If you're doing a nonlinear warping, then having bits of the skull remain or parts of the brain missing is fairly problematic...

Things that I've found somewhat useful, if you have a particularly dark image or non-uniformities, you can try 3dUnifize before 3dSkullStrip. You can also use optibet (script). I've written a rough script that uses the same idea of optibet, but with AFNI-only tools below that you're welcome to.

Finally if none of those seem terribly good (though optibet tends to work well for me), the Freesurfer skull stripping as part of their pipeline works quite well. I have a few projects that use the brain.nii file coming out of the Freesurfer followed by @SUMA_Make_Spec_FS with decent results.

#!/bin/bash

# based off procedures in:
# Lutkenhoff, E. S., Rosenberg, M., Chiang, J., Zhang, K., Pickard, J. D., Owen, A. D., & Monti, M. M. (2014).  Optimized Brain Extraction for Pathological Brains (optiBET).  PLOSone 9(12): e115551.  DOI:10.1371/journal.pone. 0115551.  

# ---------------------------- OUTLINE ------------------------------
# 1. SkullStrip with 3dSkullStrip
# 2. Warp to MNI space with @auto_tlrc and/or 3dQwarp
# 3. Back-project brain only-mask from +tlrc to +orig
# 4. Mask out brain tissue with back-projected brain-only mask
# -------------------------------------------------------------------

if [ $# -lt 2 ]; then
	echo "@optiSS.sh"
	echo "USAGE: optiSS.sh <input> <output> <options>"
	echo "<options> not currently implemented. Sorry!"
	exit;
fi

if [ -e $2 ]; then
	echo "Final file $2 already exists.  I cannot overwrite it."
	exit;
fi

afnidirtemp=`which 3dSkullStrip`
afnidir=`echo $afnidirtemp | awk -F "3dSkullStrip" '{print $1}'`

# ---------------------------- STEP 1: Extraction ------------------------------
echo "Step 1: SKull Strip & Unifize"
3dSkullStrip -prefix tmp.s0 -input $1 -orig_vol
3dUnifize -prefix tmp.s1 -input tmp.s0+orig -GM 

# ---------------------------- STEP 2: Warp to MNI ------------------------------
echo "Step 2: Affine warp to Template"
@auto_tlrc -base MNI152_T1_2009c+tlrc.HEAD -input tmp.s1+orig -no_ss 

# ----------------------- STEP 3: Nonlinear Warp to MNI -------------------------
echo "Step 3: Nonlinear Warp to Template"
3dQwarp -base ${afnidir}/MNI152_T1_2009c+tlrc.HEAD -source tmp.s1+tlrc -prefix tmp.s3 \
-pblur -maxlev 3

# ----------------------- STEP 4: Nonlinear Warp to MNI -------------------------
echo "Step 4: Create Mask of Template"
3dAutomask -prefix tmp.s4.mask ${afnidir}/MNI152_T1_2009c+tlrc.HEAD

# ----------------------- STEP 5: Nonlinear Warp to MNI -------------------------
echo "Step 5: Invert warp and put template in subject space"
3dNwarpApply \
-prefix tmp.s5.TT_in_subject \
-source tmp.s4.mask+tlrc \
-nwarp 'tmp.s3_WARP+tlrc.HEAD tmp.s1.Xaff12.1D' \
-iwarp \
-master tmp.s1+orig \
-interp NN

# ------------------ STEP 6: Mask original image by warp ------------------------
echo "Step 6: AND the maps of template and original image"
3dcalc -a 'tmp.s0+orig.HEAD' -b 'tmp.s5.TT_in_subject+orig' -expr 'a*b' -prefix $2

# ------------------ STEP 7: Cleanup ------------------------
echo "Step 7: Delete temporary files"
rm tmp.*

Edited 2 time(s). Last edit at 08/23/2016 08:32AM by Peter Molfese.