Tuesday, April 30, 2013

SPM Tutorial: Creating Contrast Images

Those of you who have ever entered a string of ones and negative-ones in SPM's contrast manager were creating contrast images (simultaneously converted into T-maps or F-maps), whether you knew it or not. It can be difficult to see exactly what is going on, but as part of creating a statistical map, SPM calls upon its mathematical tool, spm_imcalc_ui (or just spm_imcalc; but I find spm_imcalc_ui easier to understand and to use, and therefore I will focus on it).

While using the contrast manager is useful for creating relatively simple single-subject maps, you may want to then create images from those simpler images; for example, let's say you have created functional connectivity maps, but want to take the difference between two of those maps and feed the resulting contrast map into a second-level analysis. spm_imcalc_ui allows you to do this easily, and can be scripted, saving you precious time to do more important things, like take pictures of that cucumber salad sandwich or whatever you're eating and load it onto Twitter.

spm_imcalc_ui requires at least three inputs:

  1. A matrix of input filenames;
  2. An output file;
  3. A mathematical operation to perform on the input images.

As a simple example, let's say we use the contrast manager to create two contrast images, con_0001.img and con_0002.img. Let's then say that we want to take the difference of these image to use in a second-level analysis. First, it is usually easier to assign a variable name to each file:

P1 = 'con_0001.img'; P2 = 'con_0002.img'

And then input these into spm_imcalc_ui:

spm_imalc_ui([P1; P2], 'outputImage.img', 'i1-i2'

Note that the third argument, i1-i2, calls upon reserved SPM keywords, i.e., "i1" and "i2". i1 refers to the first input image, i2 refers to the second input image, and so on.

That's really all there is to it; and from this example you can simply add more images, and perform more complex operations if you like (e.g., make one an exponent of the other, i1.^i2). Furthermore, when you have several runs, using the contrast manager can quickly become unwieldy; you can use the contrast manager to first create an image for a single regressor by positively weighting only those betas in each run corresponding to your regressor, and then when these images are created, use spm_imcalc_ui to make your contrast images. As stated previously, this allows for more flexibility in scripting from the command line, potentially saving you thousands of man-hours in cucumber-sandwich-photo-taking endeavors.

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