niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/asegstats2table.py

@@ -0,0 +1,468 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ASEGSTATS2TABLE_METADATA = Metadata(
+    id="75e1aab6262bf11a4bb07f90323b14452beb59b8.boutiques",
+    name="asegstats2table",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Asegstats2tableParameters = typing.TypedDict('Asegstats2tableParameters', {
+    "__STYX_TYPE__": typing.Literal["asegstats2table"],
+    "subjects": typing.NotRequired[list[str] | None],
+    "inputs": typing.NotRequired[list[str] | None],
+    "tablefile": str,
+    "subjectsfile": typing.NotRequired[InputPathType | None],
+    "qdec": typing.NotRequired[InputPathType | None],
+    "qdec_long": typing.NotRequired[InputPathType | None],
+    "fsgd": typing.NotRequired[InputPathType | None],
+    "maxsegno": typing.NotRequired[list[str] | None],
+    "segids_from_file": typing.NotRequired[InputPathType | None],
+    "segno_include": typing.NotRequired[list[str] | None],
+    "segno_exclude": typing.NotRequired[list[str] | None],
+    "measure": typing.NotRequired[str | None],
+    "delimiter": typing.NotRequired[str | None],
+    "statsfile": typing.NotRequired[str | None],
+    "subdir": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "write_etiv": bool,
+    "debug": bool,
+    "transpose_flag": bool,
+    "common_segs_flag": bool,
+    "all_segs_flag": bool,
+    "no_vol_extras_flag": bool,
+    "skip_missing_flag": bool,
+    "replace53_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 {
+        "asegstats2table": asegstats2table_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 {
+        "asegstats2table": asegstats2table_outputs,
+    }.get(t)
+
+
+class Asegstats2tableOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `asegstats2table(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_table: OutputPathType
+    """The resulting table file with segmentation data."""
+
+
+def asegstats2table_params(
+    tablefile: str,
+    subjects: list[str] | None = None,
+    inputs: list[str] | None = None,
+    subjectsfile: InputPathType | None = None,
+    qdec: InputPathType | None = None,
+    qdec_long: InputPathType | None = None,
+    fsgd: InputPathType | None = None,
+    maxsegno: list[str] | None = None,
+    segids_from_file: InputPathType | None = None,
+    segno_include: list[str] | None = None,
+    segno_exclude: list[str] | None = None,
+    measure: str | None = None,
+    delimiter: str | None = None,
+    statsfile: str | None = None,
+    subdir: str | None = None,
+    scale: float | None = None,
+    write_etiv: bool = False,
+    debug: bool = False,
+    transpose_flag: bool = False,
+    common_segs_flag: bool = False,
+    all_segs_flag: bool = False,
+    no_vol_extras_flag: bool = False,
+    skip_missing_flag: bool = False,
+    replace53_flag: bool = False,
+) -> Asegstats2tableParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tablefile: The output table file.
+        subjects: List of subjects.
+        inputs: List of input stat files.
+        subjectsfile: Name of the file which has the list of subjects (one\
+            subject per line).
+        qdec: Name of the qdec table which has the column of subjects ids\
+            (fsid).
+        qdec_long: Name of the longitudinal qdec table with column of tp ids\
+            (fsid) and subject templates (fsid-base).
+        fsgd: Name of the FSGD file to extract subjects from.
+        maxsegno: Specify the maximum segmentation number.
+        segids_from_file: Output only the segmentations present in the\
+            specified file.
+        segno_include: Include only the specified segmentation IDs.
+        segno_exclude: Exclude the specified segmentation IDs.
+        measure: Measure to report: default is volume (alternative: mean, std).
+        delimiter: Delimiter between measures in the table. Default is tab\
+            (alternative: comma, space, semicolon).
+        statsfile: Use specified stats file instead of 'aseg.stats'.
+        subdir: Use specified subdir instead of 'stats/'.
+        scale: Scale factor for all values written to output file. Default is\
+            1.
+        write_etiv: Report volume as percent estimated total intracranial\
+            volume.
+        debug: Increase verbosity for debugging purposes.
+        transpose_flag: Transpose the table: subjects in columns and\
+            segmentations in rows.
+        common_segs_flag: Output only the segmentations common to all stats\
+            files.
+        all_segs_flag: Output all segmentations in the stats files given.
+        no_vol_extras_flag: Do not include global volume measures like\
+            BrainSegVol.
+        skip_missing_flag: Skip subjects that do not have a stats file.
+        replace53_flag: Replace 5.3 structure names with later names.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "asegstats2table",
+        "tablefile": tablefile,
+        "write_etiv": write_etiv,
+        "debug": debug,
+        "transpose_flag": transpose_flag,
+        "common_segs_flag": common_segs_flag,
+        "all_segs_flag": all_segs_flag,
+        "no_vol_extras_flag": no_vol_extras_flag,
+        "skip_missing_flag": skip_missing_flag,
+        "replace53_flag": replace53_flag,
+    }
+    if subjects is not None:
+        params["subjects"] = subjects
+    if inputs is not None:
+        params["inputs"] = inputs
+    if subjectsfile is not None:
+        params["subjectsfile"] = subjectsfile
+    if qdec is not None:
+        params["qdec"] = qdec
+    if qdec_long is not None:
+        params["qdec_long"] = qdec_long
+    if fsgd is not None:
+        params["fsgd"] = fsgd
+    if maxsegno is not None:
+        params["maxsegno"] = maxsegno
+    if segids_from_file is not None:
+        params["segids_from_file"] = segids_from_file
+    if segno_include is not None:
+        params["segno_include"] = segno_include
+    if segno_exclude is not None:
+        params["segno_exclude"] = segno_exclude
+    if measure is not None:
+        params["measure"] = measure
+    if delimiter is not None:
+        params["delimiter"] = delimiter
+    if statsfile is not None:
+        params["statsfile"] = statsfile
+    if subdir is not None:
+        params["subdir"] = subdir
+    if scale is not None:
+        params["scale"] = scale
+    return params
+
+
+def asegstats2table_cargs(
+    params: Asegstats2tableParameters,
+    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("asegstats2table")
+    if params.get("subjects") is not None:
+        cargs.extend([
+            "--subjects",
+            *params.get("subjects")
+        ])
+    if params.get("inputs") is not None:
+        cargs.extend([
+            "--inputs",
+            *params.get("inputs")
+        ])
+    cargs.extend([
+        "--tablefile",
+        params.get("tablefile")
+    ])
+    if params.get("subjectsfile") is not None:
+        cargs.extend([
+            "--subjectsfile",
+            execution.input_file(params.get("subjectsfile"))
+        ])
+    if params.get("qdec") is not None:
+        cargs.extend([
+            "--qdec",
+            execution.input_file(params.get("qdec"))
+        ])
+    if params.get("qdec_long") is not None:
+        cargs.extend([
+            "--qdec-long",
+            execution.input_file(params.get("qdec_long"))
+        ])
+    if params.get("fsgd") is not None:
+        cargs.extend([
+            "--fsgd",
+            execution.input_file(params.get("fsgd"))
+        ])
+    if params.get("maxsegno") is not None:
+        cargs.extend([
+            "--maxsegno",
+            *params.get("maxsegno")
+        ])
+    if params.get("segids_from_file") is not None:
+        cargs.extend([
+            "--segids-from-file",
+            execution.input_file(params.get("segids_from_file"))
+        ])
+    if params.get("segno_include") is not None:
+        cargs.extend([
+            "--segno",
+            *params.get("segno_include")
+        ])
+    if params.get("segno_exclude") is not None:
+        cargs.extend([
+            "--no-segno",
+            *params.get("segno_exclude")
+        ])
+    if params.get("measure") is not None:
+        cargs.extend([
+            "--meas",
+            params.get("measure")
+        ])
+    if params.get("delimiter") is not None:
+        cargs.extend([
+            "--delimiter",
+            params.get("delimiter")
+        ])
+    if params.get("statsfile") is not None:
+        cargs.extend([
+            "--statsfile",
+            params.get("statsfile")
+        ])
+    if params.get("subdir") is not None:
+        cargs.extend([
+            "--subdir",
+            params.get("subdir")
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "--scale",
+            str(params.get("scale"))
+        ])
+    if params.get("write_etiv"):
+        cargs.append("--etiv")
+    if params.get("debug"):
+        cargs.append("--debug")
+    if params.get("transpose_flag"):
+        cargs.append("--transpose")
+    if params.get("common_segs_flag"):
+        cargs.append("--common-segs")
+    if params.get("all_segs_flag"):
+        cargs.append("--all-segs")
+    if params.get("no_vol_extras_flag"):
+        cargs.append("--no-vol-extras")
+    if params.get("skip_missing_flag"):
+        cargs.append("--skip")
+    if params.get("replace53_flag"):
+        cargs.append("--replace53")
+    return cargs
+
+
+def asegstats2table_outputs(
+    params: Asegstats2tableParameters,
+    execution: Execution,
+) -> Asegstats2tableOutputs:
+    """
+    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 = Asegstats2tableOutputs(
+        root=execution.output_file("."),
+        output_table=execution.output_file(params.get("tablefile")),
+    )
+    return ret
+
+
+def asegstats2table_execute(
+    params: Asegstats2tableParameters,
+    execution: Execution,
+) -> Asegstats2tableOutputs:
+    """
+    Converts a subcortical stats file created by recon-all and/or mri_segstats
+    (e.g., aseg.stats) into a table.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Asegstats2tableOutputs`).
+    """
+    params = execution.params(params)
+    cargs = asegstats2table_cargs(params, execution)
+    ret = asegstats2table_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def asegstats2table(
+    tablefile: str,
+    subjects: list[str] | None = None,
+    inputs: list[str] | None = None,
+    subjectsfile: InputPathType | None = None,
+    qdec: InputPathType | None = None,
+    qdec_long: InputPathType | None = None,
+    fsgd: InputPathType | None = None,
+    maxsegno: list[str] | None = None,
+    segids_from_file: InputPathType | None = None,
+    segno_include: list[str] | None = None,
+    segno_exclude: list[str] | None = None,
+    measure: str | None = None,
+    delimiter: str | None = None,
+    statsfile: str | None = None,
+    subdir: str | None = None,
+    scale: float | None = None,
+    write_etiv: bool = False,
+    debug: bool = False,
+    transpose_flag: bool = False,
+    common_segs_flag: bool = False,
+    all_segs_flag: bool = False,
+    no_vol_extras_flag: bool = False,
+    skip_missing_flag: bool = False,
+    replace53_flag: bool = False,
+    runner: Runner | None = None,
+) -> Asegstats2tableOutputs:
+    """
+    Converts a subcortical stats file created by recon-all and/or mri_segstats
+    (e.g., aseg.stats) into a table.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        tablefile: The output table file.
+        subjects: List of subjects.
+        inputs: List of input stat files.
+        subjectsfile: Name of the file which has the list of subjects (one\
+            subject per line).
+        qdec: Name of the qdec table which has the column of subjects ids\
+            (fsid).
+        qdec_long: Name of the longitudinal qdec table with column of tp ids\
+            (fsid) and subject templates (fsid-base).
+        fsgd: Name of the FSGD file to extract subjects from.
+        maxsegno: Specify the maximum segmentation number.
+        segids_from_file: Output only the segmentations present in the\
+            specified file.
+        segno_include: Include only the specified segmentation IDs.
+        segno_exclude: Exclude the specified segmentation IDs.
+        measure: Measure to report: default is volume (alternative: mean, std).
+        delimiter: Delimiter between measures in the table. Default is tab\
+            (alternative: comma, space, semicolon).
+        statsfile: Use specified stats file instead of 'aseg.stats'.
+        subdir: Use specified subdir instead of 'stats/'.
+        scale: Scale factor for all values written to output file. Default is\
+            1.
+        write_etiv: Report volume as percent estimated total intracranial\
+            volume.
+        debug: Increase verbosity for debugging purposes.
+        transpose_flag: Transpose the table: subjects in columns and\
+            segmentations in rows.
+        common_segs_flag: Output only the segmentations common to all stats\
+            files.
+        all_segs_flag: Output all segmentations in the stats files given.
+        no_vol_extras_flag: Do not include global volume measures like\
+            BrainSegVol.
+        skip_missing_flag: Skip subjects that do not have a stats file.
+        replace53_flag: Replace 5.3 structure names with later names.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Asegstats2tableOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ASEGSTATS2TABLE_METADATA)
+    params = asegstats2table_params(
+        subjects=subjects,
+        inputs=inputs,
+        tablefile=tablefile,
+        subjectsfile=subjectsfile,
+        qdec=qdec,
+        qdec_long=qdec_long,
+        fsgd=fsgd,
+        maxsegno=maxsegno,
+        segids_from_file=segids_from_file,
+        segno_include=segno_include,
+        segno_exclude=segno_exclude,
+        measure=measure,
+        delimiter=delimiter,
+        statsfile=statsfile,
+        subdir=subdir,
+        scale=scale,
+        write_etiv=write_etiv,
+        debug=debug,
+        transpose_flag=transpose_flag,
+        common_segs_flag=common_segs_flag,
+        all_segs_flag=all_segs_flag,
+        no_vol_extras_flag=no_vol_extras_flag,
+        skip_missing_flag=skip_missing_flag,
+        replace53_flag=replace53_flag,
+    )
+    return asegstats2table_execute(params, execution)
+
+
+__all__ = [
+    "ASEGSTATS2TABLE_METADATA",
+    "Asegstats2tableOutputs",
+    "Asegstats2tableParameters",
+    "asegstats2table",
+    "asegstats2table_params",
+]

niwrap_freesurfer/freesurfer/asegstatsdiff.py

@@ -0,0 +1,197 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ASEGSTATSDIFF_METADATA = Metadata(
+    id="10487227e273c61c9beadcb9b38d15804d6724e3.boutiques",
+    name="asegstatsdiff",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+AsegstatsdiffParameters = typing.TypedDict('AsegstatsdiffParameters', {
+    "__STYX_TYPE__": typing.Literal["asegstatsdiff"],
+    "subject1": str,
+    "subject2": str,
+    "outdir": 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 {
+        "asegstatsdiff": asegstatsdiff_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 {
+        "asegstatsdiff": asegstatsdiff_outputs,
+    }.get(t)
+
+
+class AsegstatsdiffOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `asegstatsdiff(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    asegstats_output: OutputPathType | None
+    """Output table with percent differences added."""
+
+
+def asegstatsdiff_params(
+    subject1: str,
+    subject2: str,
+    outdir: str | None = None,
+) -> AsegstatsdiffParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject1: The first subject to be compared.
+        subject2: The second subject to be compared.
+        outdir: Optionally specify a directory to write the output\
+            asegstats.txt.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "asegstatsdiff",
+        "subject1": subject1,
+        "subject2": subject2,
+    }
+    if outdir is not None:
+        params["outdir"] = outdir
+    return params
+
+
+def asegstatsdiff_cargs(
+    params: AsegstatsdiffParameters,
+    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("asegstatsdiff")
+    cargs.append(params.get("subject1"))
+    if params.get("outdir") is not None:
+        cargs.append(params.get("subject2") + params.get("outdir"))
+    return cargs
+
+
+def asegstatsdiff_outputs(
+    params: AsegstatsdiffParameters,
+    execution: Execution,
+) -> AsegstatsdiffOutputs:
+    """
+    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 = AsegstatsdiffOutputs(
+        root=execution.output_file("."),
+        asegstats_output=execution.output_file(params.get("outdir") + "/asegstats.txt") if (params.get("outdir") is not None) else None,
+    )
+    return ret
+
+
+def asegstatsdiff_execute(
+    params: AsegstatsdiffParameters,
+    execution: Execution,
+) -> AsegstatsdiffOutputs:
+    """
+    Compute and report percentage differences in aseg morphometry data between two
+    subjects.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AsegstatsdiffOutputs`).
+    """
+    params = execution.params(params)
+    cargs = asegstatsdiff_cargs(params, execution)
+    ret = asegstatsdiff_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def asegstatsdiff(
+    subject1: str,
+    subject2: str,
+    outdir: str | None = None,
+    runner: Runner | None = None,
+) -> AsegstatsdiffOutputs:
+    """
+    Compute and report percentage differences in aseg morphometry data between two
+    subjects.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject1: The first subject to be compared.
+        subject2: The second subject to be compared.
+        outdir: Optionally specify a directory to write the output\
+            asegstats.txt.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AsegstatsdiffOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ASEGSTATSDIFF_METADATA)
+    params = asegstatsdiff_params(
+        subject1=subject1,
+        subject2=subject2,
+        outdir=outdir,
+    )
+    return asegstatsdiff_execute(params, execution)
+
+
+__all__ = [
+    "ASEGSTATSDIFF_METADATA",
+    "AsegstatsdiffOutputs",
+    "AsegstatsdiffParameters",
+    "asegstatsdiff",
+    "asegstatsdiff_params",
+]