mne.bem.make_flash_bem

mne.bem.make_flash_bem(subject, overwrite=False, show=True, subjects_dir=None, copy=True, *, flash5_img=None, register=True, verbose=None)

Create 3-Layer BEM model from prepared flash MRI images.

Parameters:

subjectstr

Subject name.

overwritebool

Write over existing .surf files in bem folder.

showbool

Show surfaces to visually inspect all three BEM surfaces (recommended).

subjects_dirpath-like | None

The path to the directory containing the FreeSurfer subjects reconstructions. If None, defaults to the SUBJECTS_DIR environment variable.

copybool

If True (default), use copies instead of symlinks for surfaces (if they do not already exist).

New in version 0.18.

Changed in version 1.1: Use copies instead of symlinks.

flash5_imgNone | path-like | Nifti1Image

The path to the synthesized flash 5 MRI image or the image itself. If None (default), the path defaults to mri/flash/parameter_maps/flash5.mgz within the subject reconstruction. If not present the image is copied or written to the default location.

New in version 1.1.0.

registerbool

Register the flash 5 image with T1.mgz file. If False, we assume that the images are already coregistered.

New in version 1.1.0.

verbosebool | str | int | None

Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.

See also

convert_flash_mris

Notes

This program assumes that FreeSurfer is installed and sourced properly.

This function extracts the BEM surfaces (outer skull, inner skull, and outer skin) from a FLASH 5 MRI image synthesized from multiecho FLASH images acquired with spin angles of 5 and 30 degrees.