@clip_volume


Usage 1: A script to clip regions of a volume

   @clip_volume <-input VOL> <-below Zmm> [ [-and/-or] <-above Zmm> ]

   Mandatory parameters:
      -input VOL: Volume to clip
    + At least one of the options below:
      -below Zmm: Set to 0 slices below Zmm
                  Zmm (and all other coordinates) are in RAI
                  as displayed by AFNI on the top left corner
                  of the AFNI controller
      -above Zmm: Set to 0 slices above Zmm
      -left  Xmm: Set to 0 slices left of Xmm
      -right  Xmm: Set to 0 slices right of Xmm
      -anterior Ymm: Set to 0 slices anterior to Ymm
      -posterior Ymm: Set to 0 slices posterior to Ymm
    + Or the box option:
      -box Cx Cy Cz Dx Dy Dz: Clip the volume to a box
                              centered at Cx, Cy, Cz (RAI mm),
                              and of dimensions Dx Dy Dz (RAI mm)
      -mask_box Cx Cy Cz Dx Dy Dz: Same as -box, but set all values
                              inside of box to 1.
      Example:
         @clip_volume -mask_box 20.671 -10.016 23.362 10 10 10 \
                      -input seg_no_spat.c+orig.BRIK \
                      -prefix small_box_volume -crop_greedy

      Note:
         If you are not cropping the output, you might consider
         using 3dUndump instead.

    Optional parameters:
      -and (default): Combine with next clipping planes using 'and'
      -or           : Combine with next clipping planes using 'or'
         Note: These two parameters affect the clipping options that
               come after after them. Unfortunately they are used
               to build a mask of what is to be kept in the end, rather
               than what is to be removed, so they can be confusing.
               A '-and' multiplies the mask by what is to be kept from
               the next cut, and a '-or' adds to it.
      -verb         : Verbose, show command
      -crop_allzero : Crop the output volume with 3dAutobox -noclust
                      This would keep 3dAutobox from removing any
                      slices unless they are all zeros
      -crop_greedy  : Crop the output volume with 3dAutobox
                      In addition to what you specified for cropping,
                      slices with a few non zero voxels might also get
                      chopped off by 3dAutobox
      -crop : Same as -crop_greedy, kept for backward compatibility
      -crop_npad NPAD: set 3dAutobox's -npad option to NPAD
                       Option is meaningless without -crop options
                       Use NPAD to fatten the volume a little after
                       cropping
      -prefix PRFX  : Use PRFX for output prefix. Default is the
                      input prefix with _clp suffixed to it.
      -followers DSET1 DSET2 ...: Apply the same treatment to the
                      follower datasets. Note that cropped or clipped
                      versions are all named automatically by affixing
                      _clp to their prefix.

Example:
@clip_volume -below -30 -above 53 -left 20 -right -13 -anterior -15 \
             -posterior 42 -input ABanat+orig. -verb -prefix sample

Written by Ziad S. Saad (saadz@mail.nih.gov)
                        SSCC/NIMH/NIH/DHHS