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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.

If you are installing pre-compiled binaries, start here.

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 | tee myRegOutput.txt

If you run antsRegistrationSyNQuick.sh or antsRegistrationSyN.sh, it will print the full ANTs command, which you can further modify. In the above example, the command (and its output) will be stored in myRegOutput.txt as well as being printed to the screen.