Checking data with Neuromag tools

 Data can be explored with Graph: 

 (0) How to start Graph: 
     - type 'graph' (from a shell) or double-click on the homonymous icon
     - Go to File > Load settings to load the *.setup file that you need (see below)
     - Go to File > Open Diskfile to load your *.fif data

 (1) Checking triggers and/or stimuli timing:


 (2) Checking continuous RAW data and the performance of MaxFilter:
     - Open a basic setup (for example /neurospin/meg/meg_rep/tools/graph_tools/graph_basic/general-averager.setup), load your data;
     - Explore all time points, all sensors and mark those that are bad or that present small abnormalities. You can shift between
       groups of sensors by Displays > Selection. To facilitate zapping among sensors, click on the dashed line at the top of the
       selection window to tear the window off the main window. Adjust the scale (set 'Autoscale', top right of main window) when 
       shifting from gradiometers to magnetometers.
     - Time chunks that are buggy or unnecessary for your analysis can be taken out of MaxFilter processing (see MaxFilter 2.1 manual,
       pages 18-20)
     - It is strongly advised to check the performance of MaxFilter processing by comparing the data before and after MaxFilter 
       processing, especially at sensors/time intervals that look noisy in the raw data (see Analysis with Maxfilter). 
       One way to do this is to open graph twice, load the raw data on one window and the MaxFiltered data on the other window
       and compare the signal at the same channels and time segments (be careful to select the same scale!). 

 (3) Preprocessing your data (PCA-based removal of ECG and EOG artifacts): 
     (NOTE: this procedure will be included in MaxFilter soon!)

 -> Load the triplet display by the command: (load "/neurospin/meg/meg_rep/tools/graph_tools/graph_PCA/triplet-ecg.lsp")

 -> Load the setup by "File/Load Settings" and selecting:  "/neurospin/meg/meg_rep/tools/graph_tools/graph_PCA/ecg-pca.setup"

 -> Load your Maxfiltered raw data by "File/Open diskfile"

 -> Check that the cardiac QRS complex is detected for most beats. Adjust the threshold in the widget "ecg-threshold" if needed.

 -> Average over the beats by command: (average 0 100) which uses the first 100 seconds of the file

 -> The Xplotter display should now show the cardiac artefact.

 -> Run PCA by: (pca-on-widget "to-pca" -0.2 0.4)

 -> Open "Commands/SSP dialog" and choose "Actions/Add PCA fields/5 vectors"

 -> Select the matrix in "Vector pool", select "Edit/Edit name" to rename to something like "PCA-ECG-grads", and select
 "Edit/Explode". You should have   now have 5 lines instead of 1 in the vector pool. These lines correspond to the 5 'strongest'
 principal components.

 -> Select the topmost line and click on the arrow to copy it to the "SSP vectors" list. 
 Right after the copying, the signals on the plotter display
 change to reflect the projected version of the data. Add more components until the artefact is no longer visible.

 -> Save the vector set you determined sufficient for removing the cardiac artefact: delete the unnecessary vectors from the 
 pool, invoke "File/Save",and give a filename that ends with ".fif".

 -> You may now use the SSP operators (the vector sets) on Matlab, MNE, Brainstorm and the Neuromag software. For these, 
 the vector sets have to be combined into a single operator where the vectors are augmented to the full dimensionality
 of the data; for example, the 102-dimensional magnetometer vectors should be padded to 306-dimensional space 
 (or even more if EEG is included) by inserting zeros at appropriate locations. The xfit program (Neuromag software) is
 able to do this; use it for Neuromag software, MNE and Brainstorm. For Matlab, Lucie has written a function that does a similar
 combination.

 -> Repeat the procedure for EOG artefacts. 
 Note that if your ECG or EOG electrodes are missing or too noisy, you can select one of the MEG sensor as the basis of your
 rejection procedure.


 (4) Checking AVG data: