niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/stat_normalize.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+STAT_NORMALIZE_METADATA = Metadata(
+    id="8f7cdbd11149e9374f79034222936da63d116040.boutiques",
+    name="stat_normalize",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+StatNormalizeParameters = typing.TypedDict('StatNormalizeParameters', {
+    "__STYX_TYPE__": typing.Literal["stat_normalize"],
+    "input_sv_prefix": str,
+    "output_sv_prefix": str,
+    "resolution": typing.NotRequired[float | None],
+    "field_of_view": typing.NotRequired[float | None],
+    "sph_avg": typing.NotRequired[str | None],
+    "xfm_file": typing.NotRequired[str | None],
+    "fix_xfm_flag": bool,
+    "float2int_option": 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 {
+        "stat_normalize": stat_normalize_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 StatNormalizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `stat_normalize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def stat_normalize_params(
+    input_sv_prefix: str,
+    output_sv_prefix: str,
+    resolution: float | None = None,
+    field_of_view: float | None = None,
+    sph_avg: str | None = None,
+    xfm_file: str | None = None,
+    fix_xfm_flag: bool = False,
+    float2int_option: str | None = None,
+) -> StatNormalizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_sv_prefix: Input subject volume prefix.
+        output_sv_prefix: Output subject volume prefix.
+        resolution: Set output resolution in mm (default is 8mm).
+        field_of_view: Set output field of view (default is 256).
+        sph_avg: Average in spherical coordinates by specifying hemisphere and\
+            surface.
+        xfm_file: Use specified transform file (subjid/mri/transforms/xfmfile).
+        fix_xfm_flag: Fix transform for non-zero center of original volume.
+        float2int_option: Specify float to int conversion to tkregister or\
+            round.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "stat_normalize",
+        "input_sv_prefix": input_sv_prefix,
+        "output_sv_prefix": output_sv_prefix,
+        "fix_xfm_flag": fix_xfm_flag,
+    }
+    if resolution is not None:
+        params["resolution"] = resolution
+    if field_of_view is not None:
+        params["field_of_view"] = field_of_view
+    if sph_avg is not None:
+        params["sph_avg"] = sph_avg
+    if xfm_file is not None:
+        params["xfm_file"] = xfm_file
+    if float2int_option is not None:
+        params["float2int_option"] = float2int_option
+    return params
+
+
+def stat_normalize_cargs(
+    params: StatNormalizeParameters,
+    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("stat_normalize")
+    cargs.append(params.get("input_sv_prefix"))
+    cargs.append(params.get("output_sv_prefix"))
+    if params.get("resolution") is not None:
+        cargs.extend([
+            "-r",
+            str(params.get("resolution"))
+        ])
+    if params.get("field_of_view") is not None:
+        cargs.extend([
+            "-f",
+            str(params.get("field_of_view"))
+        ])
+    if params.get("sph_avg") is not None:
+        cargs.extend([
+            "-S",
+            params.get("sph_avg")
+        ])
+    if params.get("xfm_file") is not None:
+        cargs.extend([
+            "-x",
+            params.get("xfm_file")
+        ])
+    if params.get("fix_xfm_flag"):
+        cargs.append("-i")
+    if params.get("float2int_option") is not None:
+        cargs.extend([
+            "-c",
+            params.get("float2int_option")
+        ])
+    return cargs
+
+
+def stat_normalize_outputs(
+    params: StatNormalizeParameters,
+    execution: Execution,
+) -> StatNormalizeOutputs:
+    """
+    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 = StatNormalizeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def stat_normalize_execute(
+    params: StatNormalizeParameters,
+    execution: Execution,
+) -> StatNormalizeOutputs:
+    """
+    This program will convert and average a sequence of volume-based statistics in
+    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 `StatNormalizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = stat_normalize_cargs(params, execution)
+    ret = stat_normalize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def stat_normalize(
+    input_sv_prefix: str,
+    output_sv_prefix: str,
+    resolution: float | None = None,
+    field_of_view: float | None = None,
+    sph_avg: str | None = None,
+    xfm_file: str | None = None,
+    fix_xfm_flag: bool = False,
+    float2int_option: str | None = None,
+    runner: Runner | None = None,
+) -> StatNormalizeOutputs:
+    """
+    This program will convert and average a sequence of volume-based statistics in
+    Talairach space.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_sv_prefix: Input subject volume prefix.
+        output_sv_prefix: Output subject volume prefix.
+        resolution: Set output resolution in mm (default is 8mm).
+        field_of_view: Set output field of view (default is 256).
+        sph_avg: Average in spherical coordinates by specifying hemisphere and\
+            surface.
+        xfm_file: Use specified transform file (subjid/mri/transforms/xfmfile).
+        fix_xfm_flag: Fix transform for non-zero center of original volume.
+        float2int_option: Specify float to int conversion to tkregister or\
+            round.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `StatNormalizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STAT_NORMALIZE_METADATA)
+    params = stat_normalize_params(
+        input_sv_prefix=input_sv_prefix,
+        output_sv_prefix=output_sv_prefix,
+        resolution=resolution,
+        field_of_view=field_of_view,
+        sph_avg=sph_avg,
+        xfm_file=xfm_file,
+        fix_xfm_flag=fix_xfm_flag,
+        float2int_option=float2int_option,
+    )
+    return stat_normalize_execute(params, execution)
+
+
+__all__ = [
+    "STAT_NORMALIZE_METADATA",
+    "StatNormalizeOutputs",
+    "StatNormalizeParameters",
+    "stat_normalize",
+    "stat_normalize_params",
+]

niwrap_freesurfer/freesurfer/stattablediff.py

@@ -0,0 +1,281 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+STATTABLEDIFF_METADATA = Metadata(
+    id="1700b5a4affda702434ee9916d498190f06c350c.boutiques",
+    name="stattablediff",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+StattablediffParameters = typing.TypedDict('StattablediffParameters', {
+    "__STYX_TYPE__": typing.Literal["stattablediff"],
+    "t1": InputPathType,
+    "t2": InputPathType,
+    "output": str,
+    "percent_diff": bool,
+    "percent_diff_t1": bool,
+    "percent_diff_t2": bool,
+    "multiply": typing.NotRequired[float | None],
+    "divide": typing.NotRequired[float | None],
+    "common": bool,
+    "remove_exvivo": bool,
+    "diff_subjects": bool,
+    "noreplace53": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "stattablediff": stattablediff_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 {
+        "stattablediff": stattablediff_outputs,
+    }.get(t)
+
+
+class StattablediffOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `stattablediff(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_diff_table: OutputPathType
+    """Generated table of differences"""
+
+
+def stattablediff_params(
+    t1: InputPathType,
+    t2: InputPathType,
+    output: str,
+    percent_diff: bool = False,
+    percent_diff_t1: bool = False,
+    percent_diff_t2: bool = False,
+    multiply: float | None = None,
+    divide: float | None = None,
+    common: bool = False,
+    remove_exvivo: bool = False,
+    diff_subjects: bool = False,
+    noreplace53: bool = False,
+) -> StattablediffParameters:
+    """
+    Build parameters.
+    
+    Args:
+        t1: Input table 1 (output of asegstats2table or aparcstats2table).
+        t2: Input table 2 (output of asegstats2table or aparcstats2table).
+        output: Output file for the table of differences.
+        percent_diff: Compute percent difference with respect to mean of tables.
+        percent_diff_t1: Compute percent difference with respect to table 1.
+        percent_diff_t2: Compute percent difference with respect to table 2.
+        multiply: Multiply by mulval.
+        divide: Divide by divval.
+        common: Compute difference on common segments (may reorder).
+        remove_exvivo: Remove the string '_exvivo' from the column header.
+        diff_subjects: Compare subjects with different names.
+        noreplace53: Do not replace 5.3 structure names with later names.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "stattablediff",
+        "t1": t1,
+        "t2": t2,
+        "output": output,
+        "percent_diff": percent_diff,
+        "percent_diff_t1": percent_diff_t1,
+        "percent_diff_t2": percent_diff_t2,
+        "common": common,
+        "remove_exvivo": remove_exvivo,
+        "diff_subjects": diff_subjects,
+        "noreplace53": noreplace53,
+    }
+    if multiply is not None:
+        params["multiply"] = multiply
+    if divide is not None:
+        params["divide"] = divide
+    return params
+
+
+def stattablediff_cargs(
+    params: StattablediffParameters,
+    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("stattablediff")
+    cargs.append(execution.input_file(params.get("t1")))
+    cargs.append(execution.input_file(params.get("t2")))
+    cargs.append(params.get("output"))
+    if params.get("percent_diff"):
+        cargs.append("--percent")
+    if params.get("percent_diff_t1"):
+        cargs.append("--percent1")
+    if params.get("percent_diff_t2"):
+        cargs.append("--percent2")
+    if params.get("multiply") is not None:
+        cargs.extend([
+            "--mul",
+            str(params.get("multiply"))
+        ])
+    if params.get("divide") is not None:
+        cargs.extend([
+            "--div",
+            str(params.get("divide"))
+        ])
+    if params.get("common"):
+        cargs.append("--common")
+    if params.get("remove_exvivo"):
+        cargs.append("--rm-exvivo")
+    if params.get("diff_subjects"):
+        cargs.append("--diff-subjs")
+    if params.get("noreplace53"):
+        cargs.append("--noreplace53")
+    return cargs
+
+
+def stattablediff_outputs(
+    params: StattablediffParameters,
+    execution: Execution,
+) -> StattablediffOutputs:
+    """
+    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 = StattablediffOutputs(
+        root=execution.output_file("."),
+        output_diff_table=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def stattablediff_execute(
+    params: StattablediffParameters,
+    execution: Execution,
+) -> StattablediffOutputs:
+    """
+    Creates a table of the differences between two stats tables.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `StattablediffOutputs`).
+    """
+    params = execution.params(params)
+    cargs = stattablediff_cargs(params, execution)
+    ret = stattablediff_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def stattablediff(
+    t1: InputPathType,
+    t2: InputPathType,
+    output: str,
+    percent_diff: bool = False,
+    percent_diff_t1: bool = False,
+    percent_diff_t2: bool = False,
+    multiply: float | None = None,
+    divide: float | None = None,
+    common: bool = False,
+    remove_exvivo: bool = False,
+    diff_subjects: bool = False,
+    noreplace53: bool = False,
+    runner: Runner | None = None,
+) -> StattablediffOutputs:
+    """
+    Creates a table of the differences between two stats tables.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        t1: Input table 1 (output of asegstats2table or aparcstats2table).
+        t2: Input table 2 (output of asegstats2table or aparcstats2table).
+        output: Output file for the table of differences.
+        percent_diff: Compute percent difference with respect to mean of tables.
+        percent_diff_t1: Compute percent difference with respect to table 1.
+        percent_diff_t2: Compute percent difference with respect to table 2.
+        multiply: Multiply by mulval.
+        divide: Divide by divval.
+        common: Compute difference on common segments (may reorder).
+        remove_exvivo: Remove the string '_exvivo' from the column header.
+        diff_subjects: Compare subjects with different names.
+        noreplace53: Do not replace 5.3 structure names with later names.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `StattablediffOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STATTABLEDIFF_METADATA)
+    params = stattablediff_params(
+        t1=t1,
+        t2=t2,
+        output=output,
+        percent_diff=percent_diff,
+        percent_diff_t1=percent_diff_t1,
+        percent_diff_t2=percent_diff_t2,
+        multiply=multiply,
+        divide=divide,
+        common=common,
+        remove_exvivo=remove_exvivo,
+        diff_subjects=diff_subjects,
+        noreplace53=noreplace53,
+    )
+    return stattablediff_execute(params, execution)
+
+
+__all__ = [
+    "STATTABLEDIFF_METADATA",
+    "StattablediffOutputs",
+    "StattablediffParameters",
+    "stattablediff",
+    "stattablediff_params",
+]

niwrap_freesurfer/freesurfer/stem2fname.py

@@ -0,0 +1,179 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+STEM2FNAME_METADATA = Metadata(
+    id="b941ff1daaefec18565e73dea38778f44521acf7.boutiques",
+    name="stem2fname",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Stem2fnameParameters = typing.TypedDict('Stem2fnameParameters', {
+    "__STYX_TYPE__": typing.Literal["stem2fname"],
+    "stem": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "stem2fname": stem2fname_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 {
+        "stem2fname": stem2fname_outputs,
+    }.get(t)
+
+
+class Stem2fnameOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `stem2fname(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Full filename with the detected format. Format could be one of mgh, mgz,
+    nii, nii.gz, bhdr, img, or w."""
+
+
+def stem2fname_params(
+    stem: str,
+) -> Stem2fnameParameters:
+    """
+    Build parameters.
+    
+    Args:
+        stem: The stem of the file (without extension).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "stem2fname",
+        "stem": stem,
+    }
+    return params
+
+
+def stem2fname_cargs(
+    params: Stem2fnameParameters,
+    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("stem2fname")
+    cargs.append(params.get("stem"))
+    return cargs
+
+
+def stem2fname_outputs(
+    params: Stem2fnameParameters,
+    execution: Execution,
+) -> Stem2fnameOutputs:
+    """
+    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 = Stem2fnameOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("stem") + ".[FORMAT]"),
+    )
+    return ret
+
+
+def stem2fname_execute(
+    params: Stem2fnameParameters,
+    execution: Execution,
+) -> Stem2fnameOutputs:
+    """
+    Determines the full filename with extension for a given file stem by checking
+    various formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Stem2fnameOutputs`).
+    """
+    params = execution.params(params)
+    cargs = stem2fname_cargs(params, execution)
+    ret = stem2fname_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def stem2fname(
+    stem: str,
+    runner: Runner | None = None,
+) -> Stem2fnameOutputs:
+    """
+    Determines the full filename with extension for a given file stem by checking
+    various formats.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        stem: The stem of the file (without extension).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Stem2fnameOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STEM2FNAME_METADATA)
+    params = stem2fname_params(
+        stem=stem,
+    )
+    return stem2fname_execute(params, execution)
+
+
+__all__ = [
+    "STEM2FNAME_METADATA",
+    "Stem2fnameOutputs",
+    "Stem2fnameParameters",
+    "stem2fname",
+    "stem2fname_params",
+]