MEG Data Acquisition

Creating a BEM model for source localization

After running freesurfer on a subject's T1 anatomy we next need to create a BEM model.

 cd /home/jyeatman/git/mnefun/bin
 python run_mne_bem.py --subject NLR_201_GS --layers 1 --overwrite

Aligning MEG sensor data to the BEM model

Open mne_analyze to compute the coordinate alignment. In mne_analyze load the subject's surface and digitizer data:

 File -> Load Surface -> Select Inflated
 File -> Load Digitizer Data -> sss_fif -> select any raw file

Next adjust how these digitized points align with the scalp in the MRI

 Adjust -> Coordinate Alignment
 View -> Show viewer

Within the viewer window click the "Options" button. Within the "Viewer Options" dialogue check "digitizer data" and "HPI and landmarks only". Click Options -> check Digitizer Data and HPI and landmarks only, Click each Fiducial location and then click "Align using fiducials" Save Default Make a "trans" folder within the subject's directory Move transform file and rename subj-trans.fif

2. To visualize source localized data

mne_analyze

3. File -> Load Surface -> Select Inflated

4. File-> Open

To adjust sensor plots: Adjust -> Scales To adjust source visualization: Adjust -> Estimates