@SSwarper¶
Contents
Script to skull-strip and warp to the MNI 2009 template.
Usage: @SSwarper T1dataset SubID [minp]
T1dataset = a T1-weighted dataset, not skull-stripped,
with resolution about 1 mm.
SubID = name code for output datasets (e.g., 'sub007').
minp = optional: minimum patch size on final 3dQwarp
(if not given, 11 is used)
The template dataset MNI152_2009_template.nii.gz is supplied
with AFNI binaries and is described later in this help.
Outputs:
--------
Suppose the SubID is 'sub007' (because you scanned Bond, James Bond?).
Then the outputs from this script will be
anatU.sub007.nii = intensity uniform-ized original dataset;
anatS.sub007.nii = first pass skull-stripped original dataset;
anatSS.sub007.nii = second pass skull-stripped original dataset;
anatQQ.sub007.nii = skull-stripped dataset nonlinearly warped to
MNI template space;
anatQQ.sub007.aff12.1D = affine matrix to transform original dataset
to MNI 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 MNI 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 MNI 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 tpath = `@FindAfniDsetPath MNI152_2009_template.nii.gz`
if( "$tpath" == "" ) exit 1
afni_proc.py [...other stuff here...] \
-copy_anat anatSS.${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 $tpath/MNI152_2009_template.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
anatQQ.${subj}.nii \
anatQQ.aff12.1D \
anatQQ.${subj}_WARP.nii
The Template Dataset
--------------------
The file MNI152_2009_template.nii.gz has 5 volumes:
[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).
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.
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Author: Bob, Bob, there is one Bob, He spells it B-O-B.
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