This script has dual purposes for processing a given subject's
anatomical volume:
    + to skull-strip the brain, and
    + to calculate the warp to a reference template/standard space.
Automatic snapshots of the registration are created, as well, to help
the QC process.

This program cordially ties in directly with, so you can
run it beforehand, check the results, and then provide both the
skull-stripped volume and the warps to the processing program.  That
is convenient!

Current version = 2.72
Authorship      = RW Cox

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


    sswarper2             \
        -input   AA          \
        -base    BB          \
        -subid   SS          \
       {-odir    OD}         \
       {-mask_ss MS}         \
       {-minp    MP}         \
       {-nolite}             \
       {-skipwarp}           \
       {-unifize_off}        \
       {-extra_qc_off}       \
       {-jump_to_extra_qc}   \
       {-cost_aff CA}        \
       {-cost_nl_init CNI}   \
       {-cost_nl_final CNF}  \
       {-deoblique}          \
       {-deoblique_refitly}  \
       {-warpscale WS}       \
       {-SSopt 'strings'     \
       {-aniso_off}          \
       {-ceil_off}           \
       {-verb}               \

where (note: many of the options with 'no' and 'off' in their name are
really just included for backwards compatibility, as this program has
grown/improved over time):

  -input  AA :(req) an anatomical dataset, *not* skull-stripped, with
              resolution about 1 mm.

  -base   BB :(req) a base template dataset, with contrast similar to
              the input AA dset, probably from some kind of standard
              NB: this dataset is not *just* a standard template,
              because it is not a single volume-- read about its
              composition in the NOTES on the 'The Template Dataset',
              The program first checks if the dset BB exists as
              specified; if not, then if just the filename has been
              provided it searches the AFNI_GLOBAL_SESSION,
              AFNI_PLUGINPATH, and afni bin directory (in that order)
              for the named dataset.

  -subid  SS :(req) name code for output datasets (e.g., 'sub007').

  -odir   OD :(opt) output directory for all files from this program
              (def: directory of the '-input AA').

 -mask_ss MS :(opt) if you have a mask already to start with, then you
              can also input it to help with the alignment.  For
              example, if you are running FreeSurfer's recon-all with
              @SUMA_Make_Spec_FS, you might find the 'fs_parc_wb_mask*'
              dset a useful MS dset to input.

  -minp   MP :(opt) minimum patch size on final 3dQwarp (def: 11).

  -nolite    :(opt) Do not use the '-lite' option with 3dQwarp; This
              option is used for backward compatibility, if you want
              to run 3dQwarp the same way as older versions of the
              predecessor '@SSwarper'.  The new way (starting Jan 2019)
              is to use the '-lite' option with 3dQwarp to speed up
              the calculations.  (def: use '-lite' for faster

  -skipwarp  :(opt) Do not compute past the output of anatSS.{subid}.nii.
              This option is used if you just want the skull-stripped
              result in original coordinates, without the warping
              to the template space (anatQQ). The script will run faster.

  -deoblique :(opt) apply obliquity information to deoblique the input
              volume ('3dWarp -deoblique -wsinc5 ...'), as an initial step.
              This might introduce the need to overcome a large rotation
              during the alignment, though!

  -deoblique_refitly :(opt) purge obliquity information to deoblique
              the input volume (copy, and then '3drefit -deoblique ...'),
              as an initial step.  This might help when data sets are
              very... oblique.

  -warpscale WS :(opt) opt to control flexibility of warps in 3dQwarp and
              how they adjust with patch size;  see 3dQwarp's help for
              more info. Allowed values of WS are in range [0.1, 1.0].
              (def: 1.0)

  -giant_move :(opt) when starting the initial alignment to the template,
              apply the same parameter expansions to 3dAllineate that
     does with the same option flag.  This
              might be useful if the brain has a very large angle away
              from "typical" ones, etc.

  -unifize_off :(opt) don't start with a 3dUnifize command to try reduce
              effects of brightness inhomogeneities.  Probably only
              useful if unifizing has been previously performed on the
              input dset.

  -aniso_off :(opt) don't preprocess with a 3danisosmooth command to
              try reduce effects of weird things (in a technical
              sense).  Possible that this will never be used in the
              history of running this program.

  -ceil_off  :(opt) by default, after anisosmoothing, this program
              will apply put a ceiling on values in the dset, to get rid
              of possible outliers (ceil = 98%ile of non-zero voxels in
              the whole volume).  This option will turn that off.

  -extra_qc_off :(opt) don't make extra QC images QC*jpg (for some
              unknown reason).

  -jump_to_extra_qc :(opt) just make the two QC*jpg images from a
              previous run of sswarper2.  These QC*jpg images are new
              QC output (as of late Feb, 2020), so this might be
              useful to add a quick check to previously run data.
              This command would just be tacked on to previously
              executed one.

  -cost_aff CA :(opt) specify cost function for affine (3dAllineate)
              part of alignment.  Here, 'CA' would be just the name of
              the cost function to be provided after '-cost ..' (def:
              is now "lpa+ZZ").

  -cost_nl_init CNI
             :(opt) specify cost function for initial nonlinear
              (3dQwarp) part of alignment.  Here, 'CNI' would be the
              cost function name to be provided (def: is now "lpa").

  -cost_nl_final CNF
             :(opt) specify cost function for final nonlinear
              (3dQwarp) parts of alignment.  Here, 'CNF' would be the
              cost function to be provided (def: is now "pcl").  This
              is separate from the initial nonlinear warp cost values
              '-cost_nl_init ..', because using those here might be
              pretty slow; however, using "lpa" here might help

  -tmp_name_rand :(opt) the default prefix for temporary/intermediate
              files is junk_ssw.  However, if you want to have
              randomly-named intermediate files, you can by using this
              option.  They will be called 'junk.SSwarper_[rand string]'.
              This option might be useful if you run multiple cases in
              the same directory, in which case some confusion over
              intermediate stuff might happen.

  -echo      :(opt) Run the script with "set echo", for extra verbosity
              in the terminal output.  Mainly for debugging times.

  -verb      :(opt) Apply the '-verb' option to 3dQwarp, to get more
              verbose progress information - mostly used for debugging.

  -noclean   :(opt) Do not delete the 'junk' files at the end of
              computations - mostly used for debugging and testing.

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


If you are reading this message, then several reference data sets
(base volumes) for sswarper2 now exist within the AFNI realm. Oh, what
a time it is to be alive.  A current list includes:

+ MNI152_2009_template_SSW.nii.gz
+ TT_N27_SSW.nii.gz
+ HaskinsPeds_NL_template1.0_SSW.nii.gz

Some of these are distributed with the AFNI binaries, and other may be
found online. You can make other reference base templates in whatever
space you prefer, but note that it must have several subvolumes of
information included-- see NOTES on the 'The Template Dataset', below
(which also contains a link to the sswarper2 template tutorial online

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


Suppose the -prefix is 'sub007' (because you scanned Bond, JamesBond?).
Then the outputs from this script will be"

  anatDO.sub007.nii       = deobliqued version of original dataset;
                            (*only if* using '-deoblique' opt);
  anatU.sub007.nii        = intensity uniform-ized original dataset
                            (or, if '-unifize_off' used, a copy of orig dset);
  anatUA.sub007.nii       = anisotropically smoothed version of the above
                            (or, if '-aniso_off' used, a copy of anatU.*.nii)
  anatUAC.sub007.nii      = ceiling-capped ver of the above (at 98%ile of
                            non-zero values)
                            (or, if '-ceil_off' used, a copy of anatUA.*.nii)
  anatSS.sub007.nii       = second pass skull-stripped original dataset;
                            * note that anatS and anatSS are 'original'
                              in the sense that they are aligned with
                              the input dataset - however, they have been
                              unifized and weakly smoothed: they are
                              stripped versions of anatUAC; if you want
                              a skull-stripped copy of the input with
                              no other processing, use a command like
                                3dcalc -a INPUTDATASET        \
                                       -b anatSS.sub007.nii   \
                                       -expr 'a*step(b)'      \
                                       -prefix anatSSorig.sub007.nii
  anatQQ.sub007.nii       = skull-stripped dataset nonlinearly warped to
                            the base template space;
  anatQQ.sub007.aff12.1D  = affine matrix to transform original dataset
                            to base template space;
  anatQQ.sub007_WARP.nii  = incremental warp from affine transformation
                            to nonlinearly aligned dataset;
  AMsub007.jpg            = 3x3 snapshot image of the anatQQ.sub007.nii
                            dataset with the edges from the base template
                            overlaid -- to check the alignment;
  MAsub007.jpg            = similar to the above, with the roles of the
                            template and the anatomical datasets reversed.
  QC_anatQQ.sub007.jpg    = like AM*.jpg, but 3 rows of 8 slices
  QC_anatSS.sub007.jpg    = check skullstripping in orig space: ulay is
                            input dset, and olay is mask of
                            skullstripped output (anatSS* dset)

* The .aff12.1D and _WARP.nii transformations need to be catenated to get
  the full warp from original space to the base space; example:
    3dNwarpApply -nwarp 'anatQQ.sub007_WARP.nii anatQQ.sub007.aff12.1D' ...

* It is important to examine (at least) the two .jpg snapshot images to
  make sure that the skull-stripping and nonlinear warping worked well.

* The inputs needed for the '-tlrc_NL_warped_dsets' option to
  are (in this order):
    anatQQ.sub007.nii anatQQ.sub007.aff12.1D anatQQ.sub007_WARP.nii

* When B-O-B uses this script for skull-stripping plus warping, He
  gives these options (among others), after running
  sswarper2 successfully -- here, 'subj' is the subject

  |  set btemplate = MNI152_2009_template_SSW.nii.gz
  |  set tpath = `@FindAfniDsetPath ${btemplate}`
  |  if( "$tpath" == "" ) exit 1
  |                                                  \
  |    [...other stuff here: processing blocks, options...]        \
  |    -copy_anat anatSS.${subj}.nii                               \
  |    -anat_has_skull no                                          \
  |    -align_opts_aea -ginormous_move -deoblique on -cost lpc+ZZ  \
  |    -volreg_align_to MIN_OUTLIER                                \
  |    -volreg_align_e2a                                           \
  |    -volreg_tlrc_warp -tlrc_base $tpath/$btemplate              \
  |    -tlrc_NL_warp                                               \
  |    -tlrc_NL_warped_dsets                                       \
  |       anatQQ.${subj}.nii                                       \
  |       anatQQ.${subj}.aff12.1D                                  \
  |       anatQQ.${subj}_WARP.nii

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


The Template dataset

Any reference base template dataset, such as
MNI152_2009_template_SSW.nii.gz, must have the first *4* volumes here
(and can have the optional 5th for later uses, as described):
  [0] = skull-stripped template brain volume
  [1] = skull-on template brain volume
  [2] = weight mask for nonlinear registration, with the
        brain given greater weight than the skull
  [3] = binary mask for the brain
  [4] = binary mask for gray matter plus some CSF (slightly dilated)
        ++ this volume is not used in this script
        ++ it is intended for use in restricting FMRI analyses
           to the 'interesting' parts of the brain
        ++ this mask should be resampled to your EPI spatial
           resolution (see program 3dfractionize), and then
           combined with a mask from your experiment reflecting
           your EPI brain coverage (see program 3dmask_tool).

More information about making these (with scripts) is provided on
the Interweb:

You Know My Methods, Watson

#1: Uniform-ize the input dataset's intensity via 3dUnifize.
     ==> anatU.sub007.nii
#2: ** now skipped **
#3: Nonlinearly warp (3dQwarp) the result from #1 to the skull-on
    template, driving the warping to a medium level of refinement.
#4: Use a slightly dilated brain mask from the template to
    crop off the non-brain tissue resulting from #3 (3dcalc).
#5: Warp the output of #4 back to original anatomical space,
    along with the template brain mask, and combine those
    with the output of #2 to get a better skull-stripped
    result in original space (3dNwarpApply and 3dcalc).
     ==> anatSS.sub007.nii
#6  Restart the nonlinear warping, registering the output
    of #5 to the skull-off template brain volume (3dQwarp).
     ==> anatQQ.sub007.nii (et cetera)
#7  Use @snapshot_volreg3 to make the pretty pictures.
     ==> AMsub007.jpg and MAsub007.jpg

Temporary files

If the script crashes for some reason, it might leave behind files
whose names start with 'junk.SSwarper' -- you should delete these
files manually.


  1) Run the program, deciding what the main output directory will be
  called (e.g., based on the subject ID):

    sswarper2                                    \
        -input  anat_t1w.nii.gz                  \
        -base   MNI152_2009_template_SSW.nii.gz  \
        -subid  sub-001                          \
        -odir   group/o.aw_sub-001

  2) You can input a mask to be used instead of skullstripping.  For
  example, a good one might be the parcellation-derived (but filled
  in) mask from @SUMA_Make_Spec_FS after running FS's recon-all
  (though you will have to resample it from the FS output grid to that
  of your input anatomical):

    sswarper2                                     \
        -input   anat_t1w.nii.gz                  \
        -mask_ss fs_parc_wb_mask_RES.nii.gz       \
        -base    MNI152_2009_template_SSW.nii.gz  \
        -subid   sub-001                          \
        -odir    group/o.aw_sub-001

# -------------------------------------------------------
  Author: Bob, Bob, there is one Bob, He spells it B-O-B.
# -------------------------------------------------------