Group analysis

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

• use the FEAT GUI to create a group-level map of task-related BOLD activation
  
• locate and understand results using the html reports and fsleyes
  

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

Prerequisite: Before you start group analysis, you should have flanker.feat output folders that you created for sub-001, sub-002, and sub-003.

Group analysis GUI: Our group analysis will determine the average activation across subjects for each of our contrasts that we made within-subjects (e.g., con>baseline, neu>baseline, inc>baseline, errors>baseline, inc>nue, con>neu).

• In terminal, move yourself to your data folder by typing cd ~/fmriLab/
• Type fsl and click on FEAT FMRI analysis
• In the top-left menu, select Higher-level analysis:
  

Set input and output on Data tab:

• Keep default of Inputs are lower-level FEAT directories
• Keep Number of inputs to 3, because we have 3 subjects
• Click to Select FEAT directories and select each of your flanker.feat folders:
  

• Keep Use lower-level copes as default, these are the six contrasts we set for the single-subject analyses
• Specify output directory to be in derivatives with the name group_n3:
  

Setup group model on Stats tab:

• Select Fixed effects, which computes an average generalizable to only this set of participants. This is most appropriate if you have less than 10 subjects.
• Select Model setup wizard and keep the default of single-group average and click Process:
  

Our group model: Now what does the red line represent?

Post-stats tab: all settings here can stay as default.

Click Go:

• An html output report will come up in your browser, or you can find it in the output folder you specified
• Once done, navigate to Results and click on Lower-level contrast 3 (inc)
• You should see the map below:
  

• Click on the image in the html report, let's talk about the table you see below:
  

• Just like with single-subject analyses, we can also use fsleyes 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: e.g., cd ~/fmriLab/flankerData_n4/group_n3.gfeat/cope3.feat/
  • Open fsleyes through the terminal with settings for viewing FEAT output: fsleyes -ad /opt/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz thresh_zstat1.nii.gz
  • Change your color scale to orange->yellow
  • Show your cluster table by selecting: View-> Layouts -> FEAT Mode
  • 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.
  • See information from neuroanatomy atlases by selecting: Settings -> Ortho View 1 -> Atlas panel
  • You should see a display like below in fsleyes.

For your next fMRI task analysis technical assignment, you will need to complete the single-subject task analysis for sub-004 and create a new group analysis that includes all subjects in your dataset (sub-001, sub-002, sub-003, sub-004)