The purpose of this function is to help convert an anatomical data
    set from DICOM files into a volume.  Ummm, yep, that's about it.

    (But it will be done in a way to fit in line with other
    processing, particularly with DTI analysis, so it might not be
    *totally* useless; more options while converting might be added
    over time, as well.)

    REQUIRES: AFNI (which should now contain dcm2niix_afni, the
    version of dcm2niix [by C. Rorden] distributed in AFNI).

    Ver. 3.5 (PA Taylor, Feb 12, 2019)



  fat_proc_convert_dcm_anat  \
        {-indir  DIR_IN  | -innii  NII_IN}     \
        -prefix  PPP                           \
        {-workdir WWW}                         \
        {-orient  ORIENT}                      \
        {-no_clean}                            \
        {-reorig_reorient_off}                 \
        {-qc_prefix    QCPREF}                 \
        {-no_cmd_out}                          \

    -indir  DIR_IN  :input as dicom directory; DIR_IN should contain
                     only DICOM files; all will be selected.
    -innii  NII_IN  :input as NIFTI file (zipped or unzipped fine).
                     Alternative to '-indir ..'. The point of this option
                     is to have all other "niceifying" steps applied
                     to an already-converted volume.

    -prefix   PPP   :set prefix (and path) for output data; required.

    -workdir  WWW   :specify a working directory, which can be removed;
                     (default name = '__WORKING_convert_dcm_anat').

    -orient  ORIENT :optional chance to reset orientation of the volume
                     files (default is currently 'RAI').
                    :switch to turn of the nicety of putting (0, 0, 0)
                     at brain's center of mass (-> 'reorigin' calc) and to
                     not reorient data (-> 'reorient' calc).  Could lead
                     to weirdness later on down the road, depending on the
                     data and headers (ergo, not recommended.)

  -qc_prefix QCPREF :can set the prefix of the QC image files separately
                     (default is '').
   -no_qc_view      :can turn off generating QC image files (why?)
   -no_cmd_out      :don't save the command line call of this program
                     and the location where it was run (otherwise, it is
                     saved by default in the ODIR/).


  OUTPUTS: a single anatomical volume in the DIR_OUT.
           In some cases of anatomical volume acquisition, the DICOMS
           get converted to more than one format of volumetric output
           (one total acquired volume, one centered around the head,
           etc.); these usually have different formats of file name,
           starting with '2*', 'co*' and 'o*'.  Basically, the '2*' is
           chosen for outputting, and the others are stored in a
           subdirectory called DIR_OUT/WWW/.



    fat_proc_convert_dcm_anat  \
       -indir  "ANAT_DICOMS"                 \
       -prefix outdir/anat                   \
       -orient RAI

    fat_proc_convert_dcm_anat  \
       -innii  t1w.nii.gz                    \
       -prefix outdir/anat                   \
       -orient RAI