Module Detail Information

Name:3D SkullStrip
Type: Module
Short URL:
http://bit.ly/1C54ScS
Description:A program to extract the brain from surrounding tissue from MRI T1-weighted images. The fully automated process consists of three steps: 1. Preprocessing of volume to remove gross spatial image non-uniformity artifacts and reposition the brain in a reasonable manner for convenience. 2. Expand a spherical surface iteratively until it envelopes the brain. This is a modified version of the BET algorithm: Fast robust automated brain extraction, by Stephen M. Smith, HBM 2002 v 17:3 pp 143-155 Modifications include the use of: Outer brain surface Expansion driven by data inside and outside the surface Avoidance of eyes and ventricles. A set of operations to avoid the clipping of certain brain areas and reduce leakage into the skull in heavily shaded data. Two additional processing stages to ensure convergence and reduction of clipped areas. Use of 3d edge detection, see Deriche and Monga references in 3dedge3 -help. 3. The creation of various masks and surfaces modeling brain and portions of the skull. Common examples of usage: 3dSkullStrip -input VOL -prefix VOL_PREFIX Vanilla mode, should work for most datasets. 3dSkullStrip -input VOL -prefix VOL_PREFIX -push_to_edge Adds an agressive push to brain edges. Use this option when the chunks of gray matter are not included. This option might cause the mask to leak into non-brain areas. 3dSkullStrip -input VOL -surface_coil -prefix VOL_PREFIX -monkey Vanilla mode, for use with monkey data. 3dSkullStrip -input VOL -prefix VOL_PREFIX -ld 30 Use a denser mesh, in the cases where you have lots of csf between gyri. Also helps when some of the brain is clipped close to regions of high curvature. Tips- I ran the program with the default parameters on 200+ datasets. The results were quite good in all but a couple of instances, here are some tips on fixing trouble spots: Clipping in frontal areas, close to the eye balls: Try -push_to_edge option first. Can also try -no_avoid_eyes option. Clipping in general: Try -push_to_edge option first. Can also use lower -shrink_fac, start with 0.5 then 0.4 Problems down below: Piece of cerbellum missing, reduce -shrink_fac_bot_lim from default value. Leakage in lower areas, increase -shrink_fac_bot_lim from default value. Some lobules are not included: Use a denser mesh. Start with -ld 30. If that still fails, try even higher density (like -ld 50) and increase iterations (say to -niter 750). Expect the program to take much longer in that case. Instead of using denser meshes, you could try blurring the data before skull stripping. Something like -blur_fwhm 2 did wonders for some of my data with the default options of 3dSkullStrip. Blurring is a lot faster than increasing mesh density. Use also a smaller -shrink_fac is you have lots of CSF between gyri. Massive chunks missing: If brain has very large ventricles and lots of CSF between gyri, the ventricles will keep attracting the surface inwards. In such cases, use the -visual option to see what is happening and try these options to reduce the severity of the skull: -blur_fwhm 2 -use_skull Eye Candy Mode- You can run BrainWarp and have it send successive iterations to SUMA and AFNI. This is very helpful in following the progression of the algorithm and determining the source of trouble, if any. Example: afni -niml -yesplugouts & suma -niml & 3dSkullStrip -input Anat+orig -o_ply anat_brain -visual
Executable:
/3dSkullStrip
Input Parameters:
 - Input File
 - Output Type
 - Spatial Normalization
 - No Spatial Normalization
 - Write Spatnorm Volume
 - Specify Spatial Resolution
 - Number of Iterations
 - LD
 - Shrink Factor
 - Varation of Shrink Factor
 - No Variation of Shrink Factor
 - Shrink Factor Bottom Limit
 - Pushout
 - No Pushout
 - Speed of Expansion
 - Fill Holes
 - Nearest Neighbor Smooth
 - Smooth Final Surface
 - Avoid Ventricles
 - Don't Avoid Ventricles
 - Initial Sphere Radius
 - Avoid Eyes
 - Don't Avoid Eyes
 - Use Edge
 - Don't Use Edge
 - Push To Edge
 - Don't Push To Edge
 - Use Skull
 - Do Not Use Skull
 - Send No Skull
 - Percentage Intersect
 - No Intersection Testing
 - Max Intersection Iterations
 - Blur FWHM
 - Interactive
 - Demo Pause
 - Talk SUMA
 - Refresh Rate
 - Send kth Element
 - sh (SUMA)
 - NI Text
 - NI Binary
 - Feed AFNI
 - Visual
 - Debug
 - Node Debug
 - Save Brain Contour File (Debug)
 - Save Brain Hull File (Debug)
 - Save Skull Outer File (Debug)
 - No Transforms
 - Trace (Debug)
 - Extreme Trace (Debug)
 - No Memory Trace (Debug)
 - Memory Trace (Debug)
Output Parameters:
 - Output Prefix (Surface)
 - Output Prefix (Volume)
File size:65.71 KB
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