Head Model and Source Space Creation in MNE
Make sure you've typed
mne_setup_2.6.1_32bit (depending on version, latest version mne_setup_2.7.1_32bit) freesurfer_4.3.0 (depending on version, latest version freesurfer_5.1.0) setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces.
After this step, you should realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set). It is briefly described below.
The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the MNE manual or reading papers.
{{{#!/bin/sh
SUBJECTS_DIR='</myMRIdirectory/>' # root directory for MRI data
for SUBJECT in Subject1 Subject2 Subject3 # use your list of subject names here do
- # creates surfaces necessary for BEM head models mne_watershed_bem --overwrite --subject $SUBJECT ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_inner_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skin_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_brain_surface' $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf # creates fiff-files for MNE describing MRI data mne_setup_mri --overwrite --subject $SUBJECT # create a source space from the cortical surface created in Freesurfer mne_setup_source_space --spacing 5 --overwrite --subject $SUBJECT
done }}} You've got to create the links ("ln -s..."), such that MNE uses the newly created surfaces in the following analyses.
Aligning MEG and MRI coordinate systems
This is a brief summary of how to align MEG and MRI coordinate systems. For more information see the MNE manual (chapter 12.11).
If you have several fiff-files per participant(e.g. averages for different conditions), and if these files contain the same sensor configuration (e.g. if averages are from the same block, or from different blocks but were interpolated using the -trans option in maxfilter), then this procedure has to be applied only once per subject. If you have different fiff-files per subject with different sensor configurations, then you have to do this for each file separately.
Make sure you've typed
mne_setup_2.6.0 (depending on version, latest version mne_setup_2.7.1_32bit) setenv SUBJECTS_DIR </myMRIdirectory/>
before proceeding.
1) Start mne_analyze ("vglrun mne_analyze").
2) Load a surface file (File -> Load Surface, choose inflated).
3) Load a fiff-file containing digitiser data (raw or averaged file; File -> Load digitizer data).
4) Open the viewer (View -> Show Viewer).
5) Click on "Options". Hide the cortex, make the skin transparent, show the digitiser data.
6) Choose Adjust -> Coordinate Alignment. Define approximate landmarks (LAP, RAP, Nasion) by clicking at their labels, then at their approximate locations in the viewer. The click "Align Using Fiducials".
7) Use the "ICP Align" option multiple times until the transformation matrix doesn't change significantly any more. You can remove outliers using the "Omit/Discard" option (e.g. choose 10 or 5 mm, then ICP align again).
8) When you are happy, click "Save default".
The coordinate transform will automatically be invoked in future operation within MNE.