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Make Design Matrix for IR1

Page history last edited by PBworks 13 years, 6 months ago

(1) First, you'll need to define two text files encoding two orthogonal regressors. Each of these files will have exactly 84 lines, one per scan.


In the IR1 paradigm, there are equal numbers of RealWord scans as there are FalseFont scans, so for the contrast "RealWord-FalseFont" place a 1 for RealWord scans and a -1 for FalseFont scans. Place a 0 for Fix scans. You'll probably want to also include an orthogonal regressor for the contrast "(RealWord and FalseFont) - Fix", where there is a -2 for Fix scans and a 1 for either RealWord and FalseFont scans.


If there had been a differing number of RealWord and FalseFont scans, it's a little trickier. Say there were N RealWord scans and M FalseFont scans. Then you could place a M for RealWord scans and a -N for FalseFont scans. You want the sum of all of the numbers in the text file to equal zero.


For your convenience, here are pre-made text files that you can just download and save into your tutorial directory, if you'd rather not make them by hand (but at least look at their contents in a text editor like Notepad or gedit!):




(2) Invoke MEDx, and open up a New Folder.


(3) Select Toolbox --> Functional --> Correlation Analysis.


(4) In the Correlation Analysis dialog box, under General Parameters, set Length of Time Series (in scans) to 84. The IR1 paradigm has only 84 scans, after dropping the initial 5 "dummy" scans.


(5) Click on the Waveform Creation tab.


(6) Change Shape to Custom.


(7) Set Custom File to point to the full path to the RealWordAndFalseFontMinusFix.txt file, e.g.




If you like, you can click on the little button (has an icon of a folder) to the right of the white entry box to browse to the file.


(8) Click on the Load Custom File button. The waveform displayed in the white panel should change to show the "(RealWord and FalseFont) - Fix" contrast.


(9) Click on the Add button. This opens up another column in the Design Matrix, in which we can add the other regressor.


(10) Repeat steps 6 through 8, but this time for the file RealWordMinusFalseFont.txt. After clicking on the Load Custom File, then click on the Save button in the lower left corner.


(11) In the Select a File dialog box, save the Design Matrix into a file in your tutorial directory. Name the file DesignMatrix.vst. (The vst extension indicates that it's in VEST format, which is an idiosyncratic MEDx format.) Clicking on the OK button performs the save and dismisses this dialog box.


(12) Select Image --> Open Image... and load in the 84 spatially normalized image volumes (Sn*.hdr). They should appear in a new Group page named New Group.


(13) Back in the Correlation Analysis dialog box, click on the Multiple Regression tab.


(14) Set Time Series Group to the Group page containing your 84 scans (New Group).


(15) Set Input Model File to point to the Design Matrix file you created in step 11.


(16) Turn off Model Probability and Parameter Probability (we rarely use these). Leave Model F and r^2 and Parameter Estimate, t and Z-Score selected.


(17) Leave Apply Temporal Autocorrelation Correction selected. Change Hemodynamic Lag (secs) to 5, and TR (secs)** to 3. Then click on the OK button. This will cause Multiple Regression to be performed.




Return to Analysis 2: Multiple Regression

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