This tutorial will demonstrate how to create a mask of the functional activation within a region of interest. I used fsl and Ubuntu for this tutorial.

For each step (especially the first time creating a mask) it is suggested to open and quality check within fslview.

• Open Group level activation for condition desired in fslview
  • thresh_zstat#.nii.gz
  • Open on top of bg_image.nii.gz
• Add atlas in fslview
  • Tools –> Toolbars –> Atlas Tools
• Add structures desired from atlas
  • Click Structures… (under Atlas Tools box at bottom)
  • Choose Atlas
    • Cerebellar Atlas in MNI152 space after normalization with FNIRT
    • Choose Structures desired
    • Press “+” to add to Overlay Settings
    • Press Ok to close window when done choosing structures
    • The structures chosen will appear on the image and in the Overlay Settings box. These are the anatomical ROIs and the Intensity is displayed as a probability. For this tutorial, we want only the area in which the probability is above 50% and want the structure to be binary.
    • Increase Min to 50 if you would like to view the structure as it will look once thresholded
• Save the region as a mask
  • Be sure the correct structure is highlighted in Overlay Settings
  • File –> Save As… –> ReName_Structure_When_Saving
    • Choose a name for the structure that will be descriptive enough
    • Ex. For Right Amygdala, use mask-Ramy.nii.gz
  • Check the file type in your saved location. You want this to be nii.gz
    • If the file is .img or .hdr, change the file type
    • In the Terminal:
    • fslchfiletype [filename2]
    • Ex. fslchfiletype NIFTI_GZ mask-Ramy.img
• Treshold the newly created mask
  • In the Terminal:
    • fslmaths [filename2]
    • Ex. fslmaths mask-Ramy.nii.gz -thr 50 -bin mask-Ramy-b
    • -thr : threshold
      
    • -bin : binary
• If you would like to combine two structures (ie. Create mask for Right and Left amygdala and combine into one mask)
  • In the Terminal:
  • Fslmaths -add [filename2]
  • Ex. Fslmaths mask-Lamy-b.nii.gz -add mask-Ramy-b.nii.gz mask-BIamy
• Multiply the mask by the activation
  • This will allow the mask to take on the intensity of the activation
    fslmaths -mul [filename2]
  • Ex. Fslmaths thresh_zstat1.nii.gz -mul mask-Biamy.nii.gz mask-fia-biamy
    • fia: Functional In Anatomical
  • If you would also like to make this mask binary:
    • fslmaths -mul -bin [filename2]
    • Ex. Fslmaths thresh_zstat1.nii.gz -mul mask-Biamy.nii.gz -bin mask-fia-biamy-bin
• Run fsl-featquery.py to extract the information of this newly created mask from each individual participant
• This will output a csv that can be read and analyzed in R

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