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BIAC TOOLS

Loading an image into a variable

Viewing an image

Calculating a Difference Image

If we are worried about checking an image for excessive motion, then we should calculate a difference image using showsrs2 in matlab. To calculate a difference image:

temp = readmr('functionalfilename.nii');

What are we looking for? A difference image basically calculates the “difference” between each image, and shows the change as various shades of grey. So, if we see a single, opaque sheet of grey, this means that there is no change from one slice to the next, meaning that there was no motion, and we are good! Seeing an outline of a brain, or anything that isn’t matte grey, means that there was motion/change from one slice to the next, and this isn’t good. FSL uses McFlirt to correct for motion, and can handle small amounts of it in any direction. However, what it doesn’t like is huge changes that completely reorient the brain, like a drastic twist. We could see something like this with the difference image.