@SSwarper~¶
OVERVIEW¶
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 afni_proc.py, 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 = 1.41
Authorship = RW Cox
# -----------------------------------------------------------------
USAGE¶
@SSwarper \
-input AA \
-base BB \
-subid SS \
{-odir OD} \
{-minp MP} \
{-nolite} \
{-skipwarp} \
{-unifize_off} \
{-skullstrip_off} \
{-aniso_off} \
{-verb} \
{-noclean}
where:
-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
template.
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',
below.
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').
-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 @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 calculations).
-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.
-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.
-skullstrip_off :(opt) don't preprocess with a 3dSkullstrip command
to roughly isolated brain in the beginning. This might
be useful with macaque dsets.
-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.
# -----------------------------------------------------------------
REFERENCE DATASETS¶
If you are reading this message, then several reference data sets
(base volumes) for @SSwarper 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 @SSwarper template tutorial online
help).
# ----------------------------------------------------------------------
OUTPUTS¶
Suppose the -prefix is 'sub007' (because you scanned Bond, JamesBond?).
Then the outputs from this script will be"
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)
anatS.sub007.nii = first pass skull-stripped original dataset;
(or, if '-skullstrip_off' used, a copy of
anatUA.*.nii)
anatSS.sub007.nii = second pass skull-stripped original dataset;
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.
* The .aff12.1D and _WARP.nii transformations need to be catenated to get
the full warp from orginal 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 afni_proc.py
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 afni_proc.py these options (among others), after running
@SSwarper successfully -- here, 'subj' is the subject
identifier:
| set btemplate = MNI152_2009_template_SSW.nii.gz
| set tpath = `@FindAfniDsetPath ${btemplate}`
| if( "$tpath" == "" ) exit 1
| afni_proc.py \
| [...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
# -------------------------------------------------------------------
NOTES¶
- 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:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/template_atlas/sswarper_base.html
- You Know My Methods, Watson
#1: Uniform-ize the input dataset's intensity via 3dUnifize.
==> anatU.sub007.nii
#2: Strip the skull with 3dSkullStrip, with mildly agressive settings.
==> anatS.sub007.nii
#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.
# -------------------------------------------------------
Author: Bob, Bob, there is one Bob, He spells it B-O-B.
# -------------------------------------------------------
