Par0057 - elastix

Registration Description

intra-subject; Rigid transformation; B-spline transformation

Image data

Clinical 4D dynamic contrast enhanced (DCE) MR images and diffusion weighted (DW) MR images with three b-values, both with the clinical focus on the liver. The mean DCE MR images is calculated from all the DCE MR images and used as fixed image. The DW MR image with the lowest b-value is resized to the dimensions of the mean DCE MR image and used as moving image.

Application

Registration of DW MR images to the DCE MR image space.

Registration Settings

For parameter files see the Elastix Model Zoo repository on GitHub.

elastix version: 4.801

Command line calls

To used the rigid registration followed by the b-spline registration, the following command is used:

elastix -f <fixed image> -m <moving image> -p <par filename rigid> -p <par filename b-spline> -fMask <liver mask>  -out <output dir>

where is the mean DCE MR image, is the resized DW MR image with the lowest b-value, and is a liver mask created before registration to focus the registration on the liver region.

The remaining DW MR images can be transformed to the DCE MR image space by using the 'TransformParameters.1.txt' output in the function . The following command can be used:

transformix -in <moving image> -out <output dir> -tp <transform parameters>

where is the resized DW MR image.

Published in

Jansen et al. (2019) Liver segmentation and metastases detection in MR images using convolutional neural networks (submitted)

© 2020 Viktor van der Valk