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#!/usr/bin/env python
"""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: Lorenzo De Santis
# Alexandre Gramfort
import mne
from mne.bem import convert_flash_mris, make_flash_bem
def _vararg_callback(option, opt_str, value, parser):
assert value is None
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()
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