@djunct_4d_imager


# ------------------------------------------------------------------------

The program is useful for viewing the same slice across the 'time'
dimension of a 4D data set.  It is used in several of FATCAT's
fat_proc* functions (e.g., viewing DWIs).  But because it seemed so
useful, it now has some basic help for basic usage by *expert* AFNI
users!

The program outputs the following in sets of three, one for each spatial
axis:

    + an image of the same central slice across volumes along the time
      axis, with the brightness range constant across volume
      ("*onescl*" images); that is, the same grayscale in each panel
      corresponds to the same numerical value.
    + an image of the same central slice across volumes along the time
      axis, with the brightness range possibly *varying* for each
      panel across volume ("*sepscl*" images); that is, the grayscale
      value in each panel can (and likely will) correspond to *a
      different* numerical value.  Useful, for example, for checking
      details in DWIs, where the expected scale of values can change
      dramatically across volumes.
    + (with option flag) a movie version of the "onescl" images,
      showing one slice at a time.
    + (with option flag) a movie version of the "sepscl" images,
      showing one slice at a time.

The panel dimensionality in each of the above montage images is
calculated to be approximately golden ratio-ish.  (with blank panels
appended as deemed desirable; blank slices are *not* appended to the
dset, they are just added for the montage visualization).  Slice
numbers are shown in both the image panels and the movie panels.

This program is a very basic wrapper around @chauffeur_afni.  It is
useful as a quality control (QC) generator, driving AFNI functionality
to make images *and* movies of a data set while processing (working in
a virtual X11 environment using xvfb, so that this generates
images/movies even on a remote terminal).

written by PA Taylor (NIMH, NIH, USA).

# ========================================================================

-help, -h          :see helpfile (here!)
-ver               :see version number

-inset     UUU     :ulay dset (required).  Probably 4D (hence the name of
                    this program...).

-prefix    PPP     :prefix for output files (required).

-do_movie  MTYPE   :specify type of movie file.  Basically, one of two
                    options:
                      MPEG   AGIF
                    This is optional; by default, a montage of PNG images
                    is created: the same slice across the 4D set.

-no_clean          :by default, the temporary directory made by this
                    program is deleted when finishing.  Use this option
                    to keep the final intermediate files.

# ========================================================================

EXAMPLE:

    # 1) Um, just view all the volumes in a DWI acquisition, both as a
    #    montage saved as a PNG file and as an mpeg file.

    @djunct_4d_imager                 \
        -inset  MY_DWIs.nii.gz        \
        -prefix PRETTY_DWIS           \
        -do_movie AGIF