Update fMRI_04_Preprocessing

docs/fMRI_Short_Course/fMRI_04_Preprocessing

@@ -17,8 +17,9 @@ Think of preprocessing as cleaning up images. When you take a photo with a camer
 * Increase color saturation;
 * Remove shadows.
 
+.. Show a picture illustrating what this looks like with a real photo
 
-Similarly, when we preprocess fMRI data we are cleaning up the 3-dimensional images that we acquire every TR.
+Similarly, when we preprocess fMRI data we are cleaning up the 3-dimensional images that we acquire every TR. An fMRI volume contains not only the signal that we are interested in - changes in oxygenated blood - but also signals that we are not interested in, such as head motion, random drifts, breathing, and heartbeats. We call these other signals **noise**, since we want to separate them from the signal that we are interested in. Some of these can be regressed out of the data by modeling them (discussed later), whereas others can be reduced or removed by preprocessing.
 
 
 Preprocessing Steps
@@ -35,4 +36,19 @@ The major preprocessing steps are:
 * Normalization
 
 
-Different software packages will do these steps in slightly different order - for example, FSL will do normalization after the statistical model has been fit. There are also some analyses which omit certain steps - for example, people who do multi-voxel pattern analyses sometimes will not do smoothing. In any case, these represent the most common steps that are performed on a typical dataset.
+.. note::
+  Different software packages will do these steps in slightly different order - for example, FSL will normalize the statistical maps after the model has been fit. There are also analyses which omit certain steps - for example, some people who do multi-voxel pattern analyses don't smooth their data. In any case, the list above represents the most common steps that are performed on a typical dataset.
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+
+We use the term **preprocessing** because we are trying to clean up the images as best we can before fitting a model to the data. Once it has been processed, we can fit a statistical model and make claims about which conditions lead to changes in oxygenated blood.
+
+
+Brain Extraction (or "skull stripping")
+^^^^^^^^^^
+
+Since fMRI studies focus on brain tissue, our first step is to remove the skull and non-brain areas from the image. FSL has a tool for brain extraction called **bet**, or the Brain Extraction Tool. It is the first button listed on the FSL GUI:
+
+.. figure:: FSL_BET_GUI.png
+
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+