7.1.48. 3dAutomask

Link to classic view

Usage: 3dAutomask [options] dataset Input dataset is EPI 3D+time, or a skull-stripped anatomical. Output dataset is a brain-only mask dataset.

This program by itself does NOT do ‘skull-stripping’. Use program 3dSkullStrip for that purpose!

Method:
  • Uses 3dClipLevel algorithm to find clipping level.
  • Keeps only the largest connected component of the supra-threshold voxels, after an erosion/dilation step.
  • Writes result as a ‘fim’ type of functional dataset, which will be 1 inside the mask and 0 outside the mask.

Options:

-prefix ppp = Write mask into dataset with prefix ‘ppp’.
[Default == ‘automask’]
-apply_prefix ppp = Apply mask to input dataset and save
masked dataset. If an apply_prefix is given and not the usual prefix, the only output will be the applied dataset
-clfrac cc = Set the ‘clip level fraction’ to ‘cc’, which
must be a number between 0.1 and 0.9. A small ‘cc’ means to make the initial threshold for clipping (a la 3dClipLevel) smaller, which will tend to make the mask larger. [default=0.5]
-nograd = The program uses a ‘gradual’ clip level by default.
To use a fixed clip level, use ‘-nograd’. [Change to gradual clip level made 24 Oct 2006.]
-peels pp = Peel the mask ‘pp’ times, then unpeel. Designed
to clip off protuberances less than 2*pp voxels thick. [Default == 1]
-nbhrs nn = Define the number of neighbors needed for a voxel
NOT to be peeled. The 18 nearest neighbors in the 3D lattice are used, so ‘nn’ should be between 9 and 18. [Default == 17]
-q = Don’t write progress messages (i.e., be quiet).
-eclip = After creating the mask, remove exterior
voxels below the clip threshold.
-dilate nd = Dilate the mask outwards ‘nd’ times.
-erode ne = Erode the mask inwards ‘ne’ times.
-SI hh = After creating the mask, find the most superior
voxel, then zero out everything more than ‘hh’ millimeters inferior to that. hh=130 seems to be decent (i.e., for Homo Sapiens brains).
-depth DEP = Produce a dataset (DEP) that shows how many peel
operations it takes to get to a voxel in the mask. The higher the number, the deeper a voxel is located in the mask.

None of -peels, -dilate, or -erode affect this option.

  • 3dAutomask -prefix Amask Astrip+orig

  • Create a mask of edge-only voxels via
    3dcalc -a Amask+orig -b a+i -c a-i -d a+j -e a-j -f a+k -g a-k

    -expr ‘ispositive(a)*amongst(0,b,c,d,e,f,g)’ -prefix Aedge

    which will be 1 at all voxels in the brain mask that have a nearest neighbor that is NOT in the brain mask.

  • cf. ‘3dcalc -help’ DIFFERENTIAL SUBSCRIPTS for information on the ‘a+i’ et cetera inputs used above.

  • In regions where the brain mask is ‘stair-stepping’, then the voxels buried inside the corner of the steps probably won’t show up in this edge mask:

    ...00000000... ...aaa00000... ...bbbaa000... ...bbbbbaa0...

    Only the ‘a’ voxels are in this edge mask, and the ‘b’ voxels down in the corners won’t show up, because they only touch a 0 voxel on a corner, not face-on. Depending on your use for the edge mask, this effect may or may not be a problem.


++ Compile date = Dec 16 2015

Table Of Contents

This Page