niwrap-freesurfer 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/compute_label_volumes_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 COMPUTE_LABEL_VOLUMES_CSH_METADATA = Metadata(
-    id="82638ae4faa0eb9506df9c2f3a56c833cb5de288.boutiques",
+    id="f6bb92d910cd7a9b624eadf0f487558e645d0c90.boutiques",
     name="compute_label_volumes.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,6 +18,7 @@ ComputeLabelVolumesCshParameters = typing.TypedDict('ComputeLabelVolumesCshParam
     "label_vol": InputPathType,
     "output_file": str,
     "label_l": typing.NotRequired[str | None],
+    "label_l_1": typing.NotRequired[str | None],
     "version": bool,
     "help": bool,
 })
@@ -69,6 +70,7 @@ def compute_label_volumes_csh_params(
     label_vol: InputPathType,
     output_file: str,
     label_l: str | None = None,
+    label_l_1: str | None = None,
     version: bool = False,
     help_: bool = False,
 ) -> ComputeLabelVolumesCshParameters:
@@ -79,6 +81,8 @@ def compute_label_volumes_csh_params(
         label_vol: Label volume to be analyzed.
         output_file: Text file where the results are written.
         label_l: The particular label to be analyzed (case-insensitive option).
+        label_l_1: The particular label to be analyzed (case-insensitive\
+            option).
         version: Print version and exit.
         help_: Print help and exit.
     Returns:
@@ -93,6 +97,8 @@ def compute_label_volumes_csh_params(
     }
     if label_l is not None:
         params["label_l"] = label_l
+    if label_l_1 is not None:
+        params["label_l_1"] = label_l_1
     return params
 
 
@@ -110,7 +116,7 @@ def compute_label_volumes_csh_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("compute_label_volumes")
+    cargs.append("compute_label_volumes.csh")
     cargs.extend([
         "--vol",
         execution.input_file(params.get("label_vol"))
@@ -124,6 +130,11 @@ def compute_label_volumes_csh_cargs(
             "--l",
             params.get("label_l")
         ])
+    if params.get("label_l_1") is not None:
+        cargs.extend([
+            "--l",
+            params.get("label_l_1")
+        ])
     if params.get("version"):
         cargs.append("--version")
     if params.get("help"):
@@ -180,6 +191,7 @@ def compute_label_volumes_csh(
     label_vol: InputPathType,
     output_file: str,
     label_l: str | None = None,
+    label_l_1: str | None = None,
     version: bool = False,
     help_: bool = False,
     runner: Runner | None = None,
@@ -196,6 +208,8 @@ def compute_label_volumes_csh(
         label_vol: Label volume to be analyzed.
         output_file: Text file where the results are written.
         label_l: The particular label to be analyzed (case-insensitive option).
+        label_l_1: The particular label to be analyzed (case-insensitive\
+            option).
         version: Print version and exit.
         help_: Print help and exit.
         runner: Command runner.
@@ -208,6 +222,7 @@ def compute_label_volumes_csh(
         label_vol=label_vol,
         output_file=output_file,
         label_l=label_l,
+        label_l_1=label_l_1,
         version=version,
         help_=help_,
     )

niwrap_freesurfer/freesurfer/conf2hires.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONF2HIRES_METADATA = Metadata(
-    id="0daec93cecaaf674dbbc3d770b70999cf8bff082.boutiques",
+    id="2455d1a9818a72df60f5c386c53541cd8cd28eab.boutiques",
     name="conf2hires",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,14 +16,20 @@ CONF2HIRES_METADATA = Metadata(
 Conf2hiresParameters = typing.TypedDict('Conf2hiresParameters', {
     "__STYX_TYPE__": typing.Literal["conf2hires"],
     "subject": str,
+    "t2": bool,
     "no_t2": bool,
     "mm_norm_sigma": typing.NotRequired[float | None],
+    "flair": bool,
     "no_flair": bool,
     "threads": typing.NotRequired[float | None],
     "copy_bias_from_conf": bool,
     "norm_opts_rca": bool,
+    "cubic": bool,
     "trilin": bool,
+    "dev": bool,
     "no_dev": bool,
+    "bbr_con": typing.NotRequired[str | None],
+    "bbr_t1": bool,
     "bbr_t2": bool,
     "first_peak_d1": bool,
     "first_peak_d2": bool,
@@ -74,14 +80,20 @@ class Conf2hiresOutputs(typing.NamedTuple):
 
 def conf2hires_params(
     subject: str,
+    t2: bool = False,
     no_t2: bool = False,
     mm_norm_sigma: float | None = 8,
+    flair: bool = False,
     no_flair: bool = False,
     threads: float | None = None,
     copy_bias_from_conf: bool = False,
     norm_opts_rca: bool = False,
+    cubic: bool = False,
     trilin: bool = False,
+    dev: bool = False,
     no_dev: bool = False,
+    bbr_con: str | None = None,
+    bbr_t1: bool = False,
     bbr_t2: bool = False,
     first_peak_d1: bool = False,
     first_peak_d2: bool = False,
@@ -94,17 +106,23 @@ def conf2hires_params(
     
     Args:
         subject: Subject identifier.
+        t2: Enable T2 processing.
         no_t2: Disable T2 processing (default).
         mm_norm_sigma: Smoothing level for T2 mri_normalize (default is 8).
+        flair: Enable FLAIR processing.
         no_flair: Disable FLAIR processing (default).
         threads: Number of threads to use.
         copy_bias_from_conf: Copy bias field from conformed instead of\
             computing directly.
         norm_opts_rca: Compute bias directly using recon-all opts to\
             mri_normalize.
+        cubic: Use cubic normalization (applies with --copy-bias-from-conf).
         trilin: Use trilinear normalization (default, applies with\
             --copy-bias-from-conf).
+        dev: Use mris_make_surfaces.dev.
         no_dev: Do not use mris_make_surfaces.dev (default).
+        bbr_con: Set BBR contrast type (default t2).
+        bbr_t1: Set BBR contrast type to t1.
         bbr_t2: Set BBR contrast type to t2.
         first_peak_d1: Refine surface targets in MRIScomputeBorderValues()\
             using first peak method D1.
@@ -119,12 +137,17 @@ def conf2hires_params(
     params = {
         "__STYXTYPE__": "conf2hires",
         "subject": subject,
+        "t2": t2,
         "no_t2": no_t2,
+        "flair": flair,
         "no_flair": no_flair,
         "copy_bias_from_conf": copy_bias_from_conf,
         "norm_opts_rca": norm_opts_rca,
+        "cubic": cubic,
         "trilin": trilin,
+        "dev": dev,
         "no_dev": no_dev,
+        "bbr_t1": bbr_t1,
         "bbr_t2": bbr_t2,
         "first_peak_d1": first_peak_d1,
         "first_peak_d2": first_peak_d2,
@@ -134,6 +157,8 @@ def conf2hires_params(
         params["mm_norm_sigma"] = mm_norm_sigma
     if threads is not None:
         params["threads"] = threads
+    if bbr_con is not None:
+        params["bbr_con"] = bbr_con
     if stopmask is not None:
         params["stopmask"] = stopmask
     if expert is not None:
@@ -160,6 +185,8 @@ def conf2hires_cargs(
         "--s",
         params.get("subject")
     ])
+    if params.get("t2"):
+        cargs.append("--t2")
     if params.get("no_t2"):
         cargs.append("--no-t2")
     if params.get("mm_norm_sigma") is not None:
@@ -167,6 +194,8 @@ def conf2hires_cargs(
             "--mm-norm-sigma",
             str(params.get("mm_norm_sigma"))
         ])
+    if params.get("flair"):
+        cargs.append("--flair")
     if params.get("no_flair"):
         cargs.append("--no-flair")
     if params.get("threads") is not None:
@@ -178,10 +207,21 @@ def conf2hires_cargs(
         cargs.append("--copy-bias-from-conf")
     if params.get("norm_opts_rca"):
         cargs.append("--norm-opts-rca")
+    if params.get("cubic"):
+        cargs.append("--cubic")
     if params.get("trilin"):
         cargs.append("--trilin")
+    if params.get("dev"):
+        cargs.append("--dev")
     if params.get("no_dev"):
         cargs.append("--no-dev")
+    if params.get("bbr_con") is not None:
+        cargs.extend([
+            "--bbr-con",
+            params.get("bbr_con")
+        ])
+    if params.get("bbr_t1"):
+        cargs.append("--bbr-t1")
     if params.get("bbr_t2"):
         cargs.append("--bbr-t2")
     if params.get("first_peak_d1"):
@@ -249,14 +289,20 @@ def conf2hires_execute(
 
 def conf2hires(
     subject: str,
+    t2: bool = False,
     no_t2: bool = False,
     mm_norm_sigma: float | None = 8,
+    flair: bool = False,
     no_flair: bool = False,
     threads: float | None = None,
     copy_bias_from_conf: bool = False,
     norm_opts_rca: bool = False,
+    cubic: bool = False,
     trilin: bool = False,
+    dev: bool = False,
     no_dev: bool = False,
+    bbr_con: str | None = None,
+    bbr_t1: bool = False,
     bbr_t2: bool = False,
     first_peak_d1: bool = False,
     first_peak_d2: bool = False,
@@ -275,17 +321,23 @@ def conf2hires(
     
     Args:
         subject: Subject identifier.
+        t2: Enable T2 processing.
         no_t2: Disable T2 processing (default).
         mm_norm_sigma: Smoothing level for T2 mri_normalize (default is 8).
+        flair: Enable FLAIR processing.
         no_flair: Disable FLAIR processing (default).
         threads: Number of threads to use.
         copy_bias_from_conf: Copy bias field from conformed instead of\
             computing directly.
         norm_opts_rca: Compute bias directly using recon-all opts to\
             mri_normalize.
+        cubic: Use cubic normalization (applies with --copy-bias-from-conf).
         trilin: Use trilinear normalization (default, applies with\
             --copy-bias-from-conf).
+        dev: Use mris_make_surfaces.dev.
         no_dev: Do not use mris_make_surfaces.dev (default).
+        bbr_con: Set BBR contrast type (default t2).
+        bbr_t1: Set BBR contrast type to t1.
         bbr_t2: Set BBR contrast type to t2.
         first_peak_d1: Refine surface targets in MRIScomputeBorderValues()\
             using first peak method D1.
@@ -302,14 +354,20 @@ def conf2hires(
     execution = runner.start_execution(CONF2HIRES_METADATA)
     params = conf2hires_params(
         subject=subject,
+        t2=t2,
         no_t2=no_t2,
         mm_norm_sigma=mm_norm_sigma,
+        flair=flair,
         no_flair=no_flair,
         threads=threads,
         copy_bias_from_conf=copy_bias_from_conf,
         norm_opts_rca=norm_opts_rca,
+        cubic=cubic,
         trilin=trilin,
+        dev=dev,
         no_dev=no_dev,
+        bbr_con=bbr_con,
+        bbr_t1=bbr_t1,
         bbr_t2=bbr_t2,
         first_peak_d1=first_peak_d1,
         first_peak_d2=first_peak_d2,

niwrap_freesurfer/freesurfer/connected_components.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONNECTED_COMPONENTS_METADATA = Metadata(
-    id="415ac7eebb3cd7123aaeb6ad6eb398b6cc1343ba.boutiques",
+    id="f1633b5575d9dbbe6d93199947f8505bc14a7d96.boutiques",
     name="connected_components",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,9 @@ CONNECTED_COMPONENTS_METADATA = Metadata(
 
 ConnectedComponentsParameters = typing.TypedDict('ConnectedComponentsParameters', {
     "__STYX_TYPE__": typing.Literal["connected_components"],
+    "input_image": InputPathType,
+    "output_image": str,
+    "threshold": typing.NotRequired[float | None],
 })
 
 
@@ -61,17 +64,27 @@ class ConnectedComponentsOutputs(typing.NamedTuple):
 
 
 def connected_components_params(
+    input_image: InputPathType,
+    output_image: str = "output_labelled_image",
+    threshold: float | None = None,
 ) -> ConnectedComponentsParameters:
     """
     Build parameters.
     
     Args:
+        input_image: Input image file.
+        output_image: Output labeled connected components image.
+        threshold: Threshold for binarizing the input image.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "connected_components",
+        "input_image": input_image,
+        "output_image": output_image,
     }
+    if threshold is not None:
+        params["threshold"] = threshold
     return params
 
 
@@ -90,6 +103,16 @@ def connected_components_cargs(
     """
     cargs = []
     cargs.append("connected_components")
+    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.extend([
+        "-o",
+        params.get("output_image")
+    ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-t",
+            str(params.get("threshold"))
+        ])
     return cargs
 
 
@@ -108,7 +131,7 @@ def connected_components_outputs(
     """
     ret = ConnectedComponentsOutputs(
         root=execution.output_file("."),
-        output_labelled_image_file=execution.output_file("[OUTPUT_IMAGE].nii.gz"),
+        output_labelled_image_file=execution.output_file(params.get("output_image") + ".nii.gz"),
     )
     return ret
 
@@ -138,6 +161,9 @@ def connected_components_execute(
 
 
 def connected_components(
+    input_image: InputPathType,
+    output_image: str = "output_labelled_image",
+    threshold: float | None = None,
     runner: Runner | None = None,
 ) -> ConnectedComponentsOutputs:
     """
@@ -148,6 +174,9 @@ def connected_components(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        input_image: Input image file.
+        output_image: Output labeled connected components image.
+        threshold: Threshold for binarizing the input image.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ConnectedComponentsOutputs`).
@@ -155,6 +184,9 @@ def connected_components(
     runner = runner or get_global_runner()
     execution = runner.start_execution(CONNECTED_COMPONENTS_METADATA)
     params = connected_components_params(
+        input_image=input_image,
+        output_image=output_image,
+        threshold=threshold,
     )
     return connected_components_execute(params, execution)
 

niwrap_freesurfer/freesurfer/dcmdir_info_mgh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMDIR_INFO_MGH_METADATA = Metadata(
-    id="7ccff8790fdd0d584c57e3c31a9bf9ffd1e90e36.boutiques",
+    id="162f400a399c275cd7fef293d1d5ad1cd84402e4.boutiques",
     name="dcmdir-info-mgh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -112,9 +112,10 @@ def dcmdir_info_mgh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("dcmdir-info-mgh")
     cargs.extend([
         "-mgh",
-        "dcmdir-info" + params.get("dicomdir")
+        params.get("dicomdir")
     ])
     if params.get("unpackdir") is not None:
         cargs.append(params.get("unpackdir"))

niwrap_freesurfer/freesurfer/dcmdjpeg_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMDJPEG_FS_METADATA = Metadata(
-    id="72def5b0b090531bebd9d33b2cf8001287532af2.boutiques",
+    id="23277311b6d3ec67d22170dc491d01934643849c.boutiques",
     name="dcmdjpeg.fs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -260,7 +260,7 @@ def dcmdjpeg_fs_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("dcmdjpeg")
+    cargs.append("dcmdjpeg.fs")
     cargs.append(execution.input_file(params.get("input_file")))
     cargs.append(params.get("output_file"))
     if params.get("help"):

niwrap_freesurfer/freesurfer/dcmdrle_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMDRLE_FS_METADATA = Metadata(
-    id="1c6fdec3b4ee16a344e1e0d5d4e1bcbc79b17f47.boutiques",
+    id="b9eeb8b72ae777bc906cf77f646047be70b17380.boutiques",
     name="dcmdrle.fs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -221,7 +221,7 @@ def dcmdrle_fs_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("dcmdrle")
+    cargs.append("dcmdrle.fs")
     cargs.append(execution.input_file(params.get("input_file")))
     cargs.append(params.get("output_file"))
     if params.get("help"):

niwrap_freesurfer/freesurfer/dicom_rename.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DICOM_RENAME_METADATA = Metadata(
-    id="2eb87845c3a6be71bcd6bb57089f0cd879da57d4.boutiques",
+    id="967c36e6f1722cec2c2a414d9307145c8c3ca445.boutiques",
     name="dicom-rename",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,8 @@ DicomRenameParameters = typing.TypedDict('DicomRenameParameters', {
     "__STYX_TYPE__": typing.Literal["dicom-rename"],
     "input_files": list[InputPathType],
     "output_base": str,
+    "version": bool,
+    "help": bool,
 })
 
 
@@ -65,6 +67,8 @@ class DicomRenameOutputs(typing.NamedTuple):
 def dicom_rename_params(
     input_files: list[InputPathType],
     output_base: str,
+    version: bool = False,
+    help_: bool = False,
 ) -> DicomRenameParameters:
     """
     Build parameters.
@@ -73,6 +77,8 @@ def dicom_rename_params(
         input_files: Input DICOM files to be renamed.
         output_base: Base name for output files that includes series and image\
             numbers.
+        version: Print version and exit.
+        help_: Print help and exit.
     Returns:
         Parameter dictionary
     """
@@ -80,6 +86,8 @@ def dicom_rename_params(
         "__STYXTYPE__": "dicom-rename",
         "input_files": input_files,
         "output_base": output_base,
+        "version": version,
+        "help": help_,
     }
     return params
 
@@ -98,14 +106,19 @@ def dicom_rename_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("dicom-rename")
     cargs.extend([
         "-rename",
-        "dicom" + "".join([execution.input_file(f) for f in params.get("input_files")])
+        *[execution.input_file(f) for f in params.get("input_files")]
     ])
     cargs.extend([
         "--o",
         params.get("output_base")
     ])
+    if params.get("version"):
+        cargs.append("--version")
+    if params.get("help"):
+        cargs.append("--help")
     return cargs
 
 
@@ -156,6 +169,8 @@ def dicom_rename_execute(
 def dicom_rename(
     input_files: list[InputPathType],
     output_base: str,
+    version: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> DicomRenameOutputs:
     """
@@ -169,6 +184,8 @@ def dicom_rename(
         input_files: Input DICOM files to be renamed.
         output_base: Base name for output files that includes series and image\
             numbers.
+        version: Print version and exit.
+        help_: Print help and exit.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DicomRenameOutputs`).
@@ -178,6 +195,8 @@ def dicom_rename(
     params = dicom_rename_params(
         input_files=input_files,
         output_base=output_base,
+        version=version,
+        help_=help_,
     )
     return dicom_rename_execute(params, execution)
 

niwrap_freesurfer/freesurfer/dmri_bset.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_BSET_METADATA = Metadata(
-    id="a5ba928b721f328bbae969650915bdc4c218018a.boutiques",
+    id="9a9d1299f82ba59a9a11b741685458eb6f480882.boutiques",
     name="dmri_bset",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,7 @@ DmriBsetParameters = typing.TypedDict('DmriBsetParameters', {
     "__STYX_TYPE__": typing.Literal["dmri_bset"],
     "input_dwi": InputPathType,
     "output_dwi": str,
+    "b_values": typing.NotRequired[list[float] | None],
     "btol": typing.NotRequired[float | None],
     "bsort": bool,
     "bmax": typing.NotRequired[float | None],
@@ -76,6 +77,7 @@ class DmriBsetOutputs(typing.NamedTuple):
 def dmri_bset_params(
     input_dwi: InputPathType,
     output_dwi: str,
+    b_values: list[float] | None = None,
     btol: float | None = 0.05,
     bsort: bool = False,
     bmax: float | None = None,
@@ -90,6 +92,7 @@ def dmri_bset_params(
     Args:
         input_dwi: Input DWI series.
         output_dwi: Output DWI series.
+        b_values: Extract one or more b-values.
         btol: Tolerance around each single b-value (default: 0.05).
         bsort: Reorder output data by b-shell (default: maintain original\
             order).
@@ -111,6 +114,8 @@ def dmri_bset_params(
         "output_dwi": output_dwi,
         "bsort": bsort,
     }
+    if b_values is not None:
+        params["b_values"] = b_values
     if btol is not None:
         params["btol"] = btol
     if bmax is not None:
@@ -143,7 +148,11 @@ def dmri_bset_cargs(
     cargs.append("dmri_bset")
     cargs.append(execution.input_file(params.get("input_dwi")))
     cargs.append(params.get("output_dwi"))
-    cargs.append("[B_VALUES...]")
+    if params.get("b_values") is not None:
+        cargs.extend([
+            "--b",
+            *map(str, params.get("b_values"))
+        ])
     if params.get("btol") is not None:
         cargs.extend([
             "--btol",
@@ -229,6 +238,7 @@ def dmri_bset_execute(
 def dmri_bset(
     input_dwi: InputPathType,
     output_dwi: str,
+    b_values: list[float] | None = None,
     btol: float | None = 0.05,
     bsort: bool = False,
     bmax: float | None = None,
@@ -249,6 +259,7 @@ def dmri_bset(
     Args:
         input_dwi: Input DWI series.
         output_dwi: Output DWI series.
+        b_values: Extract one or more b-values.
         btol: Tolerance around each single b-value (default: 0.05).
         bsort: Reorder output data by b-shell (default: maintain original\
             order).
@@ -270,6 +281,7 @@ def dmri_bset(
     params = dmri_bset_params(
         input_dwi=input_dwi,
         output_dwi=output_dwi,
+        b_values=b_values,
         btol=btol,
         bsort=bsort,
         bmax=bmax,

niwrap_freesurfer/freesurfer/dmri_forrest.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_FORREST_METADATA = Metadata(
-    id="dd4542253804128ad899a822733de446938568c4.boutiques",
+    id="2c71c0f52e15a044282718015b50d98a2a58e574.boutiques",
     name="dmri_forrest",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -23,6 +23,7 @@ DmriForrestParameters = typing.TypedDict('DmriForrestParameters', {
     "diff_file": typing.NotRequired[InputPathType | None],
     "debug": bool,
     "checkopts": bool,
+    "help": bool,
 })
 
 
@@ -74,6 +75,7 @@ def dmri_forrest_params(
     diff_file: InputPathType | None = None,
     debug: bool = False,
     checkopts: bool = False,
+    help_: bool = False,
 ) -> DmriForrestParameters:
     """
     Build parameters.
@@ -88,6 +90,7 @@ def dmri_forrest_params(
             directory.
         debug: Turn on debugging mode.
         checkopts: Only check options and exit.
+        help_: Display help information.
     Returns:
         Parameter dictionary
     """
@@ -99,6 +102,7 @@ def dmri_forrest_params(
         "tract_files": tract_files,
         "debug": debug,
         "checkopts": checkopts,
+        "help": help_,
     }
     if seg_file is not None:
         params["seg_file"] = seg_file
@@ -152,6 +156,8 @@ def dmri_forrest_cargs(
         cargs.append("--debug")
     if params.get("checkopts"):
         cargs.append("--checkopts")
+    if params.get("help"):
+        cargs.append("--help")
     return cargs
 
 
@@ -208,6 +214,7 @@ def dmri_forrest(
     diff_file: InputPathType | None = None,
     debug: bool = False,
     checkopts: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> DmriForrestOutputs:
     """
@@ -228,6 +235,7 @@ def dmri_forrest(
             directory.
         debug: Turn on debugging mode.
         checkopts: Only check options and exit.
+        help_: Display help information.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriForrestOutputs`).
@@ -243,6 +251,7 @@ def dmri_forrest(
         diff_file=diff_file,
         debug=debug,
         checkopts=checkopts,
+        help_=help_,
     )
     return dmri_forrest_execute(params, execution)