antsASLProcessing1

Part of ants registration suite

Overview

Cannot find antsRegistration. Please $re$define $PATH in your environment. Cannot find antsApplyTransforms. Please $re$define $PATH in your environment. Cannot find antsIntermodalityIntrasubject.sh script. Please $re$define $PATH 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

Optional arguments:

: -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.