Analyzing Data in BrainVoyager

The first step in analyzing data with BrainVoyager is to specify the experimental protocol which is stored in a .prt file.  Open the FMR project dep032000_run1_sc.fmr and choose Analysis->Stimulation Protocol to bring up the following dialog (clicking the Intervals>> button to get the bottom half):

 Give the protocol a name in the Experiment box. Add and edit conditions in the Condition list frame.  The Depall experiment presented randomly ordered positive, neutral, and negative pictures for three seconds with sixteen seconds interval between the end of one picture to the start of the next . The first picture was a positive one presented at the start of the sixth scan from time 15 to 18 seconds.  The next was a neutral one from 34 to 37 seconds and the third a negative one from 53 to 56 seconds and so on until 21 of each type of picture was presented.  Since only every third picture presentation coincides exactly with a volume acquisition (occurring exactly every 3 seconds)  it is necessary to specify milliseconds in the Time units frame.  Select the positive (pos) condition and add the time intervals for the positive pictures only in the Intervals defining condition events/blocks frame.  Then do the same for the neutral and negative pictures.  Finally use File->Save Protocol to save the protocol file. Since the protocol file is an ascii text file it is fairly easy to create the time intervals in Excel and paste them into the appropriate place in a template protocol file.  By choosing Plot->Time Course Plot window..  the following display of the protocol is made:

You can check that the protocol has been  linked to the FMR project using the File->Edit FRM Infos menu and clicking on the Edit Protocol button and verifying that the proper protocol is referenced.

At this point we are ready to do some analysis using a the General Linear Model (GLM).  The first step is to create predictor time courses for each condition (picture type).  Choose Analysis->General Linear Model, Single Study from the main menu to bring up the following dialog:

Clicking the Protocol button in the center of the button group in the lower right opens the Stimulation Protocol dialog too.  By right clicking on the pos condition and left clicking on the baseline condition in the Stimulation Protocol dialog a square wave is created in the GLM window.  Clicking on the Hemodynamic RF button will convolve this square wave with a theoretical hemodynamic response function creating the predictor time course for the positive condition.  Next click the Add Pred button which will increment to predictor two in the Predictors frame and in a similar fashion create the predictor time course for the neutral condition (predictor 2) and the same for negative condition (predictor 3).  Now the GLM time course can be saved by choosing the File->Save time course menu in the Single Study General Linear Model dialog.

Let's try running the GLM on the raw VTC and on the motion corrected and filtered VTC.  Go to the Analysis->Use vtc menu item, click on the Browse button, choose dep032000_run1_sc.vtc, check the load into memory box and click OK.  Go back to the GLM single study dialog from the Analysis and load the time course created above.  Click the Go button.  The results are displayed below (the white square marks the ROI described below):

An average ROI time course can be created by right clicking in the activated region:

In addition the average hemodynamic response functions for each picture type over this ROI can be computed.  First an event average file needs to be created.  Choose Analysis->Event-related averaging ... to bring up the following dialog:

Click the Add func data button and choose the dep032000_run1_sc.vtc file, then hold down the shift key and choose the pos/neg/neu picture conditions.  Click the Generate AVG button and save to dep032000_run1_sc.AVG.  This creates an ascii file that tells BV which data files and times to use in the average calculations.  Bring up the or ROI time plot again and click the >> in the lower right to get additional options:

Click the middle Browse button across from the Event-related avg check box and choose the dep032000_run1_sc.AVG file.  The following average HRFs are computed for the ROI:

Left clicking on this graph brings up an options dialog for setting graph characteristics.

Below are the same images using the motion corrected and filtered volume time courses: