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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 compiling ANTs on Linux / Mac or compiling ANTs on Windows.

Releases since 2.4.1 include binaries for Mac and Linux, see the instructions to install pre-compiled binaries.

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.