antsASLProcessing.sh 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.sh
              -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)             
	      -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)
	      -h print help and exit

For an example usage, see process.sh. Data can be downloaded from https://dl.dropboxusercontent.com/u/25867023/asl_data.tgz.