+    return params
+
+
+def long_mris_slopes_cargs(
+    params: LongMrisSlopesParameters,
+    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("long_mris_slopes")
+    cargs.extend([
+        "--qdec",
+        execution.input_file(params.get("qdec"))
+    ])
+    cargs.extend([
+        "--meas",
+        params.get("meas")
+    ])
+    cargs.extend([
+        "--hemi",
+        params.get("hemi")
+    ])
+    cargs.extend([
+        "--sd",
+        params.get("sd")
+    ])
+    if params.get("do_avg"):
+        cargs.append("--do-avg")
+    if params.get("do_rate"):
+        cargs.append("--do-rate")
+    if params.get("do_pc1fit"):
+        cargs.append("--do-pc1fit")
+    if params.get("do_pc1"):
+        cargs.append("--do-pc1")
+    if params.get("do_spc"):
+        cargs.append("--do-spc")
+    if params.get("do_stack"):
+        cargs.append("--do-stack")
+    if params.get("do_label"):
+        cargs.append("--do-label")
+    if params.get("qcache") is not None:
+        cargs.extend([
+            "--qcache",
+            params.get("qcache")
+        ])
+    if params.get("resid") is not None:
+        cargs.extend([
+            "--resid",
+            params.get("resid")
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "--fwhm",
+            params.get("fwhm")
+        ])
+    if params.get("nosmooth"):
+        cargs.append("--nosmooth")
+    if params.get("time") is not None:
+        cargs.extend([
+            "--time",
+            params.get("time")
+        ])
+    if params.get("generic_time"):
+        cargs.append("--generic-time")
+    if params.get("in_label") is not None:
+        cargs.extend([
+            "--in-label",
+            params.get("in_label")
+        ])
+    if params.get("jac"):
+        cargs.append("--jac")
+    if params.get("name_avg") is not None:
+        cargs.extend([
+            "--name-avg",
+            params.get("name_avg")
+        ])
+    if params.get("name_rate") is not None:
+        cargs.extend([
+            "--name-rate",
+            params.get("name_rate")
+        ])
+    if params.get("name_pc1fit") is not None:
+        cargs.extend([
+            "--name-pc1fit",
+            params.get("name_pc1fit")
+        ])
+    if params.get("name_pc1") is not None:
+        cargs.extend([
+            "--name-pc1",
+            params.get("name_pc1")
+        ])
+    if params.get("name_spc") is not None:
+        cargs.extend([
+            "--name-spc",
+            params.get("name_spc")
+        ])
+    if params.get("name_resid") is not None:
+        cargs.extend([
+            "--name-resid",
+            params.get("name_resid")
+        ])
+    if params.get("out_stack") is not None:
+        cargs.extend([
+            "--out-stack",
+            params.get("out_stack")
+        ])
+    if params.get("out_label") is not None:
+        cargs.extend([
+            "--out-label",
+            params.get("out_label")
+        ])
+    if params.get("isec_labels") is not None:
+        cargs.extend([
+            "--isec-labels",
+            params.get("isec_labels")
+        ])
+    if params.get("stack_avg") is not None:
+        cargs.extend([
+            "--stack-avg",
+            params.get("stack_avg")
+        ])
+    if params.get("stack_rate") is not None:
+        cargs.extend([
+            "--stack-rate",
+            params.get("stack_rate")
+        ])
+    if params.get("stack_pc1fit") is not None:
+        cargs.extend([
+            "--stack-pc1fit",
+            params.get("stack_pc1fit")
+        ])
+    if params.get("stack_pc1") is not None:
+        cargs.extend([
+            "--stack-pc1",
+            params.get("stack_pc1")
+        ])
+    if params.get("stack_spc") is not None:
+        cargs.extend([
+            "--stack-spc",
+            params.get("stack_spc")
+        ])
+    if params.get("stack_resid") is not None:
+        cargs.extend([
+            "--stack-resid",
+            params.get("stack_resid")
+        ])
+    return cargs
+
+
+def long_mris_slopes_outputs(
+    params: LongMrisSlopesParameters,
+    execution: Execution,
+) -> LongMrisSlopesOutputs:
+    """
+    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 = LongMrisSlopesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def long_mris_slopes_execute(
+    params: LongMrisSlopesParameters,
+    execution: Execution,
+) -> LongMrisSlopesOutputs:
+    """
+    Computes slope maps (e.g., of thickness) in a longitudinal study 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 `LongMrisSlopesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = long_mris_slopes_cargs(params, execution)
+    ret = long_mris_slopes_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def long_mris_slopes(
+    qdec: InputPathType,
+    meas: str,
+    hemi: str,
+    sd: str,
+    do_avg: bool = False,
+    do_rate: bool = False,
+    do_pc1fit: bool = False,
+    do_pc1: bool = False,
+    do_spc: bool = False,
+    do_stack: bool = False,
+    do_label: bool = False,
+    qcache: str | None = None,
+    resid: str | None = None,
+    fwhm: str | None = None,
+    nosmooth: bool = False,
+    time_: str | None = None,
+    generic_time: bool = False,
+    in_label: str | None = None,
+    jac: bool = False,
+    name_avg: str | None = None,
+    name_rate: str | None = None,
+    name_pc1fit: str | None = None,
+    name_pc1: str | None = None,
+    name_spc: str | None = None,
+    name_resid: str | None = None,
+    out_stack: str | None = None,
+    out_label: str | None = None,
+    isec_labels: str | None = None,
+    stack_avg: str | None = None,
+    stack_rate: str | None = None,
+    stack_pc1fit: str | None = None,
+    stack_pc1: str | None = None,
+    stack_spc: str | None = None,
+    stack_resid: str | None = None,
+    runner: Runner | None = None,
+) -> LongMrisSlopesOutputs:
+    """
+    Computes slope maps (e.g., of thickness) in a longitudinal study using
+    FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        qdec: (REQUIRED) QDEC table file specifying the subjects and time\
+            points.
+        meas: (REQUIRED) The surface input measure (e.g. thickness).
+        hemi: (REQUIRED) Run one hemisphere: lh or rh or both.
+        sd: (REQUIRED) Full path to FreeSurfer subjects directory.
+        do_avg: Compute and output the temporal average.
+        do_rate: Compute and output the rate.
+        do_pc1fit: Compute and output the percent change (w.r.t. tp1 from\
+            linear fit).
+        do_pc1: Compute and output the percent change (w.r.t. tp1).
+        do_spc: Compute and output the symmetrized percent change (w.r.t.\
+            temporal average).
+        do_stack: Save the stacked within subject file (time series).
+        do_label: Compute and output intersected cortex label.
+        qcache: Create cache for QDEC (resample to subject <QCACHE>, e.g.\
+            fsaverage).
+        resid: Residual time point (pass 1 for tp1 etc., pass 0 for average) to\
+            export.
+        fwhm: Smoothing at specific FWHM (required for percent change).
+        nosmooth: Do not smooth the data.
+        time_: Variable name for time column variable (e.g. age) in QDEC table.
+        generic_time: Time points are ordered in QDEC file, assume\
+            time=1,2,3...
+        in_label: Use pre-existing label for smoothing and to mask the output.
+        jac: Use this flag when mapping area or volume maps to correct Jacobian.
+        name_avg: Filename (without hemi ?h) to store temporal average.
+        name_rate: Filename (without hemi ?h) to store rate.
+        name_pc1fit: Filename (without hemi ?h) to store percent change fit.
+        name_pc1: Filename (without hemi ?h) to store percent change.
+        name_spc: Filename (without hemi ?h) to store symmetrized percent\
+            change.
+        name_resid: Filename (without hemi ?h) to store residual.
+        out_stack: Filename to store stacked measure file.
+        out_label: Filename to store within-subject intersected cortex labels.
+        isec_labels: Intersect labels on <qtarget> (usually cortex labels).
+        stack_avg: Output stacked avg maps on <qtarget>.
+        stack_rate: Output stacked rate maps on <qtarget>.
+        stack_pc1fit: Output stacked PC1FIT maps on <qtarget>.
+        stack_pc1: Output stacked PC1 maps on <qtarget>.
+        stack_spc: Output stacked SPC maps on <qtarget>.
+        stack_resid: Output stacked residual maps on <qtarget>.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `LongMrisSlopesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LONG_MRIS_SLOPES_METADATA)
+    params = long_mris_slopes_params(
+        qdec=qdec,
+        meas=meas,
+        hemi=hemi,
+        sd=sd,
+        do_avg=do_avg,
+        do_rate=do_rate,
+        do_pc1fit=do_pc1fit,
+        do_pc1=do_pc1,
+        do_spc=do_spc,
+        do_stack=do_stack,
+        do_label=do_label,
+        qcache=qcache,
+        resid=resid,
+        fwhm=fwhm,
+        nosmooth=nosmooth,
+        time_=time_,
+        generic_time=generic_time,
+        in_label=in_label,
+        jac=jac,
+        name_avg=name_avg,
+        name_rate=name_rate,
+        name_pc1fit=name_pc1fit,
+        name_pc1=name_pc1,
+        name_spc=name_spc,
+        name_resid=name_resid,
+        out_stack=out_stack,
+        out_label=out_label,
+        isec_labels=isec_labels,
+        stack_avg=stack_avg,
+        stack_rate=stack_rate,
+        stack_pc1fit=stack_pc1fit,
+        stack_pc1=stack_pc1,
+        stack_spc=stack_spc,
+        stack_resid=stack_resid,
+    )
+    return long_mris_slopes_execute(params, execution)
+
+
+__all__ = [
+    "LONG_MRIS_SLOPES_METADATA",
+    "LongMrisSlopesOutputs",
+    "LongMrisSlopesParameters",
+    "long_mris_slopes",
+    "long_mris_slopes_params",
+]