NAME

       antsASLProcessing - part of ANTS registration suite

DESCRIPTION

       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.

antsASLProcessing 2.5.4+dfsg                      February 2025                             ANTSASLPROCESSING(1)