Single subject (first‐level) task analysis

By the end of this practical you should be able to:

• create and understand a model of task-related BOLD signal in the FEAT GUI
  
• understand how to test for activation differences between conditions
  
• locate and view the activation maps in fsleyes
  

Access FastX through the remote login:
https://fastx.divms.uiowa.edu:3443/

Create model of task-related BOLD signal in FEAT:

• In terminal, move yourself to your data folder cd ~/fmriLab/

• Type fsl and click on FEAT FMRI analysis

• Now instead of Preprocessing select Statistics in the drop-down menu at the top, like so:

• Then select Input is a FEAT directory and navigate to sub-001's flanker.feat directory:

• Move to the Stats tab, first turn on Add additional confound EVs and then select the outliers.txt file in your beh folder as shown:
  

• Next, click on Full model setup. We will walk through set up of this as a class, including a closer look at the structure of the input text files. However, for reference, tabs for each explanatory variable (EV) should look like what is shown below:
  

EV1:

EV2:

EV3:

EV4:

• After setting up the EVs, stay in the Full model setup window and go to the Contrasts & F-tests tab. Set up the contrasts as below, and we will discuss what this means. Click Done when setup complete.
  

• After completing the Full model setup you will get your model! Let's walk through it to understand the figure.
  

• The last tab in the FEAT GUI is Post-stats. We will leave the defaults on for now. The settings here are most relevant when we get to group-level analyses.

• Click Go. When it's finished, the results will appear within your flanker.feat directory. Your html report will then include output of brain activation maps as previewed below. We will walk through the contents of the report in class.
  

• Using fsleyes will allow us to view the results more interactively:

  • Use the html report to locate the directory where the activation maps are on your computer
  • Use the terminal to move yourself there: cd ~/fmriLab/data/bids/derivatives/sub-001/func/flanker.feat
  • Open fsleyes through the terminal with settings for viewing FEAT output: fsleyes -ad filtered_func_data.nii.gz stats/zstat1 stats/zstat2
  • You should see a display like below in fsleyes. Clicking on the buttons with arrows in the column labeled Z Max location will move your cursor to the location of that peak in brain activation. With this interactive table open, you can also view your activation maps using the Lightbox view we previewed when learning about fsleyes. Give it a try!

* Once you've completed all the steps above for `sub-001`, repeat for `sub-002`. Before next class, you should have statistical maps for the same contrasts, in the **same** order, for both subjects.