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. Set up your model using tabs for each explanatory variable (EV) like 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. Click Done when setup complete.
  

• After completing the Full model setup you will get your task model!
  

• 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.
  

• 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/flankerData_n4/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 stats/zstat3
  • In the fsleyes menu, select View -> Layouts -> FEAT mode
  • 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. Give it a try!

* Once you've completed all the steps above for `sub-001`, repeat for `sub-002` and `sub-003`. Example PDFs for their FEAT activation reports will be on our course ICON site. Before next class, you should have statistical maps for the same contrasts, in the **same** order, for both subjects.