ENH: staged act
ENH: staged act

allow stages 1 to 5 to be called separately and in order.
this permits finer grained control over the process timing.
produces identical results to and is backward compatible with
the unstaged antsCorticalThickness.  the test comparison is

#!/bin/bash
DATA_DIR=${PWD}
TEMPLATE_DIR=${DATA_DIR}/Template/
OUT_DIR=${DATA_DIR}/OutputT1Only/

bash ${ANTSPATH}antsCorticalThickness.sh -d 2 -x 25 -u 0 \
  -a ${DATA_DIR}/IXI002-Guys-0828-T1_slice90.nii.gz \
  -e ${TEMPLATE_DIR}template_slice80.nii.gz \
  -m ${TEMPLATE_DIR}template_cerebrum_mask_slice80.nii.gz \
  -p ${TEMPLATE_DIR}prior%d_slice80.nii.gz \
  -o ${OUT_DIR}example

# test stages
OUT_DIR=${DATA_DIR}/OutputT1OnlyByStage/
for stage in 1 2 3 4 5 ; do
  bash ${ANTSPATH}antsCorticalThickness.sh -d 2 -x 25 -u 0 -y $stage \
    -a ${DATA_DIR}/IXI002-Guys-0828-T1_slice90.nii.gz \
    -e ${TEMPLATE_DIR}template_slice80.nii.gz \
    -m ${TEMPLATE_DIR}template_cerebrum_mask_slice80.nii.gz \
    -p ${TEMPLATE_DIR}prior%d_slice80.nii.gz \
    -o ${OUT_DIR}example
done

which produces identical output.

fbudin69500/ANTs,dawnsong/ANTs,stnava/ANTs,fbudin69500/ANTs,fbudin69500/ANTs,dawnsong/ANTs,fbudin69500/ANTs,dawnsong/ANTs,fbudin69500/ANTs,stnava/ANTs,fbudin69500/ANTs,dawnsong/ANTs,dawnsong/ANTs,stnava/ANTs,stnava/ANTs,stnava/ANTs,stnava/ANTs,dawnsong/ANTs,dawnsong/ANTs,fbudin69500/ANTs,stnava/ANTs