https://www.ccn.ucla.edu/wiki/index.php?action=history&feed=atom&title=MR%3AProcessing%3APreprocessing%3AManualSkullStrippingMR:Processing:Preprocessing:ManualSkullStripping - Revision history2026-05-06T04:01:20ZRevision history for this page on the wikiMediaWiki 1.43.6https://www.ccn.ucla.edu/wiki/index.php?title=MR:Processing:Preprocessing:ManualSkullStripping&diff=1404&oldid=prevCcn admin: 5 revisions2014-01-16T03:43:17Z<p>5 revisions</p>
<p><b>New page</b></p><div>[[File:skullstrip.jpg|thumb|Locations of buttons important to mask editing]]<br />
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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.<br />
<br />
=Setup=<br />
*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<br />
*Overlap the mask over the anatomical image, reducing the opacity of the mask so both can be seen<br />
*Unlock the mask by clicking the box by the lock icon (left of the opacity slider) - this allows the Mask Tool to be used<br />
*Select the Mask Tool from the toolbar<br />
<br />
=Fixing the mask=<br />
*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<br />
**It is often more efficient to pick the plane with the fewest slices<br />
*Continue to the next slice, using the PageUp and PageDown keys to navigate slices<br />
*Check the other planes to confirm that the corrected mask is okay<br />
**A manually edited mask will not look perfectly smooth in all planes - that is fine!<br />
*Save the new mask (<struct>_brain_mask_corrected.nii.gz)<br />
<br />
=Creating the new skull strip=<br />
*Use fslmaths to multiply the corrected mask by the original anatomical image with the following command:<br />
$ fslmaths <struct>.nii.gz -mul <struct>_brain_mask_corrected.nii.gz <struct>_brain_corrected.nii.gz<br />
*Check that <struc>_brain_corrected.nii.gz is correct in fslview</div>Ccn admin