====== Setting up FSL ======

  * For reference, the FSL-FEAT analysis **guide** is available at [[http://www.fmrib.ox.ac.uk/fsl/feat5/]]
  * A **glossary** containing descriptions of the output files from FSL-FEAT is available at [[http://www.fmrib.ox.ac.uk/fsl/feat5/index.html]]
  * **For this exercise, you'll need to open the command terminal on the Mac and this can be done by going up to "Utilities" and selecting "Terminal". You'll open FSL via this terminal, and you'll move/copy files in this command window. You'll also use MATLAB for one part of the exercise, so go ahead and open that as well. DO NOT USE THE XTERM TERMINAL THAT OPENS WITH MATLAB.**

===== Organizing Your Data =====
** Note that on Linux/Unix systems, capitalization matters! Make sure that you correctly capitalize directory and file names. Also note that you only have write access in the "classwork" folder, so you won't be able to direct output or make new files/folders elsewhere.**


  * In /afs/acpub/project/neurobio381/classwork/Fall_2008/Students create a folder for yourself (e.g., ''mkdir yourfoldername'').  It is helpful to keep open an explorer window, and the easiest way to do this will be to double-click on the **classwork** icon on your desktop. You should be able to navigate to your folder from there.
  * From /afs/acpub/project/neurobio381/datasets/Class.01/Examples __COPY, DO NOT CUT!!!__ **ANAT_4** and **FUNC_4/Run1_Block** and paste them in your folder, renaming them **Anat** and **Func**. These are pretty big, so it may take a minute or two.
<code bash>
cp -r /afs/acpub/project/neurobio381/datasets/Class.01/Examples/ANAT_4 /afs/acpub/project/neurobio381/classwork/Fall_2008/Students/David/Anat
cp -r /afs/acpub/project/neurobio381/datasets/Class.01/Examples/FUNC_4/RUN1_Block /afs/acpub/project/neurobio381/classwork/Fall_2008/Students/David/Func
</code>

  * Create a new folder called **FSL** in your folder 


=====Preparing Your Data for Analysis=====
Before we do any processing on our data, we have to [[http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1090|reorient the the data into LAS]] and convert it from our unique BIAC format (e.g., xml headers with .img files) to [[http://nifti.nimh.nih.gov/nifti-1/|NIFTI]] format. This is easily done with a BIAC tool called **bxh2analyze**; however, this has all been done for you in this lab and it will be done for the data you acquire later this semester.

=====Extracting the Brain=====
**This removes the surrounding skull and tissue from the anatomical images.**
  - First make sure you're in the directory you created.
  - In your command terminal type: **fsl &**
  - This will bring up a GUI, click **BET brain extraction**. [[http://www.fmrib.ox.ac.uk/analysis/research/bet/bet.pdf|This tool will allow you to remove non-brain material.]]
  - For the input image select the **anat.nii.gz** file, which is in the the Anat folder you made. The output image will autmatically be called anat_brain
  - Fractional intensity should automatically be set to .5 (smaller == more conservative)
  - **Run standard brain extraction using bet2** should be the option that is automatically selected checked.
  - Click **Go**.
  - This should take about 20 seconds to run. When it finishes, you will have a new file in the Anat directory: "anat_brain.nii.gz". You should view this file in MATLAB using **showsrs2**, to see the effects of brain extraction (e.g., ''anatb=readmr('anat_brain.nii.gz')'')


====== Running FSL Analyses ======
** We'll begin with a first-level analysis (i.e., on only one run of one subject's data). To save time, we'll split this into two parts: 1.) preprocessing and 2.) stats**
  - Move (don't just copy) the run1.nii.gz file (which is in the Func folder you made) into the FSL folder. Also move the anat_brain.nii.gz file into that folder.

<code bash>
mv /afs/acpub/project/neurobio381/classwork/Fall_2008/Students/David/Func/run1.nii.gz /afs/acpub/project/neurobio381/classwork/Fall_2008/Students/David/FSL/run1.nii.gz
mv /afs/acpub/project/neurobio381/classwork/Fall_2008/Students/David/Anat/anat_brain.nii.gz /afs/acpub/project/neurobio381/classwork/Fall_2008/Students/David/FSL/anat_brain.nii.gz
</code>

  - In the command terminal, change into your FSL folder (e.g., ''cd where_ever_you_want_to_go'').
  - If FSL is not already open, type **fsl &** and click **FEAT FMRI Analysis** in the GUI. Just click once; it will take a few seconds to appear.
  - Go to this webpage - [[http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html]] - and follow along to read about each setting you are changing


===== FSL GUI settings: Preprocessing =====
  - **Pull-down menus**
    * At top, the left menu should read **First-level analysis**. The right menu should read **Full analysis**. You need to change this right menu to **Pre-stats**. You'll notice the "Stats" and "Post-Stats" tabs will be grayed out now.
  - **Misc** tab
    * Click on this tab. You should leave everything on this tab at the default settings.
  - **Data** tab
    * Click on this tab, next.
    * Make sure that **Number of Analyses** is set to **1**. 
    * Click **Select 4D Data** and select the **run1.nii.gz** file that you copied into the FSL folder earlier. Click **OK** twice, ignoring any error messages at this stage.
    * Click **Select Output Directory**, type "prestats" into the selection box, and click **OK**. 
    * Check to make sure your **Total volumes** is set to **131** (should have changed when you selected your func data)
    * Set the **TR(s)** to **2**. This is your repetition time (TR) in seconds.
    * You shouldn't have to change anything else. The defaults should be correct: **Delete Volumes = 0, High-Pass Filter cutoff (s) = 100**.
  - **Prestats** Tab 
    * **Motion correction** should be **MCFLIRT** -- [[http://www.fmrib.ox.ac.uk/analysis/techrep/tr02mj1/tr02mj1.pdf|This will remove rigid motion from the time series]]
    * **B0 unwraping** should be unchecked (gray)
    * **Slice timing correction** should be **Interleaved**
    * **BET brain extraction** should be checked (yellow) -- This is doing BET on the functional data. You did it on the anatomical earlier.
    * **Spatial smoothing** should be set to **8mm**
    * **Intensity normalization** should be unchecked (gray)
    * **Temporal filtering** should be **Highpass**
    * **Melodic ICA** should be unchecked (gray).
  - **Registration** Tab
    * **Standard space** should already be checked, with the file **/usr/local/fsl/data/standard/MNI152_T1_2mm_brain**, **Normal Search**, and **12 DOF**.
    * Click the **Main structural image** checkbox. Select your **anat_brain.nii.gz** file and then click **OK**. You should have **Normal Search** and **7 DOF** selected automatically.


Now click **Go** in the lower left of the GUI and prestats will start running. This will take about 15-20 minutes. 


===== FSL GUI settings: Stats =====

==== Step 1: Setting up your timing files ====

This is the part of analysis where you specify what happened in the experiment. For your reference, here is the description of the experimental paradigm:

**A static checkerboard is displayed for the first two TRs (4s).  Alternating blocks begin with the third TR.  The first block displays a flashing checkerboard for 10 TRs (20s).  The second block displays a static checkerboard for 10 TRs (20s).  This set of flashing/static blocks is repeated six times.  After the final static block, another 6 TRs (12s) of flashing checkerboard appeared before the run ended.**

You need to create a **three-column text file** that describes your experimental paradigm. Each line of the file consists of three values, separated by tabs. 
  * The three columns are: **Start of event (seconds)**, **Duration of event (seconds)**, and **Intensity of event**. 
  * So, for the first row of the text file, we could use: 
<code>4     20       1</code>
  * You need to create a text file that has seven rows, each corresponding to one of the blocks of visual stimuli. Save this file in your **FSL** directory as **block_3col.txt**.

<code bash>
#from within your FSL directory
touch block_3col.txt
open -a TextEdit block_3col.txt
</code>




==== Step 2: Setting up your Design in FSL====

  - **Pull-down menus**
    * At top, the left menu should read **First-level analysis**. The right menu should read **Pre-stats**. You need to change this right menu to **Stats + Post-stats**. You'll notice the "Pre-Stats" tab will be grayed out now.
  - **Misc** tab
    * Click on this tab. You should leave everything on this tab at the default settings.
  - **Data** tab
    * Click on this tab, next.
    * Make sure that **Number of Analyses** is set to **1**. 
    * Click **Select 4D Data** and select the **filtered_func_data.nii.gz** file that was created in the preprocessing step. This file will be located in the output directory from the preprocessing step (e.g., prestats.feat)
    * Click **Select Output Directory**, type "stats" into the selection box, and click **OK**. 
    * Check to make sure your **Total volumes** is set to **131** (should have changed when you selected your func data)
    * Set the **TR(s)** to **2**. This is your repetition time (TR) in seconds.
    * You shouldn't have to change anything else. The defaults should be correct: **Delete Volumes = 0, High-Pass Filter cutoff (s) = 100**.
   - Stats Tab
    * **Use FILM prewhitening** should be checked. [[http://www.fmrib.ox.ac.uk/analysis/techrep/tr01mw1/tr01mw1.pdf|This prewhitens and and does an AR(1) correction]].
    * **Add motion parameterers** should be **No**
    * To set up the design, click on **Full model setup**. 
    * In this experiment, only one thing happens: a checkerboard flashes. So, we only need one **Explanatory Variable (EV)**. Type **Flash** into the **EV name** field.
    * On the **Basic shape** pull-down menu, select **Custom (3 column format)**. When the **Filename** box pops up, select the **block_3col.txt** file that you just created.
    * On the **Convolution** pull-down menu, select **Double-Gamma HRF**. Leave **Phase** at **0** seconds. 
    * **Add temporal derivative** should be unchecked (gray).
    * **Apply temporal filtering** should be checked (yellow).

You can now click on **View Design**, and you should see something that looks like the predicted hemodynamic changes that should follow alternating blocks of activation and deactivation. Close the window that just popped up (not your main FSL window), and hit "Done".

  - Post-Stats Tab
    * The key part of this is **Thresholding**. From left to right, it should read **Cluster**, ** Z Threshold 2.3**, and **Cluster P threshold 0.05**.
  - Registration Tab
    * **Standard space** should already be checked, with the file **/usr/local/fsl/data/standard/MNI152_T1_2mm_brain**, **Normal Search**, and **12 DOF**.
    * Click the **Main structural image** checkbox. Select your **anat_brain.nii.gz** file and then click **OK**. You should have **Normal Search** and **7 DOF** selected automatically.


Now click **Go** in the lower left of the GUI and stats will start running. This will take about 5-10 minutes.




===== Looking at your FSL analyses =====
  * FSL creates HTML pages for your output; these can be viewed in Internet explorer or any other browser.
  * Both of the analyses above should have opened webpages to which FSL will write its summary output.
  * In the **Prestats** output, you will be able to see how much the subject moved (i.e., how much the data was adjusted). You can also check the registration to make sure the images were normalized properly
  * In the **Stats** output, you can see the results in the post-stats tab and the model you specified in the stats tab.