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Welcome to the ANTs wiki!

See an overview of our answers to frequently asked questions and commonly requested examples here.

To build and install ANTs, see here for Linux / Mac OS, and here for Windows.

A recommended call to antsCorticalThickness.sh:

bash ${ANTSPATH}antsCorticalThickness.sh -d $dim \
  -a $img \
  -e ${TEMPLATE_DIR}T_template0.nii.gz \
  -t ${TEMPLATE_DIR}T_template0_BrainCerebellum.nii.gz \
  -f ${TEMPLATE_DIR}T_template0_BrainCerebellumExractionMask.nii.gz \
  -m ${TEMPLATE_DIR}T_template0_BrainCerebellumProbabilityMask.nii.gz \
  -p ${TEMPLATE_DIR}Priors/priors%d.nii.gz \
  -z 0 -x 25 -g 1 -k 1 \
  -o ${OUT_DIR}/${outname}/${outname}_

Fast pairwise deformable registration:

  ${ANTSPATH}antsRegistrationSyNQuick.sh \
    -d 3 \
    -t s \
    -f fixed.nii.gz \
    -m moving.nii.gz \
    -o movingToFixed