Creating Masks In FSL

Due to a high number of requests (three), I have made some walkthroughs about how to create masks in FSL. There are a few different ways to do this:

  1. Anatomical ROI: These masks are generated from anatomical regions labeled by atlases. For example, you may decide to focus only on voxels within the V1 area of visual cortex. Using an atlas will create a mask of that region, based on the atlas-defined anatomical boundaries in a standardized space.
  2. Functional ROI (or contrast ROI): This is a mask created from a contrast thresholded at a specific statistic value. For example, you may wish to focus only on voxels that pass cluster correction for the contrast of left button presses minus right button presses.
  3. Painting ROIs: This is where the real fun starts; instead of being confined by the limitations of anatomical or contrast boundaries, let your imagination run wild and simply paint where you want to do an ROI analysis. Similar to what you did in first grade, but more high-tech and with less puking after eating your crayons. (Is it my fault that Razzmatazz Red sounds so delicious?)
Demonstrations of each approach can be found in the following videos:

 Anatomical ROIs

Functional ROIs

 ROIs created from FSLview. Pretend like you're Bob Ross.