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

niwrap_freesurfer/freesurfer/mri_head.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_HEAD_METADATA = Metadata(
-    id="fb167e02a7257ba8b9a2343709e24ec6a1664305.boutiques",
+    id="f71c8c4f81d133948a66cd2d08a048fd40c58c30.boutiques",
     name="mri_head",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,6 +18,8 @@ MriHeadParameters = typing.TypedDict('MriHeadParameters', {
     "identify": bool,
     "read": bool,
     "filename": typing.NotRequired[str | None],
+    "help": bool,
+    "usage": bool,
     "question_mark_help": bool,
 })
 
@@ -65,6 +67,8 @@ def mri_head_params(
     identify: bool = False,
     read: bool = False,
     filename: str | None = None,
+    help_: bool = False,
+    usage: bool = False,
     question_mark_help: bool = False,
 ) -> MriHeadParameters:
     """
@@ -74,6 +78,8 @@ def mri_head_params(
         identify: Identify the MRI file.
         read: Read the MRI file.
         filename: Filename for identification or reading.
+        help_: Display help information.
+        usage: Display usage information.
         question_mark_help: Display help or usage information.
     Returns:
         Parameter dictionary
@@ -82,6 +88,8 @@ def mri_head_params(
         "__STYXTYPE__": "mri_head",
         "identify": identify,
         "read": read,
+        "help": help_,
+        "usage": usage,
         "question_mark_help": question_mark_help,
     }
     if filename is not None:
@@ -110,6 +118,10 @@ def mri_head_cargs(
         cargs.append("-read")
     if params.get("filename") is not None:
         cargs.append(params.get("filename"))
+    if params.get("help"):
+        cargs.append("-h")
+    if params.get("usage"):
+        cargs.append("-u")
     if params.get("question_mark_help"):
         cargs.append("-?")
     return cargs
@@ -162,6 +174,8 @@ def mri_head(
     identify: bool = False,
     read: bool = False,
     filename: str | None = None,
+    help_: bool = False,
+    usage: bool = False,
     question_mark_help: bool = False,
     runner: Runner | None = None,
 ) -> MriHeadOutputs:
@@ -176,6 +190,8 @@ def mri_head(
         identify: Identify the MRI file.
         read: Read the MRI file.
         filename: Filename for identification or reading.
+        help_: Display help information.
+        usage: Display usage information.
         question_mark_help: Display help or usage information.
         runner: Command runner.
     Returns:
@@ -187,6 +203,8 @@ def mri_head(
         identify=identify,
         read=read,
         filename=filename,
+        help_=help_,
+        usage=usage,
         question_mark_help=question_mark_help,
     )
     return mri_head_execute(params, execution)

niwrap_freesurfer/freesurfer/mri_jacobian.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_JACOBIAN_METADATA = Metadata(
-    id="261fa5191d385d242b16ec1808b1a5ac51b44bc2.boutiques",
+    id="92cd12066432758c04574ab139770c5aabee1470.boutiques",
     name="mri_jacobian",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -24,6 +24,7 @@ MriJacobianParameters = typing.TypedDict('MriJacobianParameters', {
     "smooth_sigma": typing.NotRequired[float | None],
     "zero_mean_log": bool,
     "tm3d": bool,
+    "help1": bool,
     "help2": bool,
     "dt": bool,
     "debug_voxel": typing.NotRequired[list[float] | None],
@@ -83,6 +84,7 @@ def mri_jacobian_params(
     smooth_sigma: float | None = None,
     zero_mean_log: bool = False,
     tm3d: bool = False,
+    help1: bool = False,
     help2: bool = False,
     dt: bool = False,
     debug_voxel: list[float] | None = None,
@@ -101,6 +103,7 @@ def mri_jacobian_params(
         smooth_sigma: Smoothing Jacobian volume with sigma.
         zero_mean_log: Make log Jacobian zero mean.
         tm3d: The input morph (m3z) originated from tm3d (mri_cvs_register).
+        help1: Writing out help.
         help2: Writing out help.
         dt: DT option (description not provided in help text).
         debug_voxel: Debug voxel with specified Gx, Gy, Gz coordinates.
@@ -118,6 +121,7 @@ def mri_jacobian_params(
         "log_jacobian": log_jacobian,
         "zero_mean_log": zero_mean_log,
         "tm3d": tm3d,
+        "help1": help1,
         "help2": help2,
         "dt": dt,
         "remove": remove,
@@ -162,6 +166,8 @@ def mri_jacobian_cargs(
         cargs.append("-z")
     if params.get("tm3d"):
         cargs.append("-tm3d")
+    if params.get("help1"):
+        cargs.append("-?")
     if params.get("help2"):
         cargs.append("-u")
     if params.get("dt"):
@@ -230,6 +236,7 @@ def mri_jacobian(
     smooth_sigma: float | None = None,
     zero_mean_log: bool = False,
     tm3d: bool = False,
+    help1: bool = False,
     help2: bool = False,
     dt: bool = False,
     debug_voxel: list[float] | None = None,
@@ -253,6 +260,7 @@ def mri_jacobian(
         smooth_sigma: Smoothing Jacobian volume with sigma.
         zero_mean_log: Make log Jacobian zero mean.
         tm3d: The input morph (m3z) originated from tm3d (mri_cvs_register).
+        help1: Writing out help.
         help2: Writing out help.
         dt: DT option (description not provided in help text).
         debug_voxel: Debug voxel with specified Gx, Gy, Gz coordinates.
@@ -273,6 +281,7 @@ def mri_jacobian(
         smooth_sigma=smooth_sigma,
         zero_mean_log=zero_mean_log,
         tm3d=tm3d,
+        help1=help1,
         help2=help2,
         dt=dt,
         debug_voxel=debug_voxel,

niwrap_freesurfer/freesurfer/mri_nl_align.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_NL_ALIGN_METADATA = Metadata(
-    id="cd2a19b23e2fec00175500358afe679cc9ee7fc7.boutiques",
+    id="fd12751796479c6b953e5a2ce259ca4890ee3c30.boutiques",
     name="mri_nl_align",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -33,11 +33,13 @@ MriNlAlignParameters = typing.TypedDict('MriNlAlignParameters', {
     "erode": typing.NotRequired[float | None],
     "match_mean": typing.NotRequired[float | None],
     "intensity": typing.NotRequired[float | None],
+    "ll": typing.NotRequired[float | None],
     "noregrid_flag": bool,
     "regrid_flag": bool,
     "view": typing.NotRequired[list[float] | None],
     "levels": typing.NotRequired[float | None],
     "area_smoothness": typing.NotRequired[float | None],
+    "asmooth": typing.NotRequired[float | None],
     "area": typing.NotRequired[float | None],
     "tolerance": typing.NotRequired[float | None],
     "sigma": typing.NotRequired[float | None],
@@ -125,11 +127,13 @@ def mri_nl_align_params(
     erode: float | None = None,
     match_mean: float | None = None,
     intensity: float | None = None,
+    ll: float | None = None,
     noregrid_flag: bool = False,
     regrid_flag: bool = False,
     view: list[float] | None = None,
     levels: float | None = None,
     area_smoothness: float | None = None,
+    asmooth: float | None = None,
     area: float | None = None,
     tolerance: float | None = None,
     sigma: float | None = None,
@@ -176,11 +180,13 @@ def mri_nl_align_params(
         erode: Erode source and target image specified times before morphing.
         match_mean: Control for matching peak of intensity ratio histogram.
         intensity: Set l_log_likelihood to specified value.
+        ll: Set l_log_likelihood to specified value.
         noregrid_flag: Disable regridding.
         regrid_flag: Enable regridding.
         view: View voxel coordinates (Gx, Gy, Gz).
         levels: Set levels to specified value.
         area_smoothness: Set l_area_smoothness to specified value.
+        asmooth: Set l_area_smoothness to specified value.
         area: Set l_area to specified value.
         tolerance: Set tolerance to specified value.
         sigma: Set sigma to specified value.
@@ -240,12 +246,16 @@ def mri_nl_align_params(
         params["match_mean"] = match_mean
     if intensity is not None:
         params["intensity"] = intensity
+    if ll is not None:
+        params["ll"] = ll
     if view is not None:
         params["view"] = view
     if levels is not None:
         params["levels"] = levels
     if area_smoothness is not None:
         params["area_smoothness"] = area_smoothness
+    if asmooth is not None:
+        params["asmooth"] = asmooth
     if area is not None:
         params["area"] = area
     if tolerance is not None:
@@ -373,6 +383,11 @@ def mri_nl_align_cargs(
             "-intensity",
             str(params.get("intensity"))
         ])
+    if params.get("ll") is not None:
+        cargs.extend([
+            "-ll",
+            str(params.get("ll"))
+        ])
     if params.get("noregrid_flag"):
         cargs.append("-noregrid")
     if params.get("regrid_flag"):
@@ -392,6 +407,11 @@ def mri_nl_align_cargs(
             "-areasmoothness",
             str(params.get("area_smoothness"))
         ])
+    if params.get("asmooth") is not None:
+        cargs.extend([
+            "-asmooth",
+            str(params.get("asmooth"))
+        ])
     if params.get("area") is not None:
         cargs.extend([
             "-area",
@@ -573,11 +593,13 @@ def mri_nl_align(
     erode: float | None = None,
     match_mean: float | None = None,
     intensity: float | None = None,
+    ll: float | None = None,
     noregrid_flag: bool = False,
     regrid_flag: bool = False,
     view: list[float] | None = None,
     levels: float | None = None,
     area_smoothness: float | None = None,
+    asmooth: float | None = None,
     area: float | None = None,
     tolerance: float | None = None,
     sigma: float | None = None,
@@ -629,11 +651,13 @@ def mri_nl_align(
         erode: Erode source and target image specified times before morphing.
         match_mean: Control for matching peak of intensity ratio histogram.
         intensity: Set l_log_likelihood to specified value.
+        ll: Set l_log_likelihood to specified value.
         noregrid_flag: Disable regridding.
         regrid_flag: Enable regridding.
         view: View voxel coordinates (Gx, Gy, Gz).
         levels: Set levels to specified value.
         area_smoothness: Set l_area_smoothness to specified value.
+        asmooth: Set l_area_smoothness to specified value.
         area: Set l_area to specified value.
         tolerance: Set tolerance to specified value.
         sigma: Set sigma to specified value.
@@ -682,11 +706,13 @@ def mri_nl_align(
         erode=erode,
         match_mean=match_mean,
         intensity=intensity,
+        ll=ll,
         noregrid_flag=noregrid_flag,
         regrid_flag=regrid_flag,
         view=view,
         levels=levels,
         area_smoothness=area_smoothness,
+        asmooth=asmooth,
         area=area,
         tolerance=tolerance,
         sigma=sigma,

niwrap_freesurfer/freesurfer/mri_relabel_nonwm_hypos.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_RELABEL_NONWM_HYPOS_METADATA = Metadata(
-    id="93faec099d80076ace8a12bddc7f7a4affe02681.boutiques",
+    id="c2dc64755d5cb891179f87b8ccf2689c8f1b9dde.boutiques",
     name="mri_relabel_nonwm_hypos",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -119,11 +119,11 @@ def mri_relabel_nonwm_hypos_cargs(
     cargs.append("mri_relabel_nonwm_hypos")
     cargs.extend([
         "-i",
-        "-" + execution.input_file(params.get("inputseg"))
+        execution.input_file(params.get("inputseg"))
     ])
     cargs.extend([
         "-o",
-        "-" + params.get("outputseg")
+        params.get("outputseg")
     ])
     if params.get("segments") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/mri_reorient_lr_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_REORIENT_LR_CSH_METADATA = Metadata(
-    id="44b9d6ba4983462289bb74a35e46ca2bc4fb3a6c.boutiques",
+    id="0a6ce73f29c18581e75c6c6cc19eafd6b33ca832.boutiques",
     name="mri_reorient_LR.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -118,7 +118,7 @@ def mri_reorient_lr_csh_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_reorient_LR")
+    cargs.append("mri_reorient_LR.csh")
     cargs.extend([
         "--i",
         execution.input_file(params.get("input_vol"))

niwrap_freesurfer/freesurfer/mri_seg_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SEG_DIFF_METADATA = Metadata(
-    id="71504722501dfa1ec92d8dd0c51d3ee7e1c9740c.boutiques",
+    id="1ffa8167a31865e0a4ffb1e2d6b11eef8bdddfc0.boutiques",
     name="mri_seg_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -19,6 +19,7 @@ MriSegDiffParameters = typing.TypedDict('MriSegDiffParameters', {
     "seg2": typing.NotRequired[InputPathType | None],
     "seg": typing.NotRequired[InputPathType | None],
     "diff": str,
+    "diff_in": typing.NotRequired[InputPathType | None],
     "merged": typing.NotRequired[str | None],
     "diff_force": bool,
     "debug": bool,
@@ -76,6 +77,7 @@ def mri_seg_diff_params(
     seg1: InputPathType | None = None,
     seg2: InputPathType | None = None,
     seg: InputPathType | None = None,
+    diff_in: InputPathType | None = None,
     merged: str | None = None,
     diff_force: bool = False,
     debug: bool = False,
@@ -90,6 +92,7 @@ def mri_seg_diff_params(
         seg1: First segmentation file (e.g., unedited).
         seg2: Second segmentation file (e.g., edited).
         seg: Source segmentation file (e.g., unedited).
+        diff_in: Input diff segmentation volume.
         merged: Merged output, combining unedited with diff.
         diff_force: Force creation of a diff even if no diff is detected.
         debug: Turn on debugging.
@@ -112,6 +115,8 @@ def mri_seg_diff_params(
         params["seg2"] = seg2
     if seg is not None:
         params["seg"] = seg
+    if diff_in is not None:
+        params["diff_in"] = diff_in
     if merged is not None:
         params["merged"] = merged
     return params
@@ -151,6 +156,11 @@ def mri_seg_diff_cargs(
         "--diff",
         params.get("diff")
     ])
+    if params.get("diff_in") is not None:
+        cargs.extend([
+            "--diff-in",
+            execution.input_file(params.get("diff_in"))
+        ])
     if params.get("merged") is not None:
         cargs.extend([
             "--merged",
@@ -218,6 +228,7 @@ def mri_seg_diff(
     seg1: InputPathType | None = None,
     seg2: InputPathType | None = None,
     seg: InputPathType | None = None,
+    diff_in: InputPathType | None = None,
     merged: str | None = None,
     diff_force: bool = False,
     debug: bool = False,
@@ -238,6 +249,7 @@ def mri_seg_diff(
         seg1: First segmentation file (e.g., unedited).
         seg2: Second segmentation file (e.g., edited).
         seg: Source segmentation file (e.g., unedited).
+        diff_in: Input diff segmentation volume.
         merged: Merged output, combining unedited with diff.
         diff_force: Force creation of a diff even if no diff is detected.
         debug: Turn on debugging.
@@ -254,6 +266,7 @@ def mri_seg_diff(
         seg2=seg2,
         seg=seg,
         diff=diff,
+        diff_in=diff_in,
         merged=merged,
         diff_force=diff_force,
         debug=debug,

niwrap_freesurfer/freesurfer/mri_twoclass.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_TWOCLASS_METADATA = Metadata(
-    id="717cefa4d525f9af2426548e3f53f0a54c018c15.boutiques",
+    id="d2a42c55540746e081c5b41bbf3d232cedb5984b.boutiques",
     name="mri_twoclass",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -123,7 +123,6 @@ def mri_twoclass_cargs(
     cargs.append(params.get("output_subject"))
     cargs.append(params.get("output_volume"))
     cargs.extend(params.get("c1_subjects"))
-    cargs.append(":")
     cargs.extend(params.get("c2_subjects"))
     if params.get("f_threshold") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/mri_validate_skull_stripped.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_VALIDATE_SKULL_STRIPPED_METADATA = Metadata(
-    id="2bdfa9e2cc73998aa283c518ac64ca8fd5b27024.boutiques",
+    id="0de0265b82e5cc83b346cf1e1de5cade0f9128b2.boutiques",
     name="mri_validate_skull_stripped",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -98,7 +98,7 @@ def mri_validate_skull_stripped_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("tntester")
+    cargs.append("mri_validate_skull_stripped")
     cargs.append(execution.input_file(params.get("mri_reference")))
     cargs.append(execution.input_file(params.get("mri_test")))
     cargs.append(str(params.get("weight")))

niwrap_freesurfer/freesurfer/mri_warp_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_WARP_CONVERT_METADATA = Metadata(
-    id="36b7f6d3b0edf16e088ad567445e656a71a7dd89.boutiques",
+    id="32b2750e85eac274b020aca2c35655e2c3b86427.boutiques",
     name="mri_warp_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,7 +15,17 @@ MRI_WARP_CONVERT_METADATA = Metadata(
 
 MriWarpConvertParameters = typing.TypedDict('MriWarpConvertParameters', {
     "__STYX_TYPE__": typing.Literal["mri_warp_convert"],
+    "inm3z": typing.NotRequired[InputPathType | None],
+    "infsl": typing.NotRequired[InputPathType | None],
+    "inlps": typing.NotRequired[InputPathType | None],
+    "initk": typing.NotRequired[InputPathType | None],
+    "inras": typing.NotRequired[InputPathType | None],
     "invox": typing.NotRequired[InputPathType | None],
+    "outm3z": typing.NotRequired[str | None],
+    "outfsl": typing.NotRequired[str | None],
+    "outlps": typing.NotRequired[str | None],
+    "outitk": typing.NotRequired[str | None],
+    "outras": typing.NotRequired[str | None],
     "outvox": typing.NotRequired[str | None],
     "insrcgeom": typing.NotRequired[InputPathType | None],
     "downsample": bool,
@@ -65,7 +75,17 @@ class MriWarpConvertOutputs(typing.NamedTuple):
 
 
 def mri_warp_convert_params(
+    inm3z: InputPathType | None = None,
+    infsl: InputPathType | None = None,
+    inlps: InputPathType | None = None,
+    initk: InputPathType | None = None,
+    inras: InputPathType | None = None,
     invox: InputPathType | None = None,
+    outm3z: str | None = None,
+    outfsl: str | None = None,
+    outlps: str | None = None,
+    outitk: str | None = None,
+    outras: str | None = None,
     outvox: str | None = None,
     insrcgeom: InputPathType | None = None,
     downsample: bool = False,
@@ -74,7 +94,17 @@ def mri_warp_convert_params(
     Build parameters.
     
     Args:
+        inm3z: Input M3Z warp.
+        infsl: Input FSL warp.
+        inlps: Input LPS-to-LPS displacement field (e.g. ITK, ANTs).
+        initk: Input ITK LPS-to-LPS displacement field.
+        inras: Input RAS-to-RAS displacement field (e.g. NiftyReg).
         invox: Input file with displacements in source-voxel space.
+        outm3z: Output warp (M3Z Freesurfer format).
+        outfsl: Output warp (FSL format).
+        outlps: Output LPS-to-LPS displacement field (e.g. ITK, ANTs).
+        outitk: Output ITK LPS-to-LPS displacement field.
+        outras: Output RAS-to-RAS displacement field (e.g. NiftyReg).
         outvox: Output file with displacements in source-voxel space.
         insrcgeom: Specify source image geometry (moving volume).
         downsample: Downsample output M3Z to spacing of 2.
@@ -85,8 +115,28 @@ def mri_warp_convert_params(
         "__STYXTYPE__": "mri_warp_convert",
         "downsample": downsample,
     }
+    if inm3z is not None:
+        params["inm3z"] = inm3z
+    if infsl is not None:
+        params["infsl"] = infsl
+    if inlps is not None:
+        params["inlps"] = inlps
+    if initk is not None:
+        params["initk"] = initk
+    if inras is not None:
+        params["inras"] = inras
     if invox is not None:
         params["invox"] = invox
+    if outm3z is not None:
+        params["outm3z"] = outm3z
+    if outfsl is not None:
+        params["outfsl"] = outfsl
+    if outlps is not None:
+        params["outlps"] = outlps
+    if outitk is not None:
+        params["outitk"] = outitk
+    if outras is not None:
+        params["outras"] = outras
     if outvox is not None:
         params["outvox"] = outvox
     if insrcgeom is not None:
@@ -109,11 +159,61 @@ def mri_warp_convert_cargs(
     """
     cargs = []
     cargs.append("mri_warp_convert")
+    if params.get("inm3z") is not None:
+        cargs.extend([
+            "--inm3z",
+            execution.input_file(params.get("inm3z"))
+        ])
+    if params.get("infsl") is not None:
+        cargs.extend([
+            "--infsl",
+            execution.input_file(params.get("infsl"))
+        ])
+    if params.get("inlps") is not None:
+        cargs.extend([
+            "--inlps",
+            execution.input_file(params.get("inlps"))
+        ])
+    if params.get("initk") is not None:
+        cargs.extend([
+            "--initk",
+            execution.input_file(params.get("initk"))
+        ])
+    if params.get("inras") is not None:
+        cargs.extend([
+            "--inras",
+            execution.input_file(params.get("inras"))
+        ])
     if params.get("invox") is not None:
         cargs.extend([
             "--invox",
             execution.input_file(params.get("invox"))
         ])
+    if params.get("outm3z") is not None:
+        cargs.extend([
+            "--outm3z",
+            params.get("outm3z")
+        ])
+    if params.get("outfsl") is not None:
+        cargs.extend([
+            "--outfsl",
+            params.get("outfsl")
+        ])
+    if params.get("outlps") is not None:
+        cargs.extend([
+            "--outlps",
+            params.get("outlps")
+        ])
+    if params.get("outitk") is not None:
+        cargs.extend([
+            "--outitk",
+            params.get("outitk")
+        ])
+    if params.get("outras") is not None:
+        cargs.extend([
+            "--outras",
+            params.get("outras")
+        ])
     if params.get("outvox") is not None:
         cargs.extend([
             "--outvox",
@@ -174,7 +274,17 @@ def mri_warp_convert_execute(
 
 
 def mri_warp_convert(
+    inm3z: InputPathType | None = None,
+    infsl: InputPathType | None = None,
+    inlps: InputPathType | None = None,
+    initk: InputPathType | None = None,
+    inras: InputPathType | None = None,
     invox: InputPathType | None = None,
+    outm3z: str | None = None,
+    outfsl: str | None = None,
+    outlps: str | None = None,
+    outitk: str | None = None,
+    outras: str | None = None,
     outvox: str | None = None,
     insrcgeom: InputPathType | None = None,
     downsample: bool = False,
@@ -188,7 +298,17 @@ def mri_warp_convert(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        inm3z: Input M3Z warp.
+        infsl: Input FSL warp.
+        inlps: Input LPS-to-LPS displacement field (e.g. ITK, ANTs).
+        initk: Input ITK LPS-to-LPS displacement field.
+        inras: Input RAS-to-RAS displacement field (e.g. NiftyReg).
         invox: Input file with displacements in source-voxel space.
+        outm3z: Output warp (M3Z Freesurfer format).
+        outfsl: Output warp (FSL format).
+        outlps: Output LPS-to-LPS displacement field (e.g. ITK, ANTs).
+        outitk: Output ITK LPS-to-LPS displacement field.
+        outras: Output RAS-to-RAS displacement field (e.g. NiftyReg).
         outvox: Output file with displacements in source-voxel space.
         insrcgeom: Specify source image geometry (moving volume).
         downsample: Downsample output M3Z to spacing of 2.
@@ -199,7 +319,17 @@ def mri_warp_convert(
     runner = runner or get_global_runner()
     execution = runner.start_execution(MRI_WARP_CONVERT_METADATA)
     params = mri_warp_convert_params(
+        inm3z=inm3z,
+        infsl=infsl,
+        inlps=inlps,
+        initk=initk,
+        inras=inras,
         invox=invox,
+        outm3z=outm3z,
+        outfsl=outfsl,
+        outlps=outlps,
+        outitk=outitk,
+        outras=outras,
         outvox=outvox,
         insrcgeom=insrcgeom,
         downsample=downsample,