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

niwrap_freesurfer/freesurfer/dmri_mergepaths.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_MERGEPATHS_METADATA = Metadata(
-    id="18bc644100dca612df1989666e60cf3a4214164c.boutiques",
+    id="73d51f5dfd2648daefced42e8f22083b6b9e5b42.boutiques",
     name="dmri_mergepaths",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -116,7 +116,7 @@ def dmri_mergepaths_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("./dmri_mergepaths")
+    cargs.append("dmri_mergepaths")
     cargs.extend([execution.input_file(f) for f in params.get("input_volumes")])
     if params.get("input_directory") is not None:
         cargs.extend([

niwrap_freesurfer/freesurfer/dmri_pathstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_PATHSTATS_METADATA = Metadata(
-    id="8110c02ff2c74fe994c5787d89b13efd80585a6a.boutiques",
+    id="73f70ca60d1c2b790ac7388127c1b36f4da4bbff.boutiques",
     name="dmri_pathstats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -184,7 +184,7 @@ def dmri_pathstats_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("./dmri_pathstats")
+    cargs.append("dmri_pathstats")
     cargs.extend([
         "--intrk",
         execution.input_file(params.get("intrk"))

niwrap_freesurfer/freesurfer/dmri_stats_ac.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_STATS_AC_METADATA = Metadata(
-    id="38bce967cfc9907f2f4aad1d1246fa98b24d0792.boutiques",
+    id="9fdd3938d34618874c191c301489c6b70e1c5c5b.boutiques",
     name="dmri_stats_ac",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -122,8 +122,6 @@ def dmri_stats_ac_cargs(
         "-c",
         params.get("correspondence_file")
     ])
-    cargs.append("-m")
-    cargs.append("[NUM_MEASURES]")
     cargs.extend([
         "-m",
         *params.get("measures")

niwrap_freesurfer/freesurfer/exvivo_hemi_proc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 EXVIVO_HEMI_PROC_METADATA = Metadata(
-    id="9ef40c3f2cab9928f235df79043cbc38b92918d6.boutiques",
+    id="e3813e1b2b5ac9842148171363015c6a44f9e300.boutiques",
     name="exvivo-hemi-proc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,6 +18,7 @@ ExvivoHemiProcParameters = typing.TypedDict('ExvivoHemiProcParameters', {
     "flashdir": str,
     "outdir": str,
     "subject": str,
+    "left_hemi": bool,
     "right_hemi": bool,
     "suptent": bool,
     "no_rotate": bool,
@@ -75,6 +76,7 @@ def exvivo_hemi_proc_params(
     flashdir: str,
     outdir: str,
     subject: str,
+    left_hemi: bool = False,
     right_hemi: bool = False,
     suptent: bool = False,
     no_rotate: bool = False,
@@ -94,6 +96,7 @@ def exvivo_hemi_proc_params(
         flashdir: Path to the FLASH data directory.
         outdir: Output directory where results will be saved.
         subject: Full path to the subject.
+        left_hemi: Process left hemisphere.
         right_hemi: Process right hemisphere.
         suptent: Indicate no tentorium (cblum and bstem) in the sample.
         no_rotate: Indicate rotation is not needed.
@@ -114,6 +117,7 @@ def exvivo_hemi_proc_params(
         "flashdir": flashdir,
         "outdir": outdir,
         "subject": subject,
+        "left_hemi": left_hemi,
         "right_hemi": right_hemi,
         "suptent": suptent,
         "no_rotate": no_rotate,
@@ -159,6 +163,8 @@ def exvivo_hemi_proc_cargs(
         "--s",
         params.get("subject")
     ])
+    if params.get("left_hemi"):
+        cargs.append("--lh")
     if params.get("right_hemi"):
         cargs.append("--rh")
     if params.get("suptent"):
@@ -240,6 +246,7 @@ def exvivo_hemi_proc(
     flashdir: str,
     outdir: str,
     subject: str,
+    left_hemi: bool = False,
     right_hemi: bool = False,
     suptent: bool = False,
     no_rotate: bool = False,
@@ -264,6 +271,7 @@ def exvivo_hemi_proc(
         flashdir: Path to the FLASH data directory.
         outdir: Output directory where results will be saved.
         subject: Full path to the subject.
+        left_hemi: Process left hemisphere.
         right_hemi: Process right hemisphere.
         suptent: Indicate no tentorium (cblum and bstem) in the sample.
         no_rotate: Indicate rotation is not needed.
@@ -286,6 +294,7 @@ def exvivo_hemi_proc(
         flashdir=flashdir,
         outdir=outdir,
         subject=subject,
+        left_hemi=left_hemi,
         right_hemi=right_hemi,
         suptent=suptent,
         no_rotate=no_rotate,

niwrap_freesurfer/freesurfer/fiducials_calibration.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIDUCIALS_CALIBRATION_METADATA = Metadata(
-    id="445a4b2fe29e36b5286fe1c80268453941ab7144.boutiques",
+    id="b87cb0a61e77503c416b5bd15c7cec1c1ef97456.boutiques",
     name="fiducials_calibration",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,7 @@ FIDUCIALS_CALIBRATION_METADATA = Metadata(
 
 FiducialsCalibrationParameters = typing.TypedDict('FiducialsCalibrationParameters', {
     "__STYX_TYPE__": typing.Literal["fiducials_calibration"],
+    "qt_plugin_installation": typing.NotRequired[str | None],
 })
 
 
@@ -58,17 +59,23 @@ class FiducialsCalibrationOutputs(typing.NamedTuple):
 
 
 def fiducials_calibration_params(
+    qt_plugin_installation: str | None = "Check Qt installation and platform plugin availability",
 ) -> FiducialsCalibrationParameters:
     """
     Build parameters.
     
     Args:
+        qt_plugin_installation: This application requires a functional Qt\
+            installation. If it fails to start, reinstalling the application might\
+            fix the problem.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "fiducials_calibration",
     }
+    if qt_plugin_installation is not None:
+        params["qt_plugin_installation"] = qt_plugin_installation
     return params
 
 
@@ -87,6 +94,8 @@ def fiducials_calibration_cargs(
     """
     cargs = []
     cargs.append("fiducials_calibration")
+    if params.get("qt_plugin_installation") is not None:
+        cargs.append(params.get("qt_plugin_installation"))
     return cargs
 
 
@@ -134,6 +143,7 @@ def fiducials_calibration_execute(
 
 
 def fiducials_calibration(
+    qt_plugin_installation: str | None = "Check Qt installation and platform plugin availability",
     runner: Runner | None = None,
 ) -> FiducialsCalibrationOutputs:
     """
@@ -144,6 +154,9 @@ def fiducials_calibration(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        qt_plugin_installation: This application requires a functional Qt\
+            installation. If it fails to start, reinstalling the application might\
+            fix the problem.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FiducialsCalibrationOutputs`).
@@ -151,6 +164,7 @@ def fiducials_calibration(
     runner = runner or get_global_runner()
     execution = runner.start_execution(FIDUCIALS_CALIBRATION_METADATA)
     params = fiducials_calibration_params(
+        qt_plugin_installation=qt_plugin_installation,
     )
     return fiducials_calibration_execute(params, execution)
 

niwrap_freesurfer/freesurfer/fiducials_correction.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIDUCIALS_CORRECTION_METADATA = Metadata(
-    id="4c8ff34a05a460d57cf9bd6ab63606fa5145834f.boutiques",
+    id="6353e9d7f0b132461e7ac43f5dc929e2584cbb0a.boutiques",
     name="fiducials_correction",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -16,6 +16,7 @@ FIDUCIALS_CORRECTION_METADATA = Metadata(
 FiducialsCorrectionParameters = typing.TypedDict('FiducialsCorrectionParameters', {
     "__STYX_TYPE__": typing.Literal["fiducials_correction"],
     "input_file": InputPathType,
+    "output_file": str,
 })
 
 
@@ -63,6 +64,7 @@ class FiducialsCorrectionOutputs(typing.NamedTuple):
 
 def fiducials_correction_params(
     input_file: InputPathType,
+    output_file: str,
 ) -> FiducialsCorrectionParameters:
     """
     Build parameters.
@@ -70,12 +72,14 @@ def fiducials_correction_params(
     Args:
         input_file: Input file containing imaging data with fiducial markers to\
             correct.
+        output_file: Output file with corrected fiducial markers.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "fiducials_correction",
         "input_file": input_file,
+        "output_file": output_file,
     }
     return params
 
@@ -96,7 +100,7 @@ def fiducials_correction_cargs(
     cargs = []
     cargs.append("fiducials_correction")
     cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append("[OUTPUT_FILE]")
+    cargs.append(params.get("output_file"))
     return cargs
 
 
@@ -115,7 +119,7 @@ def fiducials_correction_outputs(
     """
     ret = FiducialsCorrectionOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("[OUTPUT_FILE]"),
+        output_file=execution.output_file(params.get("output_file")),
     )
     return ret
 
@@ -148,6 +152,7 @@ def fiducials_correction_execute(
 
 def fiducials_correction(
     input_file: InputPathType,
+    output_file: str,
     runner: Runner | None = None,
 ) -> FiducialsCorrectionOutputs:
     """
@@ -162,6 +167,7 @@ def fiducials_correction(
     Args:
         input_file: Input file containing imaging data with fiducial markers to\
             correct.
+        output_file: Output file with corrected fiducial markers.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FiducialsCorrectionOutputs`).
@@ -170,6 +176,7 @@ def fiducials_correction(
     execution = runner.start_execution(FIDUCIALS_CORRECTION_METADATA)
     params = fiducials_correction_params(
         input_file=input_file,
+        output_file=output_file,
     )
     return fiducials_correction_execute(params, execution)
 

niwrap_freesurfer/freesurfer/fix_subject_corrected_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIX_SUBJECT_CORRECTED_RH_METADATA = Metadata(
-    id="52da465b947b94728415b771545cea34c0073071.boutiques",
+    id="7b7e39c32815a5cef6cf9aad3f4046ba8b47ddb9.boutiques",
     name="fix_subject_corrected-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -93,9 +93,10 @@ def fix_subject_corrected_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("fix_subject_corrected-rh")
     cargs.extend([
         "-rh",
-        "fix_subject_corrected" + params.get("subject_dir")
+        params.get("subject_dir")
     ])
     return cargs
 

niwrap_freesurfer/freesurfer/fix_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIX_SUBJECT_RH_METADATA = Metadata(
-    id="3bb32adfbfd21f826f4e479a088d3bcfcdad5042.boutiques",
+    id="d288abc3ea82bec21208e7703917dbd10a9bc4b7.boutiques",
     name="fix_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -95,9 +95,10 @@ def fix_subject_rh_cargs(
         Command-line arguments.
     """
     cargs = []
+    cargs.append("fix_subject-rh")
     cargs.extend([
         "-rh",
-        "fix_subject" + params.get("input_directory")
+        params.get("input_directory")
     ])
     if params.get("help_flag"):
         cargs.append("--help")

niwrap_freesurfer/freesurfer/fs_check_version.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_CHECK_VERSION_METADATA = Metadata(
-    id="1bb29df8432be8183122dba0b74d19ba214f7751.boutiques",
+    id="660409ce98a2983c236b82f391b2216637f1c37f.boutiques",
     name="fs-check-version",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -18,7 +18,9 @@ FsCheckVersionParameters = typing.TypedDict('FsCheckVersionParameters', {
     "subjects_dir": str,
     "outfile": str,
     "subject": typing.NotRequired[str | None],
+    "require_match": bool,
     "no_require_match": bool,
+    "test": bool,
     "test_debug": bool,
 })
 
@@ -69,7 +71,9 @@ def fs_check_version_params(
     subjects_dir: str,
     outfile: str,
     subject: str | None = None,
+    require_match: bool = False,
     no_require_match: bool = False,
+    test: bool = False,
     test_debug: bool = False,
 ) -> FsCheckVersionParameters:
     """
@@ -79,7 +83,9 @@ def fs_check_version_params(
         subjects_dir: Subjects directory path.
         outfile: Output file path where result of version check will be written.
         subject: Subject name (optional).
+        require_match: Set REQUIRE_FS_MATCH for testing.
         no_require_match: Unset REQUIRE_FS_MATCH for testing.
+        test: Go through permutations for testing.
         test_debug: Go through permutations for debugging.
     Returns:
         Parameter dictionary
@@ -88,7 +94,9 @@ def fs_check_version_params(
         "__STYXTYPE__": "fs-check-version",
         "subjects_dir": subjects_dir,
         "outfile": outfile,
+        "require_match": require_match,
         "no_require_match": no_require_match,
+        "test": test,
         "test_debug": test_debug,
     }
     if subject is not None:
@@ -124,8 +132,12 @@ def fs_check_version_cargs(
             "--s",
             params.get("subject")
         ])
+    if params.get("require_match"):
+        cargs.append("--require-match")
     if params.get("no_require_match"):
         cargs.append("--no-require-match")
+    if params.get("test"):
+        cargs.append("--test")
     if params.get("test_debug"):
         cargs.append("--test-debug")
     return cargs
@@ -180,7 +192,9 @@ def fs_check_version(
     subjects_dir: str,
     outfile: str,
     subject: str | None = None,
+    require_match: bool = False,
     no_require_match: bool = False,
+    test: bool = False,
     test_debug: bool = False,
     runner: Runner | None = None,
 ) -> FsCheckVersionOutputs:
@@ -196,7 +210,9 @@ def fs_check_version(
         subjects_dir: Subjects directory path.
         outfile: Output file path where result of version check will be written.
         subject: Subject name (optional).
+        require_match: Set REQUIRE_FS_MATCH for testing.
         no_require_match: Unset REQUIRE_FS_MATCH for testing.
+        test: Go through permutations for testing.
         test_debug: Go through permutations for debugging.
         runner: Command runner.
     Returns:
@@ -208,7 +224,9 @@ def fs_check_version(
         subjects_dir=subjects_dir,
         outfile=outfile,
         subject=subject,
+        require_match=require_match,
         no_require_match=no_require_match,
+        test=test,
         test_debug=test_debug,
     )
     return fs_check_version_execute(params, execution)

niwrap_freesurfer/freesurfer/fs_spmreg_glnxa64.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_SPMREG_GLNXA64_METADATA = Metadata(
-    id="d96fd1d83e2b7bf77ac2922d1bead84c42091878.boutiques",
+    id="92aa0f707d8268c4082f03447b8e27b77445669e.boutiques",
     name="fs_spmreg.glnxa64",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,6 +15,8 @@ FS_SPMREG_GLNXA64_METADATA = Metadata(
 
 FsSpmregGlnxa64Parameters = typing.TypedDict('FsSpmregGlnxa64Parameters', {
     "__STYX_TYPE__": typing.Literal["fs_spmreg.glnxa64"],
+    "input_volume": InputPathType,
+    "output_matrix": str,
 })
 
 
@@ -61,16 +63,22 @@ class FsSpmregGlnxa64Outputs(typing.NamedTuple):
 
 
 def fs_spmreg_glnxa64_params(
+    input_volume: InputPathType,
+    output_matrix: str = "output.mat",
 ) -> FsSpmregGlnxa64Parameters:
     """
     Build parameters.
     
     Args:
+        input_volume: Input anatomical volume.
+        output_matrix: Output registration matrix.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "fs_spmreg.glnxa64",
+        "input_volume": input_volume,
+        "output_matrix": output_matrix,
     }
     return params
 
@@ -89,8 +97,9 @@ def fs_spmreg_glnxa64_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append("fs_spmreg")
-    cargs.append("[OPTIONS]")
+    cargs.append("fs_spmreg.glnxa64")
+    cargs.append(execution.input_file(params.get("input_volume")))
+    cargs.append(params.get("output_matrix"))
     return cargs
 
 
@@ -109,7 +118,7 @@ def fs_spmreg_glnxa64_outputs(
     """
     ret = FsSpmregGlnxa64Outputs(
         root=execution.output_file("."),
-        output_matrix_file=execution.output_file("[OUTPUT_MATRIX]"),
+        output_matrix_file=execution.output_file(params.get("output_matrix")),
     )
     return ret
 
@@ -139,6 +148,8 @@ def fs_spmreg_glnxa64_execute(
 
 
 def fs_spmreg_glnxa64(
+    input_volume: InputPathType,
+    output_matrix: str = "output.mat",
     runner: Runner | None = None,
 ) -> FsSpmregGlnxa64Outputs:
     """
@@ -149,6 +160,8 @@ def fs_spmreg_glnxa64(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        input_volume: Input anatomical volume.
+        output_matrix: Output registration matrix.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsSpmregGlnxa64Outputs`).
@@ -156,6 +169,8 @@ def fs_spmreg_glnxa64(
     runner = runner or get_global_runner()
     execution = runner.start_execution(FS_SPMREG_GLNXA64_METADATA)
     params = fs_spmreg_glnxa64_params(
+        input_volume=input_volume,
+        output_matrix=output_matrix,
     )
     return fs_spmreg_glnxa64_execute(params, execution)
 

niwrap_freesurfer/freesurfer/fs_temp_file.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_TEMP_FILE_METADATA = Metadata(
-    id="517fdbcd5c110803a94e295435754191461fd4ee.boutiques",
+    id="66a8be9a7267979a485ac7d37ceb69ea952d8f36.boutiques",
     name="fs_temp_file",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -15,9 +15,12 @@ FS_TEMP_FILE_METADATA = Metadata(
 
 FsTempFileParameters = typing.TypedDict('FsTempFileParameters', {
     "__STYX_TYPE__": typing.Literal["fs_temp_file"],
+    "base_dir": typing.NotRequired[str | None],
     "base_dir_alt": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
     "suffix_alt": typing.NotRequired[str | None],
     "scratch": bool,
+    "help": bool,
     "help_alt": bool,
 })
 
@@ -62,19 +65,25 @@ class FsTempFileOutputs(typing.NamedTuple):
 
 
 def fs_temp_file_params(
+    base_dir: str | None = None,
     base_dir_alt: str | None = None,
+    suffix: str | None = None,
     suffix_alt: str | None = None,
     scratch: bool = False,
+    help_: bool = False,
     help_alt: bool = False,
 ) -> FsTempFileParameters:
     """
     Build parameters.
     
     Args:
+        base_dir: Manually specify base temporary directory.
         base_dir_alt: Manually specify base temporary directory.
+        suffix: Optional file suffix.
         suffix_alt: Optional file suffix.
         scratch: Use /scratch directory if available, but FS_TMPDIR takes\
             priority.
+        help_: Print help text and exit.
         help_alt: Print help text and exit.
     Returns:
         Parameter dictionary
@@ -82,10 +91,15 @@ def fs_temp_file_params(
     params = {
         "__STYXTYPE__": "fs_temp_file",
         "scratch": scratch,
+        "help": help_,
         "help_alt": help_alt,
     }
+    if base_dir is not None:
+        params["base_dir"] = base_dir
     if base_dir_alt is not None:
         params["base_dir_alt"] = base_dir_alt
+    if suffix is not None:
+        params["suffix"] = suffix
     if suffix_alt is not None:
         params["suffix_alt"] = suffix_alt
     return params
@@ -106,11 +120,21 @@ def fs_temp_file_cargs(
     """
     cargs = []
     cargs.append("fs_temp_file")
+    if params.get("base_dir") is not None:
+        cargs.extend([
+            "-b",
+            params.get("base_dir")
+        ])
     if params.get("base_dir_alt") is not None:
         cargs.extend([
             "--base",
             params.get("base_dir_alt")
         ])
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-s",
+            params.get("suffix")
+        ])
     if params.get("suffix_alt") is not None:
         cargs.extend([
             "--suffix",
@@ -118,6 +142,8 @@ def fs_temp_file_cargs(
         ])
     if params.get("scratch"):
         cargs.append("--scratch")
+    if params.get("help"):
+        cargs.append("-h")
     if params.get("help_alt"):
         cargs.append("--help")
     return cargs
@@ -168,9 +194,12 @@ def fs_temp_file_execute(
 
 
 def fs_temp_file(
+    base_dir: str | None = None,
     base_dir_alt: str | None = None,
+    suffix: str | None = None,
     suffix_alt: str | None = None,
     scratch: bool = False,
+    help_: bool = False,
     help_alt: bool = False,
     runner: Runner | None = None,
 ) -> FsTempFileOutputs:
@@ -183,10 +212,13 @@ def fs_temp_file(
     URL: https://github.com/freesurfer/freesurfer
     
     Args:
+        base_dir: Manually specify base temporary directory.
         base_dir_alt: Manually specify base temporary directory.
+        suffix: Optional file suffix.
         suffix_alt: Optional file suffix.
         scratch: Use /scratch directory if available, but FS_TMPDIR takes\
             priority.
+        help_: Print help text and exit.
         help_alt: Print help text and exit.
         runner: Command runner.
     Returns:
@@ -195,9 +227,12 @@ def fs_temp_file(
     runner = runner or get_global_runner()
     execution = runner.start_execution(FS_TEMP_FILE_METADATA)
     params = fs_temp_file_params(
+        base_dir=base_dir,
         base_dir_alt=base_dir_alt,
+        suffix=suffix,
         suffix_alt=suffix_alt,
         scratch=scratch,
+        help_=help_,
         help_alt=help_alt,
     )
     return fs_temp_file_execute(params, execution)