AFNI program: 3dIntracranial
Output of -help
++ 3dIntracranial: AFNI version=AFNI_24.1.03 (Apr 18 2024) [64-bit]
++ Authored by: B. D. Ward
[7m*+ WARNING:[0m This program (3dIntracranial) is old, obsolete, and not maintained!
++ 3dSkullStrip is almost always superior to 3dIntracranial :)
3dIntracranial - performs automatic segmentation of intracranial region.
This program will strip the scalp and other non-brain tissue from a
high-resolution T1 weighted anatomical dataset.
** Nota Bene: the newer program 3dSkullStrip should also be considered
** for this functionality -- it usually works better.
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Usage:
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3dIntracranial
-anat filename => Filename of anat dataset to be segmented
[-min_val a] => Minimum voxel intensity limit
Default: Internal PDF estimate for lower bound
[-max_val b] => Maximum voxel intensity limit
Default: Internal PDF estimate for upper bound
[-min_conn m] => Minimum voxel connectivity to enter
Default: m=4
[-max_conn n] => Maximum voxel connectivity to leave
Default: n=2
[-nosmooth] => Suppress spatial smoothing of segmentation mask
[-mask] => Generate functional image mask (complement)
Default: Generate anatomical image
[-quiet] => Suppress output to screen
-prefix pname => Prefix name for file to contain segmented image
** NOTE **: The newer program 3dSkullStrip will probably give
better segmentation results than 3dIntracranial!
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Examples:
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3dIntracranial -anat elvis+orig -prefix elvis_strip
3dIntracranial -min_val 30 -max_val 350 -anat elvis+orig -prefix strip
3dIntracranial -nosmooth -quiet -anat elvis+orig -prefix elvis_strip
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++ Compile date = Apr 18 2024 {AFNI_24.1.03:linux_ubuntu_16_64}
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Thu Apr 18 14:45:35 EDT 2024