Skull stripping CT

Hello Afni gurus-

I have been trying to use a few different pieces of your code (mostly trying to use some other imaging process in conjunction with 3dcalc) to skull strip a CT similar to what 3Dskullstrip does for MRIs. Most of my attempts have either left the temporalis or have included facial musculature/orbital anatomy attached to the brain. I was wondering if you have a method to do this leaving you with only the cerebrum that I dont know about? I apologize if this has previously been asked.


CT has some advantages over MRI regarding skullstripping. If your data is in standard Hounsfeld units, you can remove skull by intensity. To get brain only, you can then use something like 3dSkullStrip.

# take data only between intensities of 830-1300
3dcalc -a CT+orig'<830..1300>' -expr a -prefix CT_noskull
# get brain only
3dSkullStrip -prefix test_CT_ns -orig_vol -input CTnoskull3+orig.

If there has been surgery done, then that can be more complicated, and you may need to try some options like the “push_to_edge” or smoothing operations.

You could try:
Skull strip the T1.
Align T1 to CT (whole head).
Apply transformation to the stripped T1.
Use that as a mask on the CT.
I hope that makes sense.
We can help further if it doesn’t work.
Thanks, Justin

I published something about this a bit ago:

Essentially what we do is:

  1. Trim to 0-100 HU.
  2. Smooth the image a bit (1mm^3 gaussian) - not always necessary, but good idea depending on the convolution filter used on the CT (aka bone scans)
  3. Run Brain extraction tool (BET) with fractional intensity threshold to 0.01 - 3dSkullStrip implements a modified version of this (I believe this is shrink_fac in 3dSkullStrip)
  4. Fill some holes

Here’s example FSL bash code: