Analysis 1: Simple t-test

(1) To do this analysis, you'll need to separate your scans into Fix, RealWord, and FalseFont groups. An easy way to do this is to use a Paradigm File. Download the Paradigm File for the IR1 task here, and save it into your tutorial directory.

If you're analyzing data for which a Paradigm File has already been defined, you can just re-use the same Paradigm File. But when you're setting up a new fMRI experiment with a new paradigm, you'll need to define a new Paradigm File. See Creating a Paradigm File for further information on how to do this.

(2) Open up a new MEDx session, and then open up a New Folder.

(3) Load the Mask image that you created in step 12 of Spatial Normalization (the one named SnMask.hdr.

(4) Also load the 84 spatially normalized, spatially smoothed, temporally filtered, motion-corrected image volumes which you created in the Spatial Normalization step. You should now be looking at a Group page showing the 84 spatially normalized scans. The name of the Group page should be New Group.

(5) Select Toolbox --> Functional --> Define Paradigm.

(6) In the Paradigm Editor window, click on the Apply Paradigm button.

(7) In the Apply Paradigm dialog box, in the Filter entry box, type in the tutorial directory, followed by *.pdgm, e.g.

and then click on the Filter button. This will cause the IR1 Paradigm File to be listed in the Files: pane. Select this file, then click on the Ok button. This will cause the IR1 paradigm information to be applied to the 84 scans.

(8) Select Page --> Page Manager..., and in the Page Manager window click on the Groups radiobutton. This will cause only Group pages to be listed. Note that in addition to the original New Group group page, you now have four new groups: Fix, RealWord, FalseFont, and All. Select Fix, and then click on the GoTo button. Note that this takes you to a new page in the MEDx folder named Fix, and that it lists the subset of 28 images that correspond to the Fix task.

(9) OK, let's do the t-test. Select Toolbox --> Functional --> Group Statistics....

(10) In the Group Statistics dialog box, click on the Between Groups tab.

(11) Set Test Group to RealWord, and Control Group to FalseFont.

(9)

stand-alone MEDx tutorial.

This tutorial actually covers many useful MEDx features, and is highly recommended. The only caveat is that it uses an obsolete (I wouldn't even say that it was ever really kosher) statistical method implemented in MEDx, called Critical Threshold, found under Toolbox --> Functional --> Final Significance --> Critical Threshold. Don't use this method. Use Cluster Detection (also under Final Significance) or False Discovery Rate (not implemented in MEDx, but implemented outside of MEDx in my own C code, and also implemented in SPM).

For some information on creating a paradigm file, see Creating a Paradigm File.

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