sswarper2¶
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 = 2.8
Authorship = RW Cox
# -----------------------------------------------------------------
USAGE¶
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} \
{-aniso_off} \
{-ceil_off} \
{-verb} \
{-noclean}
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
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').
-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
calculations).
-skipwarp :(opt) Do not compute the nonlinear parts of the
alignment. This might be useful in troubleshooting early
stages of the alignment, like when initial overlap (even
after preliminary shifting) is poor, or when affine cost
functions need to be tested out. This will not produce
detailed skullstripping or alignment, and is likely just
for trial or intermediate usage.
-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)
-post_aff_tol PAT :(opt) the tolerance (in voxel count) for the
base-source error in affine alignment. Essentially, the
code will assume that the each part of the
affine-aligned subject brain boundary is at most PAT
voxels away from the template brain boundary. The code
will mask out subject brain material outside this
tolerance to try to remove skull, face and other
non-brain material, but in some cases this might need to
be increased if there is a notable shape difference
still after affine alignment, which can be checked in
the QC images, since that would lead to artifactually
cropping the subject brain in later masking.
(def: 3)
-giant_move :(opt) when starting the initial alignment to the template,
apply the same parameter expansions to 3dAllineate that
align_epi_anat.py 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.
-start2_thr STHR :(opt) unifizing is applied to the data to normalize
brightness values a bit; then, a thresholding is applied for
an initial masking. The default value for thresholding is:
500
This applies well to most anatomicals acquired at 3T, but if
you are using 7T data, we have found that setting this to
100 is often better to avoid over-chopping, particularly in
the cerebellum.
-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
results.
-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.
# -----------------------------------------------------------------
REFERENCE DATASETS¶
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
help).
# ----------------------------------------------------------------------
OUTPUTS¶
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 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
sswarper2 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: ** 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.
EXAMPLES¶
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.
# -------------------------------------------------------
