MR:Processing:Preprocessing:ManualSkullStripping

File:Skullstrip.jpg

Locations of buttons important to mask editing

Sometimes, a fidgety subject may result in anatomical scans that don't undergo skull stripping by BET or betfunc2 correctly. Fortunately, manually editing a failed skull strip is very easy to do using fslview.

Setup

• Open up the anatomical image (<struct>.nii.gz) and the incorrect mask (<struct>_brain_mask.nii.gz) in fslview - a corrected mask will be used to create a new skull strip
• Overlap the mask over the anatomical image, reducing the opacity of the mask so both can be seen
• Unlock the mask by clicking the box by the lock icon (left of the opacity slider) - this allows the Mask Tool to be used
• Select the Mask Tool from the toolbar

Fixing the mask

• Beginning from the first slice of any plane, edit the mask using the pen, eraser, and fill tools to properly reflect areas containing brain matter
  • It is often more efficient to pick the plane with the fewest slices
• Continue to the next slice, using the PageUp and PageDown keys to navigate slices
• Check the other planes to confirm that the corrected mask is okay
  • A manually edited mask will not look perfectly smooth in all planes - that is fine!
• Save the new mask (<struct>_brain_mask_corrected.nii.gz)

Creating the new skull strip

• Use fslmaths to multiply the corrected mask by the original anatomical image with the following command:

$ fslmaths <struct>.nii.gz -mul <struct>_brain_mask_corrected.nii.gz <struct>_brain_corrected.nii.gz

• Check that <struc>_brain_corrected.nii.gz is correct in fslview