Resampling MRI images

Dr. Rahul Remanan,
CEO, Moad Computer

In this Python3 code example, a set of MRI images from one scanning session is resampled to match the imaging axis of a reference scan. The DICOM images are handled using PyDICOM. The resampling function is implemented using SimpleITK.

An example use case for this code example is as follows. Consider two MRI scans, A and B, with scan A imaged along the sagittal (longitudinal) plane and scan B along the axial (horizontal) plane.

If the reference image is set as scan A, then the scan B images will be transformed to appear as image slices along the sagittal plane; instead of the original axial plane used during the scan acquisition.

Similarly, ​if the reference image is set as scan B, then the scan A images will be transformed to appear as image slices along the axial plane; instead of the original sagittal plane used during the scan acquisition.

​The example notebook is hosted in Kaggle. The MRI scans used in this notebook are from the RSNA MICCAI brain tumor classification dataset.

Importing dependencies

MRI scan resampling function using SimpleITK

Convert to UINT8 array

Defining the data handling variables including the reference image scan

Function to save the resampled MRI images

Generating resampled images