Usage 1: A script to clip regions of a volume
@clip_volume <-input VOL> <-below Zmm> [ [-and/-or] <-above Zmm> ]
-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.
@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
If you are not cropping the output, you might consider
using 3dUndump instead.
-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
-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.
@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 (email@example.com)