3dZcutup

Usage: 3dZcutup [options] dataset
Cuts slices off a dataset in its z-direction, and writes a new
dataset.  The z-direction and number of slices in a dataset
can be determined using the 3dinfo program.
Options:
 -keep b t   = Keep slices numbered 'b' through 't', inclusive.
                 This is a mandatory option.  If you want to
                 create a single-slice dataset, this is allowed,
                 but AFNI may not display such datasets properly.
                 A single slice dataset would have b=t.  Slice
                 numbers start at 0.
 -prefix ppp = Write result into dataset with prefix 'ppp'
                 [default = 'zcutup']
Notes:
 * You can use a sub-brick selector on the input dataset.
 * 3dZcutup won't overwrite an existing dataset (I hope).
 * This program is adapted from 3dZeropad, which does the
     same thing, but along all 3 axes.
 * You can glue datasets back together in the z-direction
     using program 3dZcat.  A sample C shell script that
     uses these programs to carry out an analysis of a large
     dataset is:

  #!/bin/csh
  # Cut 3D+time dataset epi07+orig into individual slices

  foreach sl ( `count_afni -dig 2 0 20` )
    3dZcutup -prefix zcut${sl} -keep $sl $sl epi07+orig

    # Analyze this slice with 3dDeconvolve separately

    3dDeconvolve -input zcut${sl}+orig.HEAD            \
                 -num_stimts 3                         \
                 -stim_file 1 ann_response_07.1D       \
                 -stim_file 2 antiann_response_07.1D   \
                 -stim_file 3 righthand_response_07.1D \
                 -stim_label 1 annulus                 \
                 -stim_label 2 antiann                 \
                 -stim_label 3 motor                   \
                 -stim_minlag 1 0  -stim_maxlag 1 0    \
                 -stim_minlag 2 0  -stim_maxlag 2 0    \
                 -stim_minlag 3 0  -stim_maxlag 3 0    \
                 -fitts zcut${sl}_fitts                \
                 -fout -bucket zcut${sl}_stats
  end

  # Assemble slicewise outputs into final datasets

  time 3dZcat -verb -prefix zc07a_fitts zcut??_fitts+orig.HEAD
  time 3dZcat -verb -prefix zc07a_stats zcut??_stats+orig.HEAD

  # Remove individual slice datasets

  /bin/rm -f zcut*

++ Compile date = Oct 31 2024 {AFNI_24.3.06:linux_ubuntu_24_64}