Visualization of Spatial Transformation

Overview

Visualizing spatial transformations is an important quality assurance step. This tutorial describes how to create uniform grid images and how to visualize a spatial transformation by viewing the warped grid images.

Create Grid Images

The three commands below use the tool scalarGrid to create the grid images along x, y and z axes.

SVtool -target input.df.nii.gz -grid

An example of the grid images are illustrated in the figures below. From left to right are gridx.nii.gz (need to be in sagittal view), gridy.nii.gz (need to be in coronal view), and gridz.nii.gz (in axial view). In this example, the voxel space, specified by input.df.nii.gz, is 192x224x144 voxels with 1x1x1 mm spatial resolution.

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Click on each image to look at it in its original resolution

Visualize Deformation Fields

To visualize the deformation field input.df.nii.gz, simply apply this warp to the three grid images and visualize the warped grid (wgridx.nii.gz, wgridy.nii.gz, and wgridz.nii.gz) using an image viewer such as MRIcro.

deformationScalarVolume -in gridx.nii.gz -out wgridx.nii.gz -trans input.df.nii.gz -target input.df.nii.gz
deformationScalarVolume -in gridy.nii.gz -out wgridy.nii.gz -trans input.df.nii.gz -target input.df.nii.gz
deformationScalarVolume -in gridz.nii.gz -out wgridz.nii.gz -trans input.df.nii.gz -target input.df.nii.gz

The movies below, from left to right, illustrate the result of browsing through each of these images in MRIcro, along sagittal for wgridx.nii.gz, coronal for wgridy.nii.gz, and axial for wgridz.nii.gz.

Click on each image to look at it in its original resolution