Viewing image arrays

In this tutorial, we'll open a 3D CT scan for viewing.

Getting DICOMautomaton

First, download a recent build of DICOMautomaton. See installation instructions.

Loading image files

Run the program without any command-line arguments. The SDL_Viewer interactive workspace will appear. Select File > Open menu option to open the file selector.

Normally DICOM image files (CT, MR, PET, ...) would be selected, but we'll use FITS-format files here. Each image is a 2D 'slice' through the 3D volume.

Reordering images

Files lacking appropriate metadata (such as FITS files) might be loaded in the wrong order, so we'll re-order them according to the position in 3D space.

Edit the script (note the trailing ',' on the ImageSelection line) and click the Run button. (Congratulations! You just ran your first DICOMautomaton script!)

Navigating images

To navigate through the 3D volume, click on the Image Navigation sliders. Scrolling the mouse wheel, using the middle-mouse button, and ctrl-clicking on the image will also help you navigate.

Hovering the mouse over the image will cause a tooltip to appear. It contains information about the specific voxel that the mouse is hovering over.

Adjusting the image

The window and level settings and colour map can be altered in the Adjust menu.

There are several preset window and level settings, or you can adjust them directly.

There are also several colour maps to choose from.

Conclusion

This concludes the first tutorial!