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Creating the BEM meshes

Using the watershed algorithm

The watershed algorithm [Segonne et al., 2004] is part of the FreeSurfer software. The name of the program is mri_watershed. Its use in the MNE environment is facilitated by the script :ref:`mne watershed_bem`.

After mne watershed_bem has completed, the following files appear in the subject's :file:`bem/watershed` directory:

  • :file:`{<subject>}_brain_surface` contains the brain surface triangulation.
  • :file:`{<subject>}_inner_skull_surface` contains the inner skull triangulation.
  • :file:`{<subject>}_outer_skull_surface` contains the outer skull triangulation.
  • :file:`{<subject>}_outer_skin_surface` contains the scalp triangulation.

All of these surfaces are in the FreeSurfer format. In addition, there will be a file called :file:`bem/watershed/ws.mgz` which contains the brain MRI volume. Furthermore, mne watershed_bem script converts the scalp surface to fif format and saves the result to :file:`bem/{<subject>}-head.fif`.

Using FLASH images

This method depends on the availablily of MRI data acquired with a multi-echo FLASH sequence at two flip angles (5 and 30 degrees). These data can be acquired separately from the MPRAGE data employed in FreeSurfer cortical reconstructions but it is strongly recommended that they are collected at the same time with the MPRAGEs or at least with the same scanner. For easy co-registration, the images should have FOV, matrix, slice thickness, gap, and slice orientation as the MPRAGE data. For information on suitable pulse sequences, see :footcite:t:`FischlEtAl2004`.

Creation of the BEM meshes using this method involves the following steps:

  • Creating a synthetic 5-degree flip angle FLASH volume, register it with the MPRAGE data, and run the segmentation and meshing program. This step is accomplished by running the script :ref:`mne flash_bem`.
  • Inspecting the meshes with tkmedit, see :ref:`inspecting-meshes`.

Note

Different methods can be employed for the creation of the individual surfaces. For example, it may turn out that the watershed algorithm produces are better quality skin surface than the segmentation approach based on the FLASH images. If this is the case, outer_skin.surf can set to point to the corresponding watershed output file while the other surfaces can be picked from the FLASH segmentation data.

Organizing MRI data into directories

Since all images comprising the multi-echo FLASH data are contained in a single series, it is necessary to organize the images according to the echoes before proceeding to the BEM surface reconstruction. This can be accomplished by using dcm2niix or the MNE-C tool mne_organize_dicom if necessary, then use :func:`mne.bem.convert_flash_mris`.

Creating the surface tessellations

The BEM surface segmentation and tessellation is automated with the script :ref:`mne flash_bem`. It assumes that a FreeSurfer reconstruction for this subject is already in place.

Before running :ref:`mne flash_bem` do the following:

  • Create symbolic links from the directories containing the 5-degree and 30-degree flip angle FLASH series to flash05 and flash30, respectively:
    • :samp:`ln -s {<FLASH 5 series dir>} flash05`
    • :samp:`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:
    • :samp:`cp {<FLASH 5 series dir>} flash05`
    • :samp:`cp {<FLASH 30 series dir>} flash30`
  • Set the SUBJECTS_DIR and SUBJECT environment variables or pass the --subjects-dir and --subject options to mne flash_bem

Note

If mne flash_bem is run with the --noflash30 option, the :file:`flash30` directory is not needed, i.e., only the 5-degree flip angle flash data are employed.

It may take a while for mne flash_bem to complete. It uses the FreeSurfer directory structure under $SUBJECTS_DIR/$SUBJECT. The script encapsulates the following processing steps:

  • It creates an mgz file corresponding to each of the eight echoes in each of the FLASH directories in mri/flash. The files will be called :file:`mef {<flip-angle>}_{<echo-number>}.mgz`.
  • If the unwarp=True option is specified, run grad_unwarp and produce files :file:`mef {<flip-angle>}_{<echo-number>}u.mgz`. These files will be then used in the following steps.
  • It creates parameter maps in :file:`mri/flash/parameter_maps` using mri_ms_fitparms.
  • It creates a synthetic 5-degree flip angle volume in :file:`mri/flash/parameter_maps/flash5.mgz` using mri_synthesize.
  • Using fsl_rigid_register, it creates a registered 5-degree flip angle volume mri/flash/parameter_maps/flash5_reg.mgz by registering :file:`mri/flash/parameter_maps/flash5.mgz` to the T1 volume under mri.
  • Using mri_convert, it converts the flash5_reg volume to COR format under mri/flash5. If necessary, the T1 and brain volumes are also converted into the COR format.
  • It runs mri_make_bem_surfaces to create the BEM surface tessellations.
  • It creates the directory :file:`bem/flash`, moves the tri-format tringulations there and creates the corresponding FreeSurfer surface files in the same directory.
  • The COR format volumes created by mne flash_bem are removed.

If the --noflash30 option is specified to mne flash_bem, steps 3 and 4 in the above are replaced by averaging over the different echo times in 5-degree flip angle data.

Inspecting the meshes

It is advisable to check the validity of the BEM meshes before using them. This can be done with:

  • the --view option of :ref:`mne flash_bem`
  • calling :func:`mne.viz.plot_bem` directly
  • Using FreeSurfer tools tkmedit or freeview