Update and rename fMRI_04_Preprocessing to fMRI_04_Preprocessing.rst

docs/fMRI_Short_Course/fMRI_04_Preprocessing → docs/fMRI_Short_Course/fMRI_04_Preprocessing.rst

@@ -6,6 +6,9 @@ fMRI Tutorial #4: Preprocessing
 =============
 
 
+.. note::
+  This chapter is much longer than the other chapters; to make it easier to read and to find what you need it is divided into sections detailing each preprocessing step. Many of the examples are run from the ``Flanker/sub-08`` directory; I recommend navigating to that directory with your Terminal before reading the rest of the chapter.
+
 Overview
 -------------
 
@@ -17,7 +20,9 @@ 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
+.. figure:: Before_After_Editing.png
+
+  A picture we take with a camera may be dark, blurry, or noisy (left panel). After cleaning up the image by enhancing contrast, reducing blur, and increasing brightness, we end up with a more defined and clearer picture.
 
 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.
 
@@ -46,9 +51,12 @@ We use the term **preprocessing** because we are trying to clean up the images a
 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:
+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 (window A, in the figure below). If you click on this button, another window opens that allows you to specify the Input image to skullstrip and the Output image that has been skullstripped (B), and a field an expandable sub-window that allows you to specify advanced options (C).
 
 .. figure:: FSL_BET_GUI.png
 
 
+.. note::
+  For BET and many of the other FSL tools, you are required to specify an input image and an output image: Some operation is operation on the input image (skullstripping, for example) and the output image is the result of that operation. Usually the other options are set to defaults that you can override.
+