• mri_make_bem_surfaces

Index

Note!!!!

All support requests should be directed to the MNE mailing list: mne_analysis@nmr.mgh.harvard.edu (see the below note in Reporting Bugs!)

Name

mri_make_bem_surfaces - This is a tool to create BEM surfaces

Synopsis

mri_make_bem_surfaces

Outputs

Description

This tool requires two COR file directories called $SUBJECTS_DIR/$SUBJECT/mri/flash5/ and $SUBJECTS_DIR/$SUBJECT/mri/brain/ to exist (The FLASH volume should be registered to the brain volume). It then estimates from the brain and FLASH 5° volumes the three surfaces. The tool itself has been kept in FreeSurfer to assist MEEG users generate good forward models; however, it is not updated or actively worked upon (It's last substantial update was in ~2001).

Examples

Example 1

mri_make_bem_surfaces

Bugs

None

See Also

mri_watershed, mri_ms_fitparms

Links

FreeSurfer, MNE

Methods Description

A fourth order icosahedron is fit around the brain volume and smoothed. The algorithm then uses this estimate to search from 3mm to 30mm outside of this surface in the FLASH volume for the boundary with the inner skull. This new surface is then smoothed generating the "inner skull" surface. Next the thickness of the skull is estimated from the FLASH volume by searching from 3mm stepping out to 30mm for the boundary of the "outer skull" surface. A safety check is performed to make sure that the algorithm hasn't stepped beyond the head (if it does it sets the value to 3mm. This is useful for places where the skull is particularly thin e.g. Squama temporalis.). Another fourth order icosahedral surface is fit and smoothed to make up the "outer skull" surface. Finally, a fourth order icosahedral surface is fit around the entire FLASH volume to generate the "outer skin" surface.

References

Reporting Bugs

This tool is no longer supported; however, the FreeSurfer team kindly keeps it in the releases to help the MEEG community.

Author/s

DanielWakeman