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Tutorial: First-Level Within-Subject fMRI Processing and Analysis, using MEDx interactively

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on May 25, 2007 at 7:34:51 am

In this tutorial, you'll step through an within-subject first-level analysis of fMRI data very similar to what is done in the Holy Script, but in a non-automated interactive MEDx session. It may be useful to have on hand a copy of the NCSI 525 Data Analysis Lab Handout while going through this tutorial, just for the diagram on page 2. Work through steps 1 through 8 sequentially; and if you're feeling adventurous, go ahead and try step 9. Then finish off with steps 10 and 11.


  1. Set up
  2. Obtain data for tutorial via DICOM transfer
  3. Motion Correction
  4. Make a Mean Image Volume and Mask
  5. Linear Temporal Filtering
  6. Spatial Smoothing
  7. Spatial Normalization
  8. Analysis 1: Simple t-test (not yet done)
  9. Analysis 2: Multiple Regression (not yet done)
  10. Cluster Detection (not yet done)
  11. Overlays (not yet done)


In the above tutorial, I sometimes suggest looking at other tutorials in the Official Collection of MEDx Tutorials. Some of these Official Tutorials use sample data that is distributed with MEDx. On the CSL computers, type


cd $PXHOME/images



to see the sample data.

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