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Welcome to the ANTs wiki!

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

** Searching the Wiki **

The search bar on the right searches page titles and headings. For a full-text search of the wiki, use the main Github search bar at the top of the page, and select "in this repository". It will search for your terms in code, issues, and wiki pages.

** Building and installing ANTs **

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

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

*** Using ANTs ***

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.