niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/seg2recon.py

@@ -0,0 +1,344 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SEG2RECON_METADATA = Metadata(
+    id="36dfabf1fcfdc6c0dea237cf9f3d8968bf6ef6bc.boutiques",
+    name="seg2recon",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Seg2reconParameters = typing.TypedDict('Seg2reconParameters', {
+    "__STYX_TYPE__": typing.Literal["seg2recon"],
+    "subject": str,
+    "segvol": InputPathType,
+    "inputvol": InputPathType,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "ndilate": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "force_update": bool,
+    "no_cc": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "headmask": typing.NotRequired[InputPathType | None],
+    "thresh": typing.NotRequired[float | None],
+    "expert": typing.NotRequired[InputPathType | None],
+    "rca": bool,
+    "no_bias_field_cor": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "seg2recon": seg2recon_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 {
+        "seg2recon": seg2recon_outputs,
+    }.get(t)
+
+
+class Seg2reconOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `seg2recon(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    aseg_auto_mgz: OutputPathType
+    """Output aseg.auto.mgz file including corpus callosum segmentation"""
+    nu_mgz: OutputPathType
+    """Bias field corrected output nu.mgz file"""
+    brainmask_mgz: OutputPathType
+    """Output brainmask.mgz file"""
+
+
+def seg2recon_params(
+    subject: str,
+    segvol: InputPathType,
+    inputvol: InputPathType,
+    ctab: InputPathType | None = None,
+    ndilate: float | None = None,
+    threads: float | None = None,
+    force_update: bool = False,
+    no_cc: bool = False,
+    mask: InputPathType | None = None,
+    headmask: InputPathType | None = None,
+    thresh: float | None = None,
+    expert: InputPathType | None = None,
+    rca: bool = False,
+    no_bias_field_cor: bool = False,
+) -> Seg2reconParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject: Output subject directory name.
+        segvol: Aseg-type volume, e.g., from synthseg, fastsurfer, psacnn,\
+            samseg, or aseg.
+        inputvol: Input volume as would be passed to recon-all.
+        ctab: Color table for the segmentation. Uses embedded table if\
+            available, or FreeSurferColorLUT.txt if not specified.
+        ndilate: Dilate binarization of segmentation when creating brainmask.\
+            Default is 2.
+        threads: Number of threads to use for processing.
+        force_update: Force regeneration of files whether needed or not.
+        no_cc: Do not segment corpus callosum.
+        mask: Use this mask as brainmask instead of computing from\
+            segmentation.
+        headmask: Use this headmask instead of running mri_seghead.
+        thresh: Threshold for bias field estimation.
+        expert: Path to expert options file.
+        rca: Run recon-all on the output.
+        no_bias_field_cor: Do not compute or apply bias field correction.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "seg2recon",
+        "subject": subject,
+        "segvol": segvol,
+        "inputvol": inputvol,
+        "force_update": force_update,
+        "no_cc": no_cc,
+        "rca": rca,
+        "no_bias_field_cor": no_bias_field_cor,
+    }
+    if ctab is not None:
+        params["ctab"] = ctab
+    if ndilate is not None:
+        params["ndilate"] = ndilate
+    if threads is not None:
+        params["threads"] = threads
+    if mask is not None:
+        params["mask"] = mask
+    if headmask is not None:
+        params["headmask"] = headmask
+    if thresh is not None:
+        params["thresh"] = thresh
+    if expert is not None:
+        params["expert"] = expert
+    return params
+
+
+def seg2recon_cargs(
+    params: Seg2reconParameters,
+    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("seg2recon")
+    cargs.extend([
+        "-s",
+        params.get("subject")
+    ])
+    cargs.extend([
+        "-seg",
+        execution.input_file(params.get("segvol"))
+    ])
+    cargs.extend([
+        "-i",
+        execution.input_file(params.get("inputvol"))
+    ])
+    if params.get("ctab") is not None:
+        cargs.extend([
+            "-ctab",
+            execution.input_file(params.get("ctab"))
+        ])
+    if params.get("ndilate") is not None:
+        cargs.extend([
+            "--ndilate",
+            str(params.get("ndilate"))
+        ])
+    if params.get("threads") is not None:
+        cargs.extend([
+            "--threads",
+            str(params.get("threads"))
+        ])
+    if params.get("force_update"):
+        cargs.append("--force-update")
+    if params.get("no_cc"):
+        cargs.append("--no-cc")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "--m",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("headmask") is not None:
+        cargs.extend([
+            "--h",
+            execution.input_file(params.get("headmask"))
+        ])
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "--thresh",
+            str(params.get("thresh"))
+        ])
+    if params.get("expert") is not None:
+        cargs.extend([
+            "--expert",
+            execution.input_file(params.get("expert"))
+        ])
+    if params.get("rca"):
+        cargs.append("--rca")
+    if params.get("no_bias_field_cor"):
+        cargs.append("--no-bias-field-cor")
+    return cargs
+
+
+def seg2recon_outputs(
+    params: Seg2reconParameters,
+    execution: Execution,
+) -> Seg2reconOutputs:
+    """
+    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 = Seg2reconOutputs(
+        root=execution.output_file("."),
+        aseg_auto_mgz=execution.output_file(params.get("subject") + "/aseg.auto.mgz"),
+        nu_mgz=execution.output_file(params.get("subject") + "/nu.mgz"),
+        brainmask_mgz=execution.output_file(params.get("subject") + "/brainmask.mgz"),
+    )
+    return ret
+
+
+def seg2recon_execute(
+    params: Seg2reconParameters,
+    execution: Execution,
+) -> Seg2reconOutputs:
+    """
+    Creates and populates a subjects directory from an input image and segmentation
+    suitable for running recon-all.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Seg2reconOutputs`).
+    """
+    params = execution.params(params)
+    cargs = seg2recon_cargs(params, execution)
+    ret = seg2recon_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def seg2recon(
+    subject: str,
+    segvol: InputPathType,
+    inputvol: InputPathType,
+    ctab: InputPathType | None = None,
+    ndilate: float | None = None,
+    threads: float | None = None,
+    force_update: bool = False,
+    no_cc: bool = False,
+    mask: InputPathType | None = None,
+    headmask: InputPathType | None = None,
+    thresh: float | None = None,
+    expert: InputPathType | None = None,
+    rca: bool = False,
+    no_bias_field_cor: bool = False,
+    runner: Runner | None = None,
+) -> Seg2reconOutputs:
+    """
+    Creates and populates a subjects directory from an input image and segmentation
+    suitable for running recon-all.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject: Output subject directory name.
+        segvol: Aseg-type volume, e.g., from synthseg, fastsurfer, psacnn,\
+            samseg, or aseg.
+        inputvol: Input volume as would be passed to recon-all.
+        ctab: Color table for the segmentation. Uses embedded table if\
+            available, or FreeSurferColorLUT.txt if not specified.
+        ndilate: Dilate binarization of segmentation when creating brainmask.\
+            Default is 2.
+        threads: Number of threads to use for processing.
+        force_update: Force regeneration of files whether needed or not.
+        no_cc: Do not segment corpus callosum.
+        mask: Use this mask as brainmask instead of computing from\
+            segmentation.
+        headmask: Use this headmask instead of running mri_seghead.
+        thresh: Threshold for bias field estimation.
+        expert: Path to expert options file.
+        rca: Run recon-all on the output.
+        no_bias_field_cor: Do not compute or apply bias field correction.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Seg2reconOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEG2RECON_METADATA)
+    params = seg2recon_params(
+        subject=subject,
+        segvol=segvol,
+        inputvol=inputvol,
+        ctab=ctab,
+        ndilate=ndilate,
+        threads=threads,
+        force_update=force_update,
+        no_cc=no_cc,
+        mask=mask,
+        headmask=headmask,
+        thresh=thresh,
+        expert=expert,
+        rca=rca,
+        no_bias_field_cor=no_bias_field_cor,
+    )
+    return seg2recon_execute(params, execution)
+
+
+__all__ = [
+    "SEG2RECON_METADATA",
+    "Seg2reconOutputs",
+    "Seg2reconParameters",
+    "seg2recon",
+    "seg2recon_params",
+]

niwrap_freesurfer/freesurfer/segment_bs_sh.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SEGMENT_BS_SH_METADATA = Metadata(
+    id="ea5de6d87d6861bdf790a471d88443f6b20986d7.boutiques",
+    name="segmentBS.sh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+SegmentBsShParameters = typing.TypedDict('SegmentBsShParameters', {
+    "__STYX_TYPE__": typing.Literal["segmentBS.sh"],
+    "matlab_runtime": 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 {
+        "segmentBS.sh": segment_bs_sh_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 SegmentBsShOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `segment_bs_sh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def segment_bs_sh_params(
+    matlab_runtime: str | None = "/usr/local/freesurfer/MCRv97",
+) -> SegmentBsShParameters:
+    """
+    Build parameters.
+    
+    Args:
+        matlab_runtime: Path to the Matlab 2019b runtime environment; necessary\
+            for running the segmentation tool.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "segmentBS.sh",
+    }
+    if matlab_runtime is not None:
+        params["matlab_runtime"] = matlab_runtime
+    return params
+
+
+def segment_bs_sh_cargs(
+    params: SegmentBsShParameters,
+    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("segmentBS.sh")
+    if params.get("matlab_runtime") is not None:
+        cargs.append(params.get("matlab_runtime"))
+    return cargs
+
+
+def segment_bs_sh_outputs(
+    params: SegmentBsShParameters,
+    execution: Execution,
+) -> SegmentBsShOutputs:
+    """
+    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 = SegmentBsShOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def segment_bs_sh_execute(
+    params: SegmentBsShParameters,
+    execution: Execution,
+) -> SegmentBsShOutputs:
+    """
+    Segmentation tool for hippocampal/amygdala and brainstem modules.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SegmentBsShOutputs`).
+    """
+    params = execution.params(params)
+    cargs = segment_bs_sh_cargs(params, execution)
+    ret = segment_bs_sh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def segment_bs_sh(
+    matlab_runtime: str | None = "/usr/local/freesurfer/MCRv97",
+    runner: Runner | None = None,
+) -> SegmentBsShOutputs:
+    """
+    Segmentation tool for hippocampal/amygdala and brainstem modules.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        matlab_runtime: Path to the Matlab 2019b runtime environment; necessary\
+            for running the segmentation tool.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SegmentBsShOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_BS_SH_METADATA)
+    params = segment_bs_sh_params(
+        matlab_runtime=matlab_runtime,
+    )
+    return segment_bs_sh_execute(params, execution)
+
+
+__all__ = [
+    "SEGMENT_BS_SH_METADATA",
+    "SegmentBsShOutputs",
+    "SegmentBsShParameters",
+    "segment_bs_sh",
+    "segment_bs_sh_params",
+]

niwrap_freesurfer/freesurfer/segment_ha_t1_long_sh.py

@@ -0,0 +1,184 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SEGMENT_HA_T1_LONG_SH_METADATA = Metadata(
+    id="e6413cb2b0b0c7d6ddbeca885e2ef04a50aea294.boutiques",
+    name="segmentHA_T1_long.sh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+SegmentHaT1LongShParameters = typing.TypedDict('SegmentHaT1LongShParameters', {
+    "__STYX_TYPE__": typing.Literal["segmentHA_T1_long.sh"],
+    "subject_dir": str,
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "segmentHA_T1_long.sh": segment_ha_t1_long_sh_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 {
+        "segmentHA_T1_long.sh": segment_ha_t1_long_sh_outputs,
+    }.get(t)
+
+
+class SegmentHaT1LongShOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `segment_ha_t1_long_sh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dir: OutputPathType
+    """Output directory containing segmentation results"""
+
+
+def segment_ha_t1_long_sh_params(
+    subject_dir: str,
+    subject_id: str,
+) -> SegmentHaT1LongShParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_dir: Directory containing subject data.
+        subject_id: Identifier for the subject within the subject directory.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "segmentHA_T1_long.sh",
+        "subject_dir": subject_dir,
+        "subject_id": subject_id,
+    }
+    return params
+
+
+def segment_ha_t1_long_sh_cargs(
+    params: SegmentHaT1LongShParameters,
+    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("segmentHA_T1_long.sh")
+    cargs.append(params.get("subject_dir"))
+    cargs.append(params.get("subject_id"))
+    return cargs
+
+
+def segment_ha_t1_long_sh_outputs(
+    params: SegmentHaT1LongShParameters,
+    execution: Execution,
+) -> SegmentHaT1LongShOutputs:
+    """
+    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 = SegmentHaT1LongShOutputs(
+        root=execution.output_file("."),
+        output_dir=execution.output_file(params.get("subject_dir") + "/" + params.get("subject_id") + "_long_segment/output"),
+    )
+    return ret
+
+
+def segment_ha_t1_long_sh_execute(
+    params: SegmentHaT1LongShParameters,
+    execution: Execution,
+) -> SegmentHaT1LongShOutputs:
+    """
+    A script for longitudinal segmentation of the hippocampal/amygdala regions.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SegmentHaT1LongShOutputs`).
+    """
+    params = execution.params(params)
+    cargs = segment_ha_t1_long_sh_cargs(params, execution)
+    ret = segment_ha_t1_long_sh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def segment_ha_t1_long_sh(
+    subject_dir: str,
+    subject_id: str,
+    runner: Runner | None = None,
+) -> SegmentHaT1LongShOutputs:
+    """
+    A script for longitudinal segmentation of the hippocampal/amygdala regions.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        subject_dir: Directory containing subject data.
+        subject_id: Identifier for the subject within the subject directory.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SegmentHaT1LongShOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_HA_T1_LONG_SH_METADATA)
+    params = segment_ha_t1_long_sh_params(
+        subject_dir=subject_dir,
+        subject_id=subject_id,
+    )
+    return segment_ha_t1_long_sh_execute(params, execution)
+
+
+__all__ = [
+    "SEGMENT_HA_T1_LONG_SH_METADATA",
+    "SegmentHaT1LongShOutputs",
+    "SegmentHaT1LongShParameters",
+    "segment_ha_t1_long_sh",
+    "segment_ha_t1_long_sh_params",
+]