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This content is taken from the University of Basel's online course, Statistical Shape Modelling: Computing the Human Anatomy. Join the course to learn more.

Femur project: data download and preparation

We have now reached the second step of our shape modelling project. The goal in this step is to download and rigidly align the femur data you will be using in this project.

Downloading the data:

Follow the instructions on Sicas Medical Image Repository (SMIR) to download the required femur surfaces and corresponding landmarks.

In case you did not yet create your account on SMIR, please refer to the instructions provided last week in the first step of the project (Step 4.11).

Remember: on the SMIR website you will be asked to submit some information about yourself. Please make sure you are familiar with the terms and conditions and privacy policy of the website before submitting your information. Whether you follow the link and submit your personal information or not, your course progress will in no way be affected. Nor will your course marks or FutureLearn profile. For the purposes of any personal information submitted the respective third party website will be the data controller, not FutureLearn nor the University of Basel.

Aligning the data:

Once the data is downloaded, you will have to rigidly align the provided surfaces to the reference femur mesh provided in the first step of the project. To do so, proceed as follows:

  • Locate the landmarks associated with the reference mesh in the dataset provided with the Scalismo Lab tutorial. They are stored in the file datasets/femur.json.

  • Rigidly align the provided femur meshes to the given reference mesh using the landmark alignment method seen previously and the landmarks provided with the meshes. (The landmarks associated with the mesh 1.stl are stored in a file 1.json, etc.)
    Important: make sure to visualise the aligned meshes and assess that you obtained a correct alignment.

That’s it for the second step.

Take the opportunity to explore other datasets available on the SMIR repository and see if they could be useful to your field of study or work.

Did everything work out well?

Did you manage to download the femur data? Did you get a chance to explore other data available on the SMIR? If you have any problems to report or questions to ask, please use the comment function below. If things worked out well for you, help your fellow learners.

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This article is from the free online course:

Statistical Shape Modelling: Computing the Human Anatomy

University of Basel