Difference between revisions of "MEG Data Acquisition"
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| + | == Creating a BEM model for source localization == | ||
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| + | After running freesurfer on a subject's T1 anatomy we next need to create a BEM model. | ||
cd /home/jyeatman/git/mnefun/bin | cd /home/jyeatman/git/mnefun/bin | ||
python run_mne_bem.py --subject NLR_201_GS --layers 1 --overwrite | 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 Surface -> Select Inflated |
| − | File -> Load Digitizer Data -> sss_fif -> select any raw file | + | File -> Load Digitizer Data -> sss_fif -> select any raw file |
| − | Adjust -> Coordinate Alignment | + | Next adjust how these digitized points align with the scalp in the MRI |
| − | View -> Show viewer | + | 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". [[File:Viewer options.png]] | ||
Click Options -> 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" | Click each Fiducial location and then click "Align using fiducials" | ||
Revision as of 22:15, 23 October 2015
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
