7.1.305. @clip_volumeΒΆ

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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 -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

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