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 mne_watershed_bem.

After mne_watershed_bem has completed, the following files appear in the subject’s bem/watershed directory:

** <subject> _brain_surface**

Contains the brain surface triangulation.

** <subject> _inner_skull_surface**

Contains the inner skull triangulation.

** <subject> _outer_skull_surface**

Contains the outer skull triangulation.

** <subject> _outer_skin_surface**

Contains the scalp triangulation.

All of these surfaces are in the FreeSurfer format. In addition, there will be a directory called bem/watershed/ws which contains the brain MRI volume. Furthermore, mne_watershed_bem script converts the scalp surface to fif format and saves the result to bem/ <subject> -head.fif . The mne_analyze tool described Interactive analysis with mne_analyze looks for this file the visualizations involving the scalp surface.

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 reference [B. Fischl et al. and J. Jovicich et al., 2006] in Forward modeling. At the Martinos Center, use of the 1.5-T Avanto scanner (Bay 2) is recommended for best results.

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


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, can set to point to the corresponding watershed output file while the other surfaces can be picked from the FLASH segmentation data.


The mne_convert_surface C utility can be used to convert text format triangulation files into the FreeSurfer surface format.


The following sections assume that you have run the appropriate setup scripts to make both MNE and FreeSurfer software available.

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 is accomplished by the mne_organize_dicom script, which creates a directory tree with symbolic links to the original DICOM image files. To run mne_organize_dicom , proceed as follows:

  • Copy all of your images or create symbolic links to them in a single directory. The images must be in DICOM format. We will refer to this directory as <source> .

  • Create another directory to hold the output of mne_organize_dicom . We will refer to this directory as <dest> .

  • Change the working directory to <dest> .

  • Say mne_organize_dicom <source> . Depending on the total number of images in <source> this script may take quite a while to run. Progress is indicated by listing the number of images processed at 50-image intervals.

As a result, <dest> will contain several directories named <three-digit number> _ <protocol_name> corresponding to the different series of images acquired. Spaces and parenthesis in protocol names will be replaced by underscores. Under each of these directories there are one or more directories named <three-digit> number corresponding to one or more subsets of images in this series (protocol). The only subset division scheme implemented in mne_organize_dicom is that according to different echoes, typically found in multi-echo FLASH data. These second level directories will contain symbolic links pointing to the original image data.


mne_organize_dicom was developed specifically for Siemens DICOM data. Its correct behavior with DICOM files originating from other MRI scanners has not been verified at this time.


Since mne_organize_dicom processes all images, not only the FLASH data, it may be a useful preprocessing step before FreeSurfer reconstruction process as well.

Creating the surface tessellations

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

Before running mne_flash_bem do the following:

  • Run mne_organize_dicom as described above.

  • Change to the <dest> directory where mne_organize_dicom created the image directory structure.

  • Create symbolic links from the directories containing the 5-degree and 30-degree flip angle FLASH series to flash05 and flash30 , respectively:

    • 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

  • Set the SUBJECTS_DIR and SUBJECT environment variables


If mne_flash_bem is run with the --noflash30 option, the 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 mef <flip-angle> _ <echo-number> .mgz .

  • If the --unwarp option is specified, run grad_unwarp and produce files mef <flip-angle> _ <echo-number> u.mgz . These files will be then used in the following steps.

  • It creates parameter maps in mri/flash/parameter_maps using mri_ms_fitparms .

  • It creates a synthetic 5-degree flip angle volume in 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 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 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 help of tkmedit, see Setting up the boundary-element model.

Using seglab

The brain segmentation provided by FreeSurfer in the directory mri/brain can be employed to create the inner skull surface triangulation with help of seglab, the Neuromag MRI segmentation tool. The description below assumes that the user is familiar with the seglab tool. If necessary, consult the seglab manual, Neuromag P/N NM20420A-A.

The data set mri/brain typically contains tissues within or outside the skull, in particular around the eyes. These must be removed manually before the inner skull triangulation is created.The editing and triangulation can be accomplished as outlined below

1. Set up the MRIs for Neuromag software access

Run the mne_setup_mri too as described in Setting up anatomical MR images for MRIlab. As a result, the directories mri/T1-neuromag and mri/brain-neuromag are set up.

2. Load the MRI data

Open the file mri/brain-neuromag/sets/COR.fif and adjust the scaling of the data.

3. Preparatory steps

Set the minimum data value to 1 using the min3D operator. Make a backup of the data with the backup3D operator.

4. Manual editing

The maskDraw3D operation is recommended for manual editing. To use it, first employ the grow3D operator with threshold interval 2…255 and the seed point inside the brain. Then do the editing in the slicer window as described in Section 5.4.2 of the seglab manual. Note that it is enough to remove the connectivity to the extracerebral tissues rather than erasing them completely.

5. Grow again and mask

Once manual editing is complete, employ the grow3D operator again and do mask3D with the backup data to see whether the result is satisfactory. If not, undo mask3D and continue manual editing. Otherwise, undo mask3D and proceed to the next step.

6. Dilation

It is advisable to make the inner skull surface slightly bigger than the brain envelope obtained in the previous step. Therefore, apply the dilate3D operation once or twice. Use the values 1 for nbours and 26 for nhood in the first dilation and 1 and 18 in the second one, respectively.

7. Triangulation

Triangulate the resulting object with the triangulate3D operator. Use a sidelength of 5 to 6 mm. Check that the triangulation looks reasonable in the 3D viewing window.

8. Save the triangulation

Save the triangulated surface as a mesh into bem/inner_skull.tri. Select unit of measure as millimeters and employ the MRI coordinate system.

Using BrainSuite

The BrainSuite software running under the Windows operating system can also be used for BEM mesh generation. This software, written by David W. Shattuck, is distributed as a collaborative project between the Laboratory of Neuro Imaging at the University of California Los Angeles (Director: Dr. Arthur W. Toga) and the Biomedical Imaging Research Group at the University of Southern California (Director: Dr. Richard M. Leahy). For further information, see

The conversion of BrainSuite tessellation files to MNE software compatible formats is accomplished with the mne_convert_surface utility, covered in mne_convert_surface.

The workflow needed to employ the BrainSuite tessellations is:

Step 1

Using the mri_convert utility available in FreeSurfer , convert an MRI volume to the img (Analyze) format. This volume should be the T1.mgz volume or a volume registered with T1.mgz in FreeSurfer :mri_convert <volume> .mgz <volume> .img

Step 2

Transfer <volume> .mgz to a location accessible to BrainSuite , running on Windows.

Step 3

Using <volume> .img as input, create the tessellations of scalp, outer skull, and inner skull surfaces in BrainSuite .

Step 4

Transfer the dfs files containing the tessellations in the bem directory of your subject’s FreeSurfer reconstruction.

Step 5

Go to the bem directory where you placed the two dfs files. Using mne_convert_surface , convert them to the FreeSurfer surface format, e,g.: mne_convert_surface `` ``--dfs inner_skull.dfs `` ``--mghmri ../mri/T1.mgz `` ``--surf

Step 6

Using tkmedit, check that the surfaces are correct, e.g.: tkmedit -f ../mri/T1.mgz `` ``-surface


Using the mne_reduce_surface function in Matlab, reduce the number of triangles on the surfaces to 10000 - 20000. Call the output files , , and .

Step 8

Proceed to mne_setup_forward_model . Use the --surf and --noswap options.


If left and right are flipped in BrainSuite, use the --flip option in mne_convert_surface to set the coordinate transformation correctly.


The BrainSuite scalp surface can be also used for visualization in mne_analyze , see Using a high-resolution head surface tessellations.