针对pulse-transit的工具

2025-02-22 16:12:02 +08:00
commit 6bc25b4e3a
7719 changed files with 1530886 additions and 0 deletions
--- a/dist/client/mne/commands/mne_watershed_bem.py
+++ b/dist/client/mne/commands/mne_watershed_bem.py
@@ -0,0 +1,134 @@
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+"""Create BEM surfaces using the watershed algorithm included with FreeSurfer.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne watershed_bem -s sample
+
+"""
+
+import sys
+
+import mne
+from mne.bem import make_watershed_bem
+from mne.utils import _check_option
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import _add_verbose_flag, get_optparser
+
+    parser = get_optparser(__file__)
+
+    parser.add_option(
+        "-s", "--subject", dest="subject", help="Subject name (required)", default=None
+    )
+    parser.add_option(
+        "-d",
+        "--subjects-dir",
+        dest="subjects_dir",
+        help="Subjects directory",
+        default=None,
+    )
+    parser.add_option(
+        "-o",
+        "--overwrite",
+        dest="overwrite",
+        help="Write over existing files",
+        action="store_true",
+    )
+    parser.add_option(
+        "-v", "--volume", dest="volume", help="Defaults to T1", default="T1"
+    )
+    parser.add_option(
+        "-a",
+        "--atlas",
+        dest="atlas",
+        help="Specify the --atlas option for mri_watershed",
+        default=False,
+        action="store_true",
+    )
+    parser.add_option(
+        "-g",
+        "--gcaatlas",
+        dest="gcaatlas",
+        help="Specify the --brain_atlas option for mri_watershed",
+        default=False,
+        action="store_true",
+    )
+    parser.add_option(
+        "-p",
+        "--preflood",
+        dest="preflood",
+        help="Change the preflood height",
+        default=None,
+    )
+    parser.add_option(
+        "--copy",
+        dest="copy",
+        help="Use copies instead of symlinks for surfaces",
+        action="store_true",
+    )
+    parser.add_option(
+        "-t",
+        "--T1",
+        dest="T1",
+        help="Whether or not to pass the -T1 flag "
+        "(can be true, false, 0, or 1). "
+        "By default it takes the same value as gcaatlas.",
+        default=None,
+    )
+    parser.add_option(
+        "-b",
+        "--brainmask",
+        dest="brainmask",
+        help="The filename for the brainmask output file "
+        "relative to the "
+        "$SUBJECTS_DIR/$SUBJECT/bem/watershed/ directory.",
+        default="ws",
+    )
+    _add_verbose_flag(parser)
+
+    options, args = parser.parse_args()
+
+    if options.subject is None:
+        parser.print_help()
+        sys.exit(1)
+
+    subject = options.subject
+    subjects_dir = options.subjects_dir
+    overwrite = options.overwrite
+    volume = options.volume
+    atlas = options.atlas
+    gcaatlas = options.gcaatlas
+    preflood = options.preflood
+    copy = options.copy
+    brainmask = options.brainmask
+    T1 = options.T1
+    if T1 is not None:
+        T1 = T1.lower()
+        _check_option("--T1", T1, ("true", "false", "0", "1"))
+        T1 = T1 in ("true", "1")
+    verbose = options.verbose
+
+    make_watershed_bem(
+        subject=subject,
+        subjects_dir=subjects_dir,
+        overwrite=overwrite,
+        volume=volume,
+        atlas=atlas,
+        gcaatlas=gcaatlas,
+        preflood=preflood,
+        copy=copy,
+        T1=T1,
+        brainmask=brainmask,
+        verbose=verbose,
+    )
+
+
+mne.utils.run_command_if_main()