Update fMRI_04_Preprocessing.rst

docs/fMRI_Short_Course/fMRI_04_Preprocessing.rst

@@ -51,12 +51,23 @@ 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 this 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 an expandable sub-window that allows you to specify advanced options (C).
+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 this called **bet**, or the Brain Extraction Tool (along with a newer version called ``bet2``). 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 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 performed 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 work well for the majority of datasets, but which you can override if you want.
+
+
+If you launched the FSL GUI from the ``sub-08`` directory, click on the Folder icon next to the ``Input image`` field and navigate to the ``anat`` directory. Select the file ``sub-08_T1w.nii.gz`` and click the OK button. Notice that the ``Output image`` field is automatically filled in with the word ``brain`` appended to your Input image. This is FSL's default, but you can change the name if you like. For this tutorial, we will leave it as is.
+
+Now click the ``Go`` button at the bottom of the window. You will see some text written to your Terminal showing which commands are being used to run ``bet2``. It is important to understand how the GUI corresponds to the Terminal - later on we will take advantage of this by creating template through the GUI and then modifying that template in the Terminal and automating it to preprocess all of the subjects in our dataset.
 
+When the Terminal says "Finished", ``bet2`` is done. Now is a good time to **look at your data**, which we will do after each preprocessing step.
+
+.. warning::
+  Newcomers often hear the phrase "Look at your data" intoned like a mantra. Without knowing how to look at one's data, the words become meaningless at best, a false comforter at worst. Each of the preprocessing steps in this chapter will be followed by recommendations of what to look for and concrete examples of what is OK and what is a problem - and what to do about it. Although we cannot cover every possible example, as you gain experience you will develop your judgment of what is Good, what is Passable, and what is Bad.
+
 
+Click on the ``FSLeyes`` button at the bottom of the GUI. When it opens, click on ``File -> Add from File`` and hold shift to select both the original anatomical image and the skullstripped image you just created. As you saw in the `previous chapter <fMRI_03_LookingAtTheData>`, you will want to change the contrast to clearly distinguish the grey from the white matter.