Produce Functional Activation within Anatomical Mask- fMRI

November 23, 2018   

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 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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