Skull strip the T1 image

By the end of this practical you should be able to complete preprocessing on your data with the following steps:

• use FSL's bet tool to remove the brain from a T1 image
  
• use FSLeyes to check the output of bet
  

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

In the terminal move to the folder where our downloaded data is:

• A the terminal prompt type: cd fmriLab
• Type ls and you should see the data you downloaded as a folder named flankerData_n4

Using FSL's brain extraction tool to skull-strip:

• At the prompt type fsl
• Click the "BET brain extraction" button on the FSL menu
• Steps to set up BET
  • Click the yellow folder to select your defaced T1 image with skull as your Input Image
  • FSL will automatically fill in the Output Image to have the same file name as your T1 with _brain at the end
  • Expand Advanced Options
    • Select Output binary brain mask image
  • Select Go to run BET
• Example default settings
  

Checking BET:

• Use the GUI menu to open your defaced T1 and brain mask in FSLeyes
• Use the Opacity slider to make the mask transparent so you can see the brain image in the background
• Checklist
  • Top of the brain: does the mask cover the brain and not spill into the eyes or skull?
  • Bottom of the brain: does the mask "hug" the brainstem or spill into the throat?

Modifying BET settings:

• Open or go back to the BET GUI
• An advanced option that always helps: Use the dropdown menu to select Robust brain centre estimation
• If your mask was too small or large at the top of the brain, change the Fractional intensity threshold
• If your mask was too small or large at either the top or the bottom of the brain, change the Threshold gradient