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

niwrap_freesurfer/freesurfer/mris_nudge.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_NUDGE_METADATA = Metadata(
-    id="6f298ed7d045a2ce709015d0cecce0980607d9d6.boutiques",
+    id="95de4ed7ce38c1344db48e4487148e75d7cd5ac7.boutiques",
     name="mris_nudge",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -115,7 +115,6 @@ def mris_nudge_cargs(
     cargs.append(str(params.get("vertex")))
     cargs.append(str(params.get("target_val")))
     cargs.append(str(params.get("nbhd")))
-    cargs.append("[OUTPUT_SURF]")
     return cargs
 
 

niwrap_freesurfer/freesurfer/mris_place_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_PLACE_SURFACE_METADATA = Metadata(
-    id="e4e973bfe64ca5b7e38915757ccc306ea96b6327.boutiques",
+    id="e71154f3ac212ed67a529db481c0c3cb77247351.boutiques",
     name="mris_place_surface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -476,7 +476,6 @@ def mris_place_surface_cargs(
             "--fill-lat-vents",
             *map(str, params.get("fill_lateral_ventricles"))
         ])
-    cargs.append("[COST_FUNCTION_ARGS]")
     return cargs
 
 

niwrap_freesurfer/freesurfer/mris_preproc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_PREPROC_METADATA = Metadata(
-    id="dd5edb4541571b929ce3905d2cb09807c8f4d850.boutiques",
+    id="19354ad334d567c1cc3b6d8c8a574e514f9d7eec.boutiques",
     name="mris_preproc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -27,6 +27,7 @@ MrisPreprocParameters = typing.TypedDict('MrisPreprocParameters', {
     "qdec": typing.NotRequired[InputPathType | None],
     "qdec_long": typing.NotRequired[InputPathType | None],
     "surfmeasfile": typing.NotRequired[list[InputPathType] | None],
+    "volmeasfile_reg": typing.NotRequired[list[str] | None],
     "projfrac": typing.NotRequired[float | None],
     "projfrac_max": typing.NotRequired[list[float] | None],
     "projfrac_avg": typing.NotRequired[list[float] | None],
@@ -118,6 +119,7 @@ def mris_preproc_params(
     qdec: InputPathType | None = None,
     qdec_long: InputPathType | None = None,
     surfmeasfile: list[InputPathType] | None = None,
+    volmeasfile_reg: list[str] | None = None,
     projfrac: float | None = None,
     projfrac_max: list[float] | None = None,
     projfrac_avg: list[float] | None = None,
@@ -176,6 +178,8 @@ def mris_preproc_params(
             column is the "fsid".
         qdec_long: Specify list of subjects via longitudinal qdec table file.
         surfmeasfile: Specify full path to input surface measure file.
+        volmeasfile_reg: Specify full path to a volume file and its\
+            registration matrix file.
         projfrac: When sampling a volume onto the surface, sample a fraction of\
             the thickness along the surface normal.
         projfrac_max: When sampling a volume onto the surface, find max along\
@@ -261,6 +265,8 @@ def mris_preproc_params(
         params["qdec_long"] = qdec_long
     if surfmeasfile is not None:
         params["surfmeasfile"] = surfmeasfile
+    if volmeasfile_reg is not None:
+        params["volmeasfile_reg"] = volmeasfile_reg
     if projfrac is not None:
         params["projfrac"] = projfrac
     if projfrac_max is not None:
@@ -374,7 +380,11 @@ def mris_preproc_cargs(
             "--is",
             *[execution.input_file(f) for f in params.get("surfmeasfile")]
         ])
-    cargs.append("[VOLMEASFILE]")
+    if params.get("volmeasfile_reg") is not None:
+        cargs.extend([
+            "--iv",
+            *params.get("volmeasfile_reg")
+        ])
     if params.get("projfrac") is not None:
         cargs.extend([
             "--projfrac",
@@ -565,6 +575,7 @@ def mris_preproc(
     qdec: InputPathType | None = None,
     qdec_long: InputPathType | None = None,
     surfmeasfile: list[InputPathType] | None = None,
+    volmeasfile_reg: list[str] | None = None,
     projfrac: float | None = None,
     projfrac_max: list[float] | None = None,
     projfrac_avg: list[float] | None = None,
@@ -630,6 +641,8 @@ def mris_preproc(
             column is the "fsid".
         qdec_long: Specify list of subjects via longitudinal qdec table file.
         surfmeasfile: Specify full path to input surface measure file.
+        volmeasfile_reg: Specify full path to a volume file and its\
+            registration matrix file.
         projfrac: When sampling a volume onto the surface, sample a fraction of\
             the thickness along the surface normal.
         projfrac_max: When sampling a volume onto the surface, find max along\
@@ -690,6 +703,7 @@ def mris_preproc(
         qdec=qdec,
         qdec_long=qdec_long,
         surfmeasfile=surfmeasfile,
+        volmeasfile_reg=volmeasfile_reg,
         projfrac=projfrac,
         projfrac_max=projfrac_max,
         projfrac_avg=projfrac_avg,

niwrap_freesurfer/freesurfer/mris_spherical_average.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SPHERICAL_AVERAGE_METADATA = Metadata(
-    id="1428559d3a56abaf727b5871834a354591593a62.boutiques",
+    id="183c7a343e730b5d37f38ae332c84cb1365ae30e.boutiques",
     name="mris_spherical_average",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,13 +15,20 @@ MRIS_SPHERICAL_AVERAGE_METADATA = Metadata(
 
 MrisSphericalAverageParameters = typing.TypedDict('MrisSphericalAverageParameters', {
     "__STYX_TYPE__": typing.Literal["mris_spherical_average"],
-    "summary_statistics": typing.NotRequired[str | None],
     "which": typing.Literal["coords", "label", "vals", "curv", "area"],
     "fname": str,
     "hemi": typing.Literal["lh", "rh"],
     "spherical_surf": str,
     "subjects": list[str],
     "output": str,
+    "segment": bool,
+    "normalize": bool,
+    "orig": typing.NotRequired[str | None],
+    "output_subject_name": typing.NotRequired[str | None],
+    "output_subject_dir": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "average_area": bool,
+    "summary_statistics": typing.NotRequired[str | None],
 })
 
 
@@ -71,6 +78,13 @@ def mris_spherical_average_params(
     spherical_surf: str,
     subjects: list[str],
     output: str,
+    segment: bool = False,
+    normalize: bool = False,
+    orig: str | None = None,
+    output_subject_name: str | None = None,
+    output_subject_dir: str | None = None,
+    subjects_dir: str | None = None,
+    average_area: bool = False,
     summary_statistics: str | None = None,
 ) -> MrisSphericalAverageParameters:
     """
@@ -83,6 +97,16 @@ def mris_spherical_average_params(
         spherical_surf: The spherical surface file.
         subjects: List of subjects.
         output: Output file or directory.
+        segment: Only use largest connected component of label.
+        normalize: Normalize output so it can be interpreted as a probability.
+        orig: Use <name> as original surface position; default=orig.
+        output_subject_name: Use <output subject name> as the space to write\
+            the results in instead of the last subject given.
+        output_subject_dir: Use <output subject dir> as the subjects dir for\
+            the output subject.
+        subjects_dir: Set the subjects directory.
+        average_area: Compute threshold for label that will give the average\
+            label approximately the average surface area.
         summary_statistics: Generate summary statistics and write them into\
             sigavg<cond #>-<hemi>.w and sigvar<cond #>-<hemi>.w.
     Returns:
@@ -96,7 +120,18 @@ def mris_spherical_average_params(
         "spherical_surf": spherical_surf,
         "subjects": subjects,
         "output": output,
+        "segment": segment,
+        "normalize": normalize,
+        "average_area": average_area,
     }
+    if orig is not None:
+        params["orig"] = orig
+    if output_subject_name is not None:
+        params["output_subject_name"] = output_subject_name
+    if output_subject_dir is not None:
+        params["output_subject_dir"] = output_subject_dir
+    if subjects_dir is not None:
+        params["subjects_dir"] = subjects_dir
     if summary_statistics is not None:
         params["summary_statistics"] = summary_statistics
     return params
@@ -117,17 +152,43 @@ def mris_spherical_average_cargs(
     """
     cargs = []
     cargs.append("mris_spherical_average")
-    if params.get("summary_statistics") is not None:
-        cargs.extend([
-            "-s",
-            params.get("summary_statistics")
-        ])
     cargs.append(params.get("which"))
     cargs.append(params.get("fname"))
     cargs.append(params.get("hemi"))
     cargs.append(params.get("spherical_surf"))
     cargs.extend(params.get("subjects"))
     cargs.append(params.get("output"))
+    if params.get("segment"):
+        cargs.append("-segment")
+    if params.get("normalize"):
+        cargs.append("-n")
+    if params.get("orig") is not None:
+        cargs.extend([
+            "-orig",
+            params.get("orig")
+        ])
+    if params.get("output_subject_name") is not None:
+        cargs.extend([
+            "-o",
+            params.get("output_subject_name")
+        ])
+    if params.get("output_subject_dir") is not None:
+        cargs.extend([
+            "-osdir",
+            params.get("output_subject_dir")
+        ])
+    if params.get("subjects_dir") is not None:
+        cargs.extend([
+            "-sdir",
+            params.get("subjects_dir")
+        ])
+    if params.get("average_area"):
+        cargs.append("-average_area")
+    if params.get("summary_statistics") is not None:
+        cargs.extend([
+            "-s",
+            params.get("summary_statistics")
+        ])
     return cargs
 
 
@@ -181,6 +242,13 @@ def mris_spherical_average(
     spherical_surf: str,
     subjects: list[str],
     output: str,
+    segment: bool = False,
+    normalize: bool = False,
+    orig: str | None = None,
+    output_subject_name: str | None = None,
+    output_subject_dir: str | None = None,
+    subjects_dir: str | None = None,
+    average_area: bool = False,
     summary_statistics: str | None = None,
     runner: Runner | None = None,
 ) -> MrisSphericalAverageOutputs:
@@ -198,6 +266,16 @@ def mris_spherical_average(
         spherical_surf: The spherical surface file.
         subjects: List of subjects.
         output: Output file or directory.
+        segment: Only use largest connected component of label.
+        normalize: Normalize output so it can be interpreted as a probability.
+        orig: Use <name> as original surface position; default=orig.
+        output_subject_name: Use <output subject name> as the space to write\
+            the results in instead of the last subject given.
+        output_subject_dir: Use <output subject dir> as the subjects dir for\
+            the output subject.
+        subjects_dir: Set the subjects directory.
+        average_area: Compute threshold for label that will give the average\
+            label approximately the average surface area.
         summary_statistics: Generate summary statistics and write them into\
             sigavg<cond #>-<hemi>.w and sigvar<cond #>-<hemi>.w.
         runner: Command runner.
@@ -207,13 +285,20 @@ def mris_spherical_average(
     runner = runner or get_global_runner()
     execution = runner.start_execution(MRIS_SPHERICAL_AVERAGE_METADATA)
     params = mris_spherical_average_params(
-        summary_statistics=summary_statistics,
         which=which,
         fname=fname,
         hemi=hemi,
         spherical_surf=spherical_surf,
         subjects=subjects,
         output=output,
+        segment=segment,
+        normalize=normalize,
+        orig=orig,
+        output_subject_name=output_subject_name,
+        output_subject_dir=output_subject_dir,
+        subjects_dir=subjects_dir,
+        average_area=average_area,
+        summary_statistics=summary_statistics,
     )
     return mris_spherical_average_execute(params, execution)
 

niwrap_freesurfer/freesurfer/mris_thickness_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_THICKNESS_DIFF_METADATA = Metadata(
-    id="fbc123e8965a3bb3509ca33036327b032bbd57be.boutiques",
+    id="9296419cd2bc81214ca3b7a9b2157195a7f31223.boutiques",
     name="mris_thickness_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -153,10 +153,6 @@ def mris_thickness_diff_cargs(
     """
     cargs = []
     cargs.append("mris_thickness_diff")
-    cargs.append("[SURFACE1]")
-    cargs.append("[DATA1]")
-    cargs.append("[SURFACE2]")
-    cargs.append("[DATA2]")
     if params.get("src_type") is not None:
         cargs.extend([
             "-src_type",

niwrap_freesurfer/freesurfer/mris_volmask_vtk.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_VOLMASK_VTK_METADATA = Metadata(
-    id="800007184636ff21baf1531ccc9b9b9b778933b9.boutiques",
+    id="26e246fc04ff45f83eec1e536a78198e40089ef9.boutiques",
     name="mris_volmask_vtk",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -187,7 +187,7 @@ def mris_volmask_vtk_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mris_volmask")
+    cargs.append("mris_volmask_vtk")
     if params.get("cap_distance") is not None:
         cargs.extend([
             "--cap_distance",

niwrap_freesurfer/freesurfer/pctsurfcon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PCTSURFCON_METADATA = Metadata(
-    id="0e082a082c6b181a71427db52d685c35d4270743.boutiques",
+    id="ad5f62ba3adae77bc989e8136a6e5d45a335abd9.boutiques",
     name="pctsurfcon",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -147,7 +147,7 @@ def pctsurfcon_cargs(
     cargs.append("pctsurfcon")
     cargs.extend([
         "-s",
-        "-" + params.get("subject")
+        params.get("subject")
     ])
     if params.get("fsvol") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/plot_structure_stats_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PLOT_STRUCTURE_STATS_TCL_METADATA = Metadata(
-    id="a74a29bbca7b8c304af58dc63af9e2298f4ac223.boutiques",
+    id="3da14e93a6edf0e5421e7aad0c1e0f8bf5f4b087.boutiques",
     name="plot_structure_stats.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -97,7 +97,7 @@ def plot_structure_stats_tcl_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("plot_structure_stats")
+    cargs.append("plot_structure_stats.tcl")
     cargs.append(execution.input_file(params.get("input_file")))
     cargs.append(params.get("output_file"))
     return cargs

niwrap_freesurfer/freesurfer/post_recon_all.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 POST_RECON_ALL_METADATA = Metadata(
-    id="043904c04e1a7c309fb6aa5cb7234831a996fdf4.boutiques",
+    id="4506cae7a1f970c99574dc4fac8b9e2fc2792099.boutiques",
     name="post-recon-all",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,9 +16,13 @@ POST_RECON_ALL_METADATA = Metadata(
 PostReconAllParameters = typing.TypedDict('PostReconAllParameters', {
     "__STYX_TYPE__": typing.Literal["post-recon-all"],
     "subject": str,
+    "subfields": bool,
     "no_subfields": bool,
+    "subregions": bool,
     "no_subregions": bool,
+    "cvs": bool,
     "no_cvs": bool,
+    "qcache": bool,
     "no_qcache": bool,
     "no_sclimbic": bool,
     "no_hthsu": bool,
@@ -75,9 +79,13 @@ class PostReconAllOutputs(typing.NamedTuple):
 
 def post_recon_all_params(
     subject: str,
+    subfields: bool = False,
     no_subfields: bool = False,
+    subregions: bool = False,
     no_subregions: bool = False,
+    cvs: bool = False,
     no_cvs: bool = False,
+    qcache: bool = False,
     no_qcache: bool = False,
     no_sclimbic: bool = False,
     no_hthsu: bool = False,
@@ -96,9 +104,13 @@ def post_recon_all_params(
     
     Args:
         subject: Subject identifier to be processed.
+        subfields: Run subfields extraction (default behavior).
         no_subfields: Do not run subfields extraction.
+        subregions: Run subregions extraction (default behavior).
         no_subregions: Do not run subregions extraction.
+        cvs: Run CVS processing.
         no_cvs: Do not run CVS processing (default behavior).
+        qcache: Run qcache processing (default behavior).
         no_qcache: Do not run qcache processing.
         no_sclimbic: Do not run sclimbic processing.
         no_hthsu: Do not run hypothalamic subunits processing.
@@ -117,9 +129,13 @@ def post_recon_all_params(
     params = {
         "__STYXTYPE__": "post-recon-all",
         "subject": subject,
+        "subfields": subfields,
         "no_subfields": no_subfields,
+        "subregions": subregions,
         "no_subregions": no_subregions,
+        "cvs": cvs,
         "no_cvs": no_cvs,
+        "qcache": qcache,
         "no_qcache": no_qcache,
         "no_sclimbic": no_sclimbic,
         "no_hthsu": no_hthsu,
@@ -151,16 +167,25 @@ def post_recon_all_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("post-recon-all")
     cargs.extend([
         "-all",
-        "post-recon" + params.get("subject")
+        params.get("subject")
     ])
+    if params.get("subfields"):
+        cargs.append("--subfields")
     if params.get("no_subfields"):
         cargs.append("--no-subfields")
+    if params.get("subregions"):
+        cargs.append("--subregions")
     if params.get("no_subregions"):
         cargs.append("--no-subregions")
+    if params.get("cvs"):
+        cargs.append("--cvs")
     if params.get("no_cvs"):
         cargs.append("--no-cvs")
+    if params.get("qcache"):
+        cargs.append("--qcache")
     if params.get("no_qcache"):
         cargs.append("--no-qcache")
     if params.get("no_sclimbic"):
@@ -236,9 +261,13 @@ def post_recon_all_execute(
 
 def post_recon_all(
     subject: str,
+    subfields: bool = False,
     no_subfields: bool = False,
+    subregions: bool = False,
     no_subregions: bool = False,
+    cvs: bool = False,
     no_cvs: bool = False,
+    qcache: bool = False,
     no_qcache: bool = False,
     no_sclimbic: bool = False,
     no_hthsu: bool = False,
@@ -262,9 +291,13 @@ def post_recon_all(
     
     Args:
         subject: Subject identifier to be processed.
+        subfields: Run subfields extraction (default behavior).
         no_subfields: Do not run subfields extraction.
+        subregions: Run subregions extraction (default behavior).
         no_subregions: Do not run subregions extraction.
+        cvs: Run CVS processing.
         no_cvs: Do not run CVS processing (default behavior).
+        qcache: Run qcache processing (default behavior).
         no_qcache: Do not run qcache processing.
         no_sclimbic: Do not run sclimbic processing.
         no_hthsu: Do not run hypothalamic subunits processing.
@@ -285,9 +318,13 @@ def post_recon_all(
     execution = runner.start_execution(POST_RECON_ALL_METADATA)
     params = post_recon_all_params(
         subject=subject,
+        subfields=subfields,
         no_subfields=no_subfields,
+        subregions=subregions,
         no_subregions=no_subregions,
+        cvs=cvs,
         no_cvs=no_cvs,
+        qcache=qcache,
         no_qcache=no_qcache,
         no_sclimbic=no_sclimbic,
         no_hthsu=no_hthsu,

niwrap_freesurfer/freesurfer/predict_v1_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PREDICT_V1_SH_METADATA = Metadata(
-    id="9dad70e954292a5df8dae706ae1d13ad401174c0.boutiques",
+    id="fa5102ea5c78705d9124599a58b8008cca2f5a92.boutiques",
     name="predict_v1.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -20,6 +20,7 @@ PredictV1ShParameters = typing.TypedDict('PredictV1ShParameters', {
     "hemisphere": typing.NotRequired[str | None],
     "print_mode_flag": bool,
     "subjects": list[str],
+    "usage_flag": bool,
 })
 
 
@@ -68,6 +69,7 @@ def predict_v1_sh_params(
     inflated_surface_flag: bool = False,
     hemisphere: str | None = None,
     print_mode_flag: bool = False,
+    usage_flag: bool = False,
 ) -> PredictV1ShParameters:
     """
     Build parameters.
@@ -79,6 +81,7 @@ def predict_v1_sh_params(
             registration (backward compatibility).
         hemisphere: Hemisphere (rh or lh) default is both hemispheres.
         print_mode_flag: Print mode (do not run commands, just print them).
+        usage_flag: Print usage.
     Returns:
         Parameter dictionary
     """
@@ -87,6 +90,7 @@ def predict_v1_sh_params(
         "inflated_surface_flag": inflated_surface_flag,
         "print_mode_flag": print_mode_flag,
         "subjects": subjects,
+        "usage_flag": usage_flag,
     }
     if template is not None:
         params["template"] = template
@@ -124,7 +128,9 @@ def predict_v1_sh_cargs(
         ])
     if params.get("print_mode_flag"):
         cargs.append("-p")
-    cargs.append("".join(params.get("subjects")) + "...")
+    cargs.extend(params.get("subjects"))
+    if params.get("usage_flag"):
+        cargs.append("-u")
     return cargs
 
 
@@ -177,6 +183,7 @@ def predict_v1_sh(
     inflated_surface_flag: bool = False,
     hemisphere: str | None = None,
     print_mode_flag: bool = False,
+    usage_flag: bool = False,
     runner: Runner | None = None,
 ) -> PredictV1ShOutputs:
     """
@@ -193,6 +200,7 @@ def predict_v1_sh(
             registration (backward compatibility).
         hemisphere: Hemisphere (rh or lh) default is both hemispheres.
         print_mode_flag: Print mode (do not run commands, just print them).
+        usage_flag: Print usage.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PredictV1ShOutputs`).
@@ -205,6 +213,7 @@ def predict_v1_sh(
         hemisphere=hemisphere,
         print_mode_flag=print_mode_flag,
         subjects=subjects,
+        usage_flag=usage_flag,
     )
     return predict_v1_sh_execute(params, execution)