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