@afni_refacer_run


OVERVIEW

This script re-faces one input dataset, using a master shell dataset to
write over the subject's 'face' region.

The main input is the name of a T1-weighted dataset.

ver = 2.2

OUTPUTS

When running with '-mode_all', then 5 datasets will be output, all in
the same space as the input volume:

    + Three refaced/defaced volumes:
      1) a "defaced" volume (face+ears replaced with zeros)
      2) a "refaced" volume (face+ears replaced with artifical values)
      3) a "reface_plused" volume (face+ears+skull replaced with artifical
         values)

    + Two face-replacing volumes:
      4) the face+ears used to replace or remove subject data
      5) the face+ears+skull used to replace subject data

Automatic images of the re/defaced volume(s) will be created with
@chauffeur_afni, so the user can quickly evaluate results visually.

A temporary working directory is also created.  This will be cleaned
(=deleted) by default, but the user can choose to save it.

USAGE

  @afni_refacer_run                         \
    -input  DSET                            \
    -mode_{reface|reface_plus|deface|all}   \
    -prefix PPP                             \
    {-anonymize_output}                     \
    {-cost CC}                              \
    {-overwrite}                            \
    {-no_clean}                             \
    {-no_images}                            \
    {-verb_allin}

where:

 -input DSET  : (req) name of input dset; can contain path information.

     ... and one of the following modes MUST be chosen:
 -mode_deface : replace the computed face+ears voxels with all zeros
                instead of the artificial face (ears are also removed)
 -mode_reface : replace the subject's face+ears with a scaled set of
                artificial values
 -mode_reface_plus : replace the subject's face+ears+skull with a scaled
                set of artificial values (i.e., like 'refacing', but
                replacing a more complete shell around the subject's
                brain)
 -mode_all    : output three volumes: one defaced, one refaced and one
                reface_plused

 -prefix PPP  : (req) name of output dset (see NOTES for info about
                about file names, particularly when "-mode_all" is used).

 -anonymize_output : (opt) use 3drefit and nifti_tool to anonymize the
                output dsets.  **But always verify anonymization
                yourself, Dear User!** This will not be able to help
                you if you choose a non-anonymizing output file name,
                for example.

 -cost CC     : (opt) can specify any cost function that is allowed by
                3dAllineate (def: ls)

 -no_clean    : (opt) don't delete temp working dir (def: remove working
                dir)

 -no_images   : (opt) don't make pretty images to automatically view the
                results of re/defacing;  but why wouldn't you want those?

 -overwrite   : (opt) final two file outputs will overwrite any existing
                files of the same name (def: don't do this).  NB: this
                option does not apply to the working directory

 -verb_allin  : (opt) run the 3dAllineate part herein with '-verb' (for
                verbosity)

NOTES

Output file names

If the user implements one of the individual modes for either
refacing, reface_plusing or defacing, then the main output file of
interest is simply specified by their "-prefix .." choice.
Additionally, the the replacement volume in subject space will be
output, with the same name plus a suffix (either 'face' or
'face_plus').

Elif the user implements '-mode_all', then three output volumes are
created, each with the same prefix specified by their "-prefix .."
choice, with identifying suffixes and *.nii.gz extensions:
    PREFIX.deface.nii.gz
    PREFIX.reface.nii.gz
    PREFIX.reface_plus.nii.gz
Additionally, both replacement volumes will be output, having the
same prefix and relevant suffix:
    PREFIX.face.nii.gz
    PREFIX.face_plus.nii.gz

A directory of QC images will be made by default, called:
    PREFIX_QC/
This will contain images of each of the new anatomical volumes and the
replacement volumes over the original anatomical.

Requisite data sets

This script relies on having two datasets that should already be
included with AFNI binaries:
    MNI152_2009_template_SSW.nii.gz = MNI skull strip/warp template
    afni_refacer_shell.nii.gz       = dataset to replace face region
The latter dataset was made with the script @afni_refacer_make_master.

If you are missing these datasets for some reason (e.g., you build
your own AFNI binaries on your computer), you can download these from
the current/atlases directory.  Or just ask for more info on the
Message Board.


Author  - The Face of Imperial Zhark, Who is Terrible to Behold!
Modifer - PA Taylor

EXAMPLES

1) default refacing (replace face+ears+skull+etc.)

    @afni_refacer_run                     \
        -input anat+orig.                 \
        -mode_reface_plus                 \
        -prefix anat_reface_plus.nii.gz

2) reface smaller volume (replace face+ears only)

    @afni_refacer_run                     \
        -input anat+orig.                 \
        -mode_reface                      \
        -prefix anat_reface.nii.gz

3) deface = replace face+ears with zeros

    @afni_refacer_run                     \
        -input anat+orig.                 \
        -mode_deface                      \
        -prefix anat_deface.nii.gz

3) ALL = output all versions of vol: refaced, reface_plused, defaced

    @afni_refacer_run                     \
        -input anat+orig.                 \
        -mode_all                         \
        -prefix anat