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.. _ahelp_3dAutobox:

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3dAutobox
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    Usage: 3dAutobox [options] DATASET
    Computes size of a box that fits around the volume.
    Also can be used to crop the volume to that box.
    
    OPTIONS:
    --------
    -prefix PREFIX = Crop the input dataset to the size of the box, and
                     write an output dataset with PREFIX for the name.
                   * If -prefix is not used, no new volume is written out,
                     just the (x,y,z) extents of the voxels to be kept.
    
    -input DATASET = An alternate way to specify the input dataset.
                     The default method is to pass DATASET as
                     the last parameter on the command line.
    
    -noclust       = Don't do any clustering to find box. Any non-zero
                     voxel will be preserved in the cropped volume.
                     The default method uses some clustering to find the
                     cropping box, and will clip off small isolated blobs.
    
    -extent: Write to standard out the spatial extent of the box
    
    -extent_ijk    = Write out the 6 auto bbox ijk slice numbers to
                     screen:
                         imin imax jmin jmax kmin kmax
                     Note that resampling would affect the ijk vals (but
                     not necessarily the xyz ones).
                     Also note that this value is calculated before
                     any '-npad ...' option, so it would ignore that.
    
    -extent_ijk_to_file FF = Write out the 6 auto bbox ijk slice numbers to
                     a simple-formatted text file FF (single row file):
                         imin imax jmin jmax kmin kmax
                     (same notes as above apply).
    
    -extent_ijk_midslice = Write out the 3 ijk midslices of the autobox to
                     the screen:
                         imid jmid kmid
                     These are obtained via: (imin + imax)/2, etc.
    
    -extent_xyz_midslice = Write out the 3 xyz midslices of the autobox to
                     the screen:
                         xmid ymid zmid
                     These are obtained via: (xmin + xmax)/2, etc.
                     These follow the same meaning as '-extent'.
    
    -npad NNN      = Number of extra voxels to pad on each side of box,
                     since some troublesome people (that's you, LRF) want
                     this feature for no apparent reason.
                   * With this option, it is possible to get a dataset that
                     is actually bigger than the input.
                   * You can input a negative value for NNN, which will
                     crop the dataset even more than the automatic method.
    
    
    ++ Compile date = Oct 13 2022 {AFNI_22.3.03:linux_ubuntu_16_64}