initial commit

mne/commands/mne_flash_bem.py

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+"""Create 3-layer BEM model from Flash MRI images.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne flash_bem --subject=sample
+    $ mne flash_bem -s sample -n --registered -5 sample/mri/mef05.mgz -3 sample/mri/mef30.mgz
+    $ mne flash_bem -s sample -n --registered -5 sample/mri/flash/mef05_*.mgz -3 sample/mri/flash/mef30_*.mgz
+
+Notes
+-----
+This program assumes that FreeSurfer and MNE are installed and
+sourced properly.
+
+This function extracts the BEM surfaces (outer skull, inner skull, and
+outer skin) from multiecho FLASH MRI data with spin angles of 5 and 30
+degrees. The multiecho FLASH data can be input as .mgz or .nii files.
+This function assumes that the Freesurfer segmentation of the subject
+has been completed. In particular, the T1.mgz and brain.mgz MRI volumes
+should be, as usual, in the subject's mri directory.
+
+"""  # noqa E501
+
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import mne
+from mne.bem import convert_flash_mris, make_flash_bem
+
+
+def _vararg_callback(option, opt_str, value, parser):
+    assert value is None
+    del opt_str  # required for input but not used
+    value = []
+
+    for arg in parser.rargs:
+        # stop on --foo like options
+        if arg[:2] == "--" and len(arg) > 2:
+            break
+        if arg[:1] == "-" and len(arg) > 1:
+            break
+        value.append(arg)
+
+    del parser.rargs[: len(value)]
+    setattr(parser.values, option.dest, value)
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import get_optparser
+
+    parser = get_optparser(__file__)
+
+    parser.add_option(
+        "-s", "--subject", dest="subject", help="Subject name", default=None
+    )
+    parser.add_option(
+        "-d",
+        "--subjects-dir",
+        dest="subjects_dir",
+        help="Subjects directory",
+        default=None,
+    )
+    parser.add_option(
+        "-3",
+        "--flash30",
+        "--noflash30",
+        dest="flash30",
+        action="callback",
+        callback=_vararg_callback,
+        help=(
+            "The 30-degree flip angle data. If no argument do "
+            "not use flash30. If arguments are given, them as "
+            "file names."
+        ),
+    )
+    parser.add_option(
+        "-5",
+        "--flash5",
+        dest="flash5",
+        action="callback",
+        callback=_vararg_callback,
+        help=("Path to the multiecho flash 5 images. Can be one file or one per echo."),
+    )
+    parser.add_option(
+        "-r",
+        "--registered",
+        dest="registered",
+        action="store_true",
+        default=False,
+        help=(
+            "Set if the Flash MRI images have already "
+            "been registered with the T1.mgz file."
+        ),
+    )
+    parser.add_option(
+        "-n",
+        "--noconvert",
+        dest="noconvert",
+        action="store_true",
+        default=False,
+        help=(
+            "[DEPRECATED] Assume that the Flash MRI images "
+            "have already been converted to mgz files"
+        ),
+    )
+    parser.add_option(
+        "-u",
+        "--unwarp",
+        dest="unwarp",
+        action="store_true",
+        default=False,
+        help=(
+            "Run grad_unwarp with -unwarp <type> "
+            "option on each of the converted data sets"
+        ),
+    )
+    parser.add_option(
+        "-o",
+        "--overwrite",
+        dest="overwrite",
+        action="store_true",
+        default=False,
+        help="Write over existing .surf files in bem folder",
+    )
+    parser.add_option(
+        "-v",
+        "--view",
+        dest="show",
+        action="store_true",
+        help="Show BEM model in 3D for visual inspection",
+        default=False,
+    )
+    parser.add_option(
+        "--copy",
+        dest="copy",
+        help="Use copies instead of symlinks for surfaces",
+        action="store_true",
+    )
+    parser.add_option(
+        "-p",
+        "--flash-path",
+        dest="flash_path",
+        default=None,
+        help="[DEPRECATED] The directory containing flash5.mgz "
+        "files (defaults to "
+        "$SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps",
+    )
+
+    options, _ = parser.parse_args()
+
+    subject = options.subject
+    subjects_dir = options.subjects_dir
+    flash5 = options.flash5
+    if flash5 is None or len(flash5) == 0:
+        flash5 = True
+    flash30 = options.flash30
+    if flash30 is None:
+        flash30 = True
+    elif len(flash30) == 0:
+        flash30 = False
+    register = not options.registered
+    unwarp = options.unwarp
+    overwrite = options.overwrite
+    show = options.show
+    copy = options.copy
+
+    if options.subject is None:
+        parser.print_help()
+        raise RuntimeError("The subject argument must be set")
+
+    flash5_img = convert_flash_mris(
+        subject=subject,
+        subjects_dir=subjects_dir,
+        flash5=flash5,
+        flash30=flash30,
+        unwarp=unwarp,
+        verbose=True,
+    )
+    make_flash_bem(
+        subject=subject,
+        subjects_dir=subjects_dir,
+        overwrite=overwrite,
+        show=show,
+        copy=copy,
+        register=register,
+        flash5_img=flash5_img,
+        verbose=True,
+    )
+
+
+mne.utils.run_command_if_main()