Category: Checkpoint

What is a Population Average?

A population average merges together several individual specimens to form a consensus of the group being studied. A population average is useful for computing and understanding what “normal” means for a specific group. For example, what is the normal 3D shape of crania, mandible, condyle, femoral head, tibial plateau, etc.

The DCM file extension is used for DICOM which stands for Digital Imaging and Communications in Medicine. This is the common file format used to store medical imaging data when a patient undergoes a CT, MRI, PET, UltraSound, and many other types of medical scans.

Unfortunately, the IDAV Landmark Editor software is no longer maintained by UC Davis and the software download is no longer available. While the Landmark Editor has been used by thousands of researchers around the world at all the leading research institutions and museums, your best option for replacement is Stratovan Checkpoint.

Checkpoint can help you convert those large micro CT scans into files that are more manageable. The following explains how to load a stack of TIF image files from a micro CT scanner and convert them into a NifTi (.nii) file type which Checkpoint can load.

The following steps are used to create a population average from a set of input specimen based on 3D volumetric data. In the example below,
3D anatomic landmark points placed on three input specimen guide the process to create a population average.

Geometric morphometrics provides invaluable information in the areas of physical anthropology and medical research. By comparing differences in 3D anatomic structures it can help quantify an evolutionary feature or relationship, determine an organisms ontogeny or help improve diagnostics and surgical planning among many other applications.

Checkpoint facilitates shape anaysis for the tibia.  The following explains how to create a tibia population and perform a shape analysis on that population.

Checkpoint facilitates shape anaysis for the temporomandibular joint (TMJ).  The following explains how to create a population of TMJ condyles and perform a shape analysis on that population.

Converting DICOM to NIFTI with Checkpoint is a short and simple process.  Load a DICOM volume, then go to the “Export” tab.  Under the volume section, select the NIFTI file format from the list provided in “Export format”.  The “Using these units” attaches new units (i.e.

What is isosurfacing?

Isosurfacing is a visualization technique for extracting a surface from 3D volumetric data, such as a CT or MRI scan. The technique, first developed by researchers at GE called Marching Cubes,  essentially started the 3D medical visualization industry.

What is joint congruence?

Joint congruence is the measurement of two opposing joint surfaces as they relate to one another considering the 3D shape contour of each bone at their interface. For example, relating the femoral condyle to the tibial plateau or the temperomandibular condyle to the fossa.

The procrustes superimposition method calculates the procrustes average specimen, which removes scale from the specimens. The following covers the options available in Checkpoint’s Shape Analysis tab.  Under “Analysis method”, select “Generalized Procrustes Analysis”.

While a post-doc at UC Davis, I led the software development effort for the IDAV Landmark Editor in conjunction with my advisor Nina Amenta and colleague Eric Delson at Lehman College, NY.