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N/A N/A Create 3-Layers BEM model from Flash MRI images

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
    4. cd to the directory where flash05 and flash30 links are
    5. Set SUBJECTS_DIR and SUBJECT environment variables appropriately
    6. Run this script

Example usage:

$ mne flash_bem --subject sample

 __future__ print_function mne.bem convert_flash_mris make_flash_bem run N/A N/A N/A N/A mne.commands.utils get_optparser N/A parser N/A get_optparser __file__ N/A N/A N/A parser add_option -s --subject dest subject help Subject name default None N/A N/A N/A parser add_option -d --subjects-dir dest subjects_dir help Subjects directory default None N/A N/A N/A parser add_option -3 --noflash30 dest noflash30 action store_true default False help Skip the 30-degree flip angle data N/A N/A N/A 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 N/A N/A N/A 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 N/A N/A N/A parser add_option -o --overwrite dest overwrite action store_true default False help Write over existing .surf files in bem folder N/A N/A N/A parser add_option -v --view dest show action store_true help Show BEM model in 3D for visual inspection default False N/A N/A options args N/A N/A parser parse_args N/A subject N/A options subject N/A subjects_dir N/A options subjects_dir N/A flash30 N/A N/A options noflash30 N/A convert N/A N/A options noconvert N/A unwarp N/A options unwarp N/A overwrite N/A options overwrite N/A show N/A options show N/A N/A N/A options subject None N/A N/A N/A N/A parser print_help N/A N/A RuntimeError The subject argument must be set N/A N/A convert_flash_mris subject subject subjects_dir subjects_dir flash30 flash30 convert convert unwarp unwarp N/A N/A make_flash_bem subject subject subjects_dir subjects_dir overwrite overwrite show show N/A N/A is_main N/A __name__ __main__ N/A is_main N/A N/A N/A run