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 = Jan 17 2020 {AFNI_20.0.00:linux_ubuntu_16_64}