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Note: the pages below were constructed during the ARRA project cycle and are no longer actively maintained.
The Registration library is still maintained but has moved here

The Slicer Registration Case Library

Welcome to the 3DSlicer Registration Case Library. This page is under continuous development as we add and refine case examples of image registration within 3DSlicer. The goal is for you to find here a case similar enough to your particular image registration problem to provide you with registration parameters, strategies and tutorials. The library is growing by virtue of user contributions; if you have an interesting case please consider our Call for Datasets on the right. Successful registration strategies; algorithm choice and parameters vary greatly for different image contrast and content. Each listed case comprises a test dataset to try yourself, a guided step-by-step tutorial that will show you how to register the case with 3DSlicer, the solution transform so you can compare, and a custom Registration Parameter Presets file with optimized registration parameters that you can load directly into slicer.
Slicer Registration Case Library: Call for Example Datasets

Consider adding your case to the library


Registration HLogo IntraMRI.png Registration HLogo IntraDTI.png Registration HLogo IntrafMRI.png Registration HLogo IntraPET.png
The Same Subject Brain MRI collection contains structuralMRI of the same subject, e.g. aligning follow-up to baseline or a T1w and a PDw image. The Same Subject DTI collection contains cases of registering a DTI dataset with an anatomical reference, such as a high-resolution MRI. The Same Subject fMRI collection contains cases of registering a fMRI dataset with an anatomical reference, such as a high-resolution MRI. The Same Subject PET/CT/MRI collection contains cases of registering a PET or CT dataset with an MRI or CT.
Registration HLogo InterMRI.png Registration HLogo InterPET.png Registration HLogo Atlas.png
The Different Subject Brain MRI collection contains cases of co-registering MRI of (many) different subjects into a common space. This often includes non-rigid registration (image warping). The Different Subject PET/CT collection contains cases of registering PET/SPECT/CT images from different subjects, e.g. aligning a SPECT perfusion atlas with an MRI. The Different Subject Brain Atlas collection contains cases of registering an atlas to a single subject or building atlases from a collection of subjects.


Registration HLogo Abdominal.png Registration HLogo Knee.png Registration HLogo WholeBody.png Registration HLogo Animal.png
The Abdominal/Thoracic collection contains cases of breast and abdominal MRI/CT/PET, e.g. for therapeutic assessment or interventional guidance. The Musculoskeletal collection contains cases of aligning musculoskeletal images, e.g. aligning knee MRI images. The Whole Body PET/CT collection contains cases of registering different modalities of whole body imaging. The Animal MRI/CT collection contains cases of aligning animal datasets.
Registration HLogo Auxiliary.png
The Auxiliary collection contains images & data that can be useful for performing, visualizing or validating registration.

How to get started

  • 1. browse/search the library for a case similar to yours. The library is organized by organ (brain vs. non-brain), modality (MR, CT, PET), intra- vs. inter-subject). Each case also has a list of keywords, so you may try a direct search for a case matching yours. Or for all cases in a single sortable table see here.
  • 2. If you find a good match, continue with 3. below. If you cannot find a good match, consider our Call for Datasets & Registration Service.
  • 3. from the case description page, follow the links to download the data, preset file and tutorials.
  • 4. run the tutorial on your machine with your installation of slicer (v3.6 or higher recommended)
  • 5. load the preset file and try those settings on your own data
  • 5. if you do not get a satisfactory registration results with the presets, have a look at the Registration Challenges and Key Strategies section on the download page of your case. You will find recommendations there on how to venture forth. Try the recommended adjustments.
  • 6. if still unsuccessful you may have a case of interest to the library. Consider adding your case to the library for a free registration. Also consider posting a message to the slicer user group.
  • 7. if successful we'd also love to hear: We gladly add your case with full acknowledgment to the library.

Source & Format

Data is collected from a variety of sources. Most we hope to originate from user contributions. Because we want to focus on the registration problem and not be distracted by image format or other data management issues, the datasets listed here are reformatted as NRRD files. Cases under construction may be listed, and when complete a download link is added.