niwrap-freesurfer 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/inflate_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_RH_METADATA = Metadata(
-    id="c870a2dd4beffc1dccf8c6c63c1951a8bb440f30.boutiques",
+    id="28e53c36f45c8022dda8ede70eb4400f88349ad3.boutiques",
     name="inflate_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -92,10 +92,11 @@ def inflate_subject_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("inflate_subject-rh")
     if params.get("arguments") is not None:
         cargs.extend([
             "-rh",
-            "inflate_subject" + params.get("arguments")
+            params.get("arguments")
         ])
     return cargs
 

niwrap_freesurfer/freesurfer/inflate_subject_sc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_SC_METADATA = Metadata(
-    id="bdd6f4bcc49d0163426eb09c58fe6f94a9a23109.boutiques",
+    id="0813ce358c83e50fc62e002b6de9508d35f9a2be.boutiques",
     name="inflate_subject_sc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,9 @@ INFLATE_SUBJECT_SC_METADATA = Metadata(
 
 InflateSubjectScParameters = typing.TypedDict('InflateSubjectScParameters', {
     "__STYX_TYPE__": typing.Literal["inflate_subject_sc"],
+    "subject_dir": str,
+    "verbose": bool,
+    "debug": bool,
 })
 
 
@@ -61,16 +64,25 @@ class InflateSubjectScOutputs(typing.NamedTuple):
 
 
 def inflate_subject_sc_params(
+    subject_dir: str,
+    verbose: bool = False,
+    debug: bool = False,
 ) -> InflateSubjectScParameters:
     """
     Build parameters.
     
     Args:
+        subject_dir: Path to the subject directory.
+        verbose: Enable verbose output.
+        debug: Enable debug mode.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "inflate_subject_sc",
+        "subject_dir": subject_dir,
+        "verbose": verbose,
+        "debug": debug,
     }
     return params
 
@@ -90,7 +102,11 @@ def inflate_subject_sc_cargs(
     """
     cargs = []
     cargs.append("inflate_subject_sc")
-    cargs.append("[OPTIONS]")
+    cargs.append(params.get("subject_dir"))
+    if params.get("verbose"):
+        cargs.append("--verbose")
+    if params.get("debug"):
+        cargs.append("--debug")
     return cargs
 
 
@@ -109,7 +125,7 @@ def inflate_subject_sc_outputs(
     """
     ret = InflateSubjectScOutputs(
         root=execution.output_file("."),
-        inflated_output=execution.output_file("[SUBJECT_DIR]/inflated_output"),
+        inflated_output=execution.output_file(params.get("subject_dir") + "/inflated_output"),
     )
     return ret
 
@@ -140,6 +156,9 @@ def inflate_subject_sc_execute(
 
 
 def inflate_subject_sc(
+    subject_dir: str,
+    verbose: bool = False,
+    debug: bool = False,
     runner: Runner | None = None,
 ) -> InflateSubjectScOutputs:
     """
@@ -151,6 +170,9 @@ def inflate_subject_sc(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        subject_dir: Path to the subject directory.
+        verbose: Enable verbose output.
+        debug: Enable debug mode.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InflateSubjectScOutputs`).
@@ -158,6 +180,9 @@ def inflate_subject_sc(
     runner = runner or get_global_runner()
     execution = runner.start_execution(INFLATE_SUBJECT_SC_METADATA)
     params = inflate_subject_sc_params(
+        subject_dir=subject_dir,
+        verbose=verbose,
+        debug=debug,
     )
     return inflate_subject_sc_execute(params, execution)
 

niwrap_freesurfer/freesurfer/irepifitvol_glnx64.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IREPIFITVOL_GLNX64_METADATA = Metadata(
-    id="e1b3c71003d88eeb91c6bc522cbeb9c8dec5641d.boutiques",
+    id="a245c53e9539ea6eed51026dad3ae5a54dd3dcd3.boutiques",
     name="irepifitvol.glnx64",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -97,7 +97,7 @@ def irepifitvol_glnx64_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("irepifitvol")
+    cargs.append("irepifitvol.glnx64")
     cargs.append(execution.input_file(params.get("input_file")))
     cargs.append(params.get("output_file"))
     return cargs

niwrap_freesurfer/freesurfer/is_surface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IS_SURFACE_METADATA = Metadata(
-    id="6cb9d1446618fbf43c51093ee6543e6c01436b21.boutiques",
+    id="86c411bc39041a8b3eae45962259ad09e76de3b1.boutiques",
     name="is-surface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -90,9 +90,10 @@ def is_surface_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("is-surface")
     cargs.extend([
         "-surface",
-        "is" + execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile"))
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/isolate_labels_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ISOLATE_LABELS_CSH_METADATA = Metadata(
-    id="38dc57e5ac2ab0f7a3569ce5a6d3b6708f167dad.boutiques",
+    id="b99f5a36e27edd815c27d9c5646229750b881f96.boutiques",
     name="isolate_labels.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -17,6 +17,7 @@ IsolateLabelsCshParameters = typing.TypedDict('IsolateLabelsCshParameters', {
     "__STYX_TYPE__": typing.Literal["isolate_labels.csh"],
     "label_volume": InputPathType,
     "output_prefix": str,
+    "label_option": typing.NotRequired[str | None],
     "lowercase_label_option": typing.NotRequired[str | None],
     "version": bool,
     "keepval": bool,
@@ -66,6 +67,7 @@ class IsolateLabelsCshOutputs(typing.NamedTuple):
 def isolate_labels_csh_params(
     label_volume: InputPathType,
     output_prefix: str,
+    label_option: str | None = None,
     lowercase_label_option: str | None = None,
     version: bool = False,
     keepval: bool = False,
@@ -77,6 +79,8 @@ def isolate_labels_csh_params(
     Args:
         label_volume: Label volume to be analyzed.
         output_prefix: Prefix of binary label file(s).
+        label_option: The particular label to be analyzed; default is all\
+            labels.
         lowercase_label_option: The particular label to be analyzed; default is\
             all labels.
         version: Print version and exit.
@@ -93,6 +97,8 @@ def isolate_labels_csh_params(
         "keepval": keepval,
         "help": help_,
     }
+    if label_option is not None:
+        params["label_option"] = label_option
     if lowercase_label_option is not None:
         params["lowercase_label_option"] = lowercase_label_option
     return params
@@ -112,7 +118,7 @@ def isolate_labels_csh_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("isolate_labels")
+    cargs.append("isolate_labels.csh")
     cargs.extend([
         "--vol",
         execution.input_file(params.get("label_volume"))
@@ -121,6 +127,11 @@ def isolate_labels_csh_cargs(
         "--outprefix",
         params.get("output_prefix")
     ])
+    if params.get("label_option") is not None:
+        cargs.extend([
+            "--L",
+            params.get("label_option")
+        ])
     if params.get("lowercase_label_option") is not None:
         cargs.extend([
             "--l",
@@ -182,6 +193,7 @@ def isolate_labels_csh_execute(
 def isolate_labels_csh(
     label_volume: InputPathType,
     output_prefix: str,
+    label_option: str | None = None,
     lowercase_label_option: str | None = None,
     version: bool = False,
     keepval: bool = False,
@@ -199,6 +211,8 @@ def isolate_labels_csh(
     Args:
         label_volume: Label volume to be analyzed.
         output_prefix: Prefix of binary label file(s).
+        label_option: The particular label to be analyzed; default is all\
+            labels.
         lowercase_label_option: The particular label to be analyzed; default is\
             all labels.
         version: Print version and exit.
@@ -213,6 +227,7 @@ def isolate_labels_csh(
     params = isolate_labels_csh_params(
         label_volume=label_volume,
         output_prefix=output_prefix,
+        label_option=label_option,
         lowercase_label_option=lowercase_label_option,
         version=version,
         keepval=keepval,

niwrap_freesurfer/freesurfer/label_subject_flash.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL_SUBJECT_FLASH_METADATA = Metadata(
-    id="6437bdd8443156c21638b016c6209131b9efc309.boutiques",
+    id="1d6e63edc1016916b719770e029fc275fe393603.boutiques",
     name="label_subject_flash",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -109,7 +109,7 @@ def label_subject_flash_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_ca_label")
+    cargs.append("label_subject_flash")
     cargs.extend([
         "-flash",
         execution.input_file(params.get("tissue_params"))

niwrap_freesurfer/freesurfer/label_subject_mixed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL_SUBJECT_MIXED_METADATA = Metadata(
-    id="c89d204a94ff9a438c87e6af7616b21249be8dd9.boutiques",
+    id="4fa18aab4c7257494464ce9a6c1ac24cbb5a4c6e.boutiques",
     name="label_subject_mixed",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -109,7 +109,7 @@ def label_subject_mixed_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("mri_ca_label")
+    cargs.append("label_subject_mixed")
     cargs.extend([
         "-mask",
         execution.input_file(params.get("brain_mask"))

niwrap_freesurfer/freesurfer/listsubj.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LISTSUBJ_METADATA = Metadata(
-    id="e9369381138405e14a70273bc76d2a91dd2f8045.boutiques",
+    id="a18d8b3140e25407e3ae5f429d4a4ba694996847.boutiques",
     name="listsubj",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,6 +16,15 @@ LISTSUBJ_METADATA = Metadata(
 ListsubjParameters = typing.TypedDict('ListsubjParameters', {
     "__STYX_TYPE__": typing.Literal["listsubj"],
     "subject_dir": str,
+    "cross": bool,
+    "base": bool,
+    "long": bool,
+    "done": bool,
+    "error": bool,
+    "running": bool,
+    "full_path": bool,
+    "count": bool,
+    "help": bool,
 })
 
 
@@ -60,18 +69,45 @@ class ListsubjOutputs(typing.NamedTuple):
 
 def listsubj_params(
     subject_dir: str,
+    cross: bool = False,
+    base: bool = False,
+    long: bool = False,
+    done: bool = False,
+    error: bool = False,
+    running: bool = False,
+    full_path: bool = False,
+    count: bool = False,
+    help_: bool = False,
 ) -> ListsubjParameters:
     """
     Build parameters.
     
     Args:
         subject_dir: Directory where subjects are stored.
+        cross: Only cross-sectional stream.
+        base: Only base stream.
+        long: Only longitudinal stream.
+        done: Only subject IDs with scripts/recon-all.done.
+        error: Only subject IDs with scripts/recon-all.error.
+        running: Only subject IDs with scripts/IsRunning.?h.
+        full_path: Prepend full absolute path.
+        count: Print number of subjects found.
+        help_: Show this help text.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "listsubj",
         "subject_dir": subject_dir,
+        "cross": cross,
+        "base": base,
+        "long": long,
+        "done": done,
+        "error": error,
+        "running": running,
+        "full_path": full_path,
+        "count": count,
+        "help": help_,
     }
     return params
 
@@ -91,8 +127,25 @@ def listsubj_cargs(
     """
     cargs = []
     cargs.append("listsubj")
-    cargs.append("[OPTIONS]")
     cargs.append(params.get("subject_dir"))
+    if params.get("cross"):
+        cargs.append("-c")
+    if params.get("base"):
+        cargs.append("-b")
+    if params.get("long"):
+        cargs.append("-l")
+    if params.get("done"):
+        cargs.append("-d")
+    if params.get("error"):
+        cargs.append("-e")
+    if params.get("running"):
+        cargs.append("-r")
+    if params.get("full_path"):
+        cargs.append("-f")
+    if params.get("count"):
+        cargs.append("-n")
+    if params.get("help"):
+        cargs.append("-h")
     return cargs
 
 
@@ -141,6 +194,15 @@ def listsubj_execute(
 
 def listsubj(
     subject_dir: str,
+    cross: bool = False,
+    base: bool = False,
+    long: bool = False,
+    done: bool = False,
+    error: bool = False,
+    running: bool = False,
+    full_path: bool = False,
+    count: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> ListsubjOutputs:
     """
@@ -152,6 +214,15 @@ def listsubj(
     
     Args:
         subject_dir: Directory where subjects are stored.
+        cross: Only cross-sectional stream.
+        base: Only base stream.
+        long: Only longitudinal stream.
+        done: Only subject IDs with scripts/recon-all.done.
+        error: Only subject IDs with scripts/recon-all.error.
+        running: Only subject IDs with scripts/IsRunning.?h.
+        full_path: Prepend full absolute path.
+        count: Print number of subjects found.
+        help_: Show this help text.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ListsubjOutputs`).
@@ -160,6 +231,15 @@ def listsubj(
     execution = runner.start_execution(LISTSUBJ_METADATA)
     params = listsubj_params(
         subject_dir=subject_dir,
+        cross=cross,
+        base=base,
+        long=long,
+        done=done,
+        error=error,
+        running=running,
+        full_path=full_path,
+        count=count,
+        help_=help_,
     )
     return listsubj_execute(params, execution)
 

niwrap_freesurfer/freesurfer/long_stats_combine.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_STATS_COMBINE_METADATA = Metadata(
-    id="44c43a96c18b3f3b72a80aed68ec585e7b861c9d.boutiques",
+    id="75845120ecb7a42bb2814094cd14fceadf929854.boutiques",
     name="long_stats_combine",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -145,7 +145,6 @@ def long_stats_combine_cargs(
         "--sd",
         params.get("subject_dir")
     ])
-    cargs.append("--out")
     cargs.extend([
         "--outqdec",
         params.get("output_qdec")

niwrap_freesurfer/freesurfer/long_stats_tps.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_STATS_TPS_METADATA = Metadata(
-    id="bc2f340c25927fb0b4a967b198182aa268f9cf9f.boutiques",
+    id="1bcd114b81501e8287ad3b93601056a429f0aaa9.boutiques",
     name="long_stats_tps",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -126,27 +126,27 @@ def long_stats_tps_cargs(
     cargs.append("long_stats_tps")
     cargs.extend([
         "--qdec",
-        "--qdec=" + execution.input_file(params.get("qdec_table"))
+        execution.input_file(params.get("qdec_table"))
     ])
     cargs.extend([
         "--stats",
-        "--stats=" + params.get("stats_file")
+        params.get("stats_file")
     ])
     cargs.extend([
         "--meas",
-        "--meas=" + params.get("measure")
+        params.get("measure")
     ])
     cargs.extend([
         "--sd",
-        "--sd=" + params.get("subjects_dir")
+        params.get("subjects_dir")
     ])
     cargs.extend([
         "--tp",
-        "--tp=" + str(params.get("time_point"))
+        str(params.get("time_point"))
     ])
     cargs.extend([
         "--out",
-        "--out=" + params.get("output_file")
+        params.get("output_file")
     ])
     if params.get("qcolumn") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/long_submit_jobs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONG_SUBMIT_JOBS_METADATA = Metadata(
-    id="d9fdcdcc044b4b6a583cb8d7681940ebbb389e10.boutiques",
+    id="73a46d90ad07cf1b262590059e8ca43cc4fde840.boutiques",
     name="long_submit_jobs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -256,12 +256,8 @@ def long_submit_jobs_cargs(
         cargs.append("--simulate")
     if params.get("simfiles"):
         cargs.append("--simfiles")
-    cargs.append("[--skip]")
-    cargs.append("[--skiperror]")
     if params.get("check"):
         cargs.append("--check")
-    cargs.append("[--update-recon-all]")
-    cargs.append("[--use-recon-all]")
     if params.get("pause") is not None:
         cargs.extend([
             "--pause",

niwrap_freesurfer/freesurfer/longmc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LONGMC_METADATA = Metadata(
-    id="51a04d5ffd0bb81591249e8acfb084306bc3edcb.boutiques",
+    id="a60463859b66f4dac910ccf5dd67f14573c1ca1f.boutiques",
     name="longmc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,6 +18,7 @@ LongmcParameters = typing.TypedDict('LongmcParameters', {
     "cross_tp_name": str,
     "base_name": str,
     "conform_to_hires": bool,
+    "no_conform_to_hires": bool,
     "subjects_dir": str,
     "subject_name": typing.NotRequired[str | None],
     "no_force_update": bool,
@@ -68,6 +69,7 @@ def longmc_params(
     base_name: str,
     subjects_dir: str,
     conform_to_hires: bool = False,
+    no_conform_to_hires: bool = False,
     subject_name: str | None = None,
     no_force_update: bool = False,
 ) -> LongmcParameters:
@@ -79,6 +81,7 @@ def longmc_params(
         base_name: Base name for the longitudinal analysis.
         subjects_dir: Set the SUBJECTS_DIR directory.
         conform_to_hires: Option to conform input to high-resolution.
+        no_conform_to_hires: Option to not conform input to high-resolution.
         subject_name: Subject name override, must be declared after -long.
         no_force_update: Do not force update.
     Returns:
@@ -89,6 +92,7 @@ def longmc_params(
         "cross_tp_name": cross_tp_name,
         "base_name": base_name,
         "conform_to_hires": conform_to_hires,
+        "no_conform_to_hires": no_conform_to_hires,
         "subjects_dir": subjects_dir,
         "no_force_update": no_force_update,
     }
@@ -119,6 +123,8 @@ def longmc_cargs(
     cargs.append(params.get("base_name"))
     if params.get("conform_to_hires"):
         cargs.append("-conf2hires")
+    if params.get("no_conform_to_hires"):
+        cargs.append("-no-conf2hires")
     cargs.extend([
         "-sd",
         params.get("subjects_dir")
@@ -182,6 +188,7 @@ def longmc(
     base_name: str,
     subjects_dir: str,
     conform_to_hires: bool = False,
+    no_conform_to_hires: bool = False,
     subject_name: str | None = None,
     no_force_update: bool = False,
     runner: Runner | None = None,
@@ -199,6 +206,7 @@ def longmc(
         base_name: Base name for the longitudinal analysis.
         subjects_dir: Set the SUBJECTS_DIR directory.
         conform_to_hires: Option to conform input to high-resolution.
+        no_conform_to_hires: Option to not conform input to high-resolution.
         subject_name: Subject name override, must be declared after -long.
         no_force_update: Do not force update.
         runner: Command runner.
@@ -211,6 +219,7 @@ def longmc(
         cross_tp_name=cross_tp_name,
         base_name=base_name,
         conform_to_hires=conform_to_hires,
+        no_conform_to_hires=no_conform_to_hires,
         subjects_dir=subjects_dir,
         subject_name=subject_name,
         no_force_update=no_force_update,