mne_flash_bem.py

#!/usr/bin/env python
"""Create 3-layer BEM model from Flash MRI images.

Examples
--------
.. code-block:: console

    $ mne flash_bem --subject=sample

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 are inputted in DICOM format.
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.

Before running this script do the following:
(unless the --noconvert option is specified)

1. Copy all of your FLASH images in a single directory <source> and
   create a directory <dest> to hold the output of mne_organize_dicom
2. cd to <dest> and run
   $ mne_organize_dicom <source>
   to create an appropriate directory structure
3. Create symbolic links to make flash05 and flash30 point to the
   appropriate series:
   $ ln -s <FLASH 5 series dir> flash05
   $ ln -s <FLASH 30 series dir> flash30
   Some partition formats (e.g. FAT32) do not support symbolic links.
   In this case, copy the file to the appropriate series:
   $ cp <FLASH 5 series dir> flash05
   $ cp <FLASH 30 series dir> flash30
4. cd to the directory where flash05 and flash30 links are
5. Set SUBJECTS_DIR and SUBJECT environment variables appropriately
6. Run this script
"""
# Authors: Lorenzo De Santis

import mne
from mne.bem import convert_flash_mris, make_flash_bem


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", "--noflash30", dest="noflash30",
                      action="store_true", default=False,
                      help=("Skip the 30-degree flip angle data"),)
    parser.add_option("-n", "--noconvert", dest="noconvert",
                      action="store_true", default=False,
                      help=("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="The directory containing flash05.mgz and "
                      "flash30.mgz files (defaults to "
                      "$SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps")

    options, args = parser.parse_args()

    subject = options.subject
    subjects_dir = options.subjects_dir
    flash30 = not options.noflash30
    convert = not options.noconvert
    unwarp = options.unwarp
    overwrite = options.overwrite
    show = options.show
    flash_path = options.flash_path
    copy = options.copy

    if options.subject is None:
        parser.print_help()
        raise RuntimeError('The subject argument must be set')

    convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
                       flash30=flash30, convert=convert, unwarp=unwarp,
                       verbose=True)
    make_flash_bem(subject=subject, subjects_dir=subjects_dir,
                   overwrite=overwrite, show=show, flash_path=flash_path,
                   copy=copy, verbose=True)


mne.utils.run_command_if_main()