antsASLProcessing - part of ANTS registration suite
Cannot find antsRegistration. Please \(re\)define $ANTSPATH in
your environment. Cannot find antsApplyTransforms. Please \(re\)define
$ANTSPATH in your environment. Cannot find antsIntermodalityIntrasubject.sh
script. Please \(re\)define $ANTSPATH in your environment. antsASLProcessing
performs ASL processing based on ANTs tools. Preprocessing of T1 images
using antsCorticalThickness.sh is assumed. The following steps are
performed:
- 1) Calculation of average pCASL image. 2) Skull stripping of average pCASL
image. 3) Registration of average pCASL image to T1 image. 4) (Robust)
calculation of mean CBF. 5) Warping tissue priors and labels to ASL space.
6) Warping mean CBF image to template space for VBM analysis.
Usage: Required arguments: antsASLProcessing -a anatomical
image (skull stripped)
- -p brain segmentation priors (C-style, e.g. priors%d.nii.gz)
-g hard brain segmentation -x t1 brain mask -s raw
pCASL image -e brain template -l template labels -t
skull-stripped t1 to template transform prefix -o output
prefix
- -b blood T1 value (defaults to 0.67 s^-1) -r robustness
parameter (defaults to 0.95) -h print help and exit -n
number of bootstrap samples (defaults to 20) -c percent to sample
per bootstrap run (defaults to 70) -k keep tmp files, including
warps (defaults to false--takes lots of space to save) -i use
inverse warps. Warps are assumed to go in the direction of subject to
template.
- If you are instead using template to subject warps (e.g. the brain
segmentation prior warps from antsCorticalThickness.sh), use -i
(binary switch--no arguments).
- -f bootstrap with
replacement?
- takes arguments "false" or "true"; defaults to
false.