2 min read

FreeSurfer: Skull-stripping

Despite recon-all might have ended without errors sadly this not guarantee that the process has been correctly done. From time to time you might spot mild errors such as segmentation or skull-stripping failures.

The most typical you will find are skull-stripping problems. That is, for some reason, the program failed in separating the brain from other tissues such as the dura or the skull.

These failures may translate into either (1) removing too little, or (2) removing too much skull. The most common of the two is, however, the former one.

IMPORTANT, please rememeber that, if neither the skull or the dura are inside the red ribbon then this is not a problem.

Note that, in the image below, part of the skull is within the limits of what is considered as pial-surface.

So, what’s next? First, copy the subject folder as a backup. This is usually done in case your editings make things even worse. Then, open the image with:

tkmedit your_subject brainmask.mgz -aux T1.mgz -surfs

Second, go to Tools > Configure Volume Brush Info…

Select Clone in the Mode eyelid, and in Clone source choose Aux Volume.

If you prefer to change the radius or the shape (this is, circle or square) of the brush you can go to Tools > Configure Brush Info…

Now, remember that by hitting the letter n you will enter into the navigation mode. Here, you will move through slices by pressing the mouse’s wheel and sliding back and forth. If while pressing right click you move the mouse you will zoom in and out the image. Instead, with the left click you will just move the image.

To enter editing mode just press the a key. Erase voxels by right-clicking on them. To clone voxels from the auxiliary volume (this is, the T1.mgz) just click the mouse’s wheel.

Beware, there’s nothing like CTRL and Z here. If you make a mistake, clone the voxels you accidentally removed.

Once you’re done with the editing, go to File > Save main volume… and that’s it. Close tkmedit and type the following to re-run the recon-all without the skull-stripping step, because you’ve already done this manually.

recon-all -s <subject_edited> -autorecon-pial 

NOTE: You can fix a bad skull-stripping via watershed modifications or the gcut tool. However, and in all my clumsiness, neither of these have ever done a good job for me. So perhaps you want to check the wiki by yourself and see how it works for you.