Applied Neurobiological Imaging, Dr. Katherine L. Narr

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Creating Results Figures Using SPM5

Written by Liberty Hamilton, October 18th, 2007. Email email lhamilto at loni dot ucla dot edu or email narr at loni dot ucla dot edu with questions.

This protocol assumes that you have already performed your basic data analysis in SPM5, including your basic models design and estimation of the data.

Start Up Matlab

  1. Start up matlab as before by typing matlab at the command prompt. If matlab and spm are installed on your local computer, you may run spm locally. Otherwise, you will have to run on one of the cerebro or cerebellum nodes (ask Rico).
  2. Type spm pet in the matlab terminal to start up SPM5 in the PET/SPECT mode (although we're not looking at PET data, we are using 4D data, so this option is most appropriate).

Viewing Results

  1. When Estimation is complete (you will see "Done" in the lower left window), you can run T- and F-contrasts to look at your data. Click the "Results" button to start, and select the SPM.mat file that was created in the Design Matrix step.


  2. Enter t-contrasts in the SPM contrast manager. First click the "t-contrasts" radio button, then click the button "Define new contrast...".
  3. Enter a name for the contrast (controls>patients, for example), and then type the contrast weights vector. Since controls are our first group, controls>patients would be [1 -1]. For patients>controls, you would enter [-1 1]. You can see your contrasts in the Design matrix image to the right. In the image below, you can see the first two columns represent patients and controls, and the following three columns are covariates.

    define contrast

  4. Click OK.
  5. Select "no" on masking with other contrasts.
  6. Select FDR and enter a value of 0.05. (Or select none, if your effect doesn't survive FDR). FWE (Family-wise Error) is the most conservative of the correction methods.
  7. Use the "volume" and "overlays" options to investigate results.

Viewing Your Results

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