Adjusting and Saving 3D Slicer Scenes

We finally describe how the projection of scenes created with 3D Slicer can be optimized, and how they can be saved. Projection adjustment is critical, since the usually non-spatial third dimension needs to be manually scaled to harmonize with the extent of the spatial axes.

Adjusting Scene Projections

The position and extent of models displayed in the 3D scene can be controled by transformation matrices. Such a matrix can be used to, e.g., optimize the display of the iso-intensity surfaces created above. View the datased from, e.g., the "L" perspective to better understand the need for this: the models only occupy a small fraction of the volume available. The dynamic range available of the display is not well exploited.

Go to the 'Data' panel to subject all models, as well as the volumes, to a transformation matrix. Click on the first entry of the list shown in the panel, scroll down to the bottom of the list, and click on the last entry while holding 'shift'. All list entries should be highlighted. Then, click 'Add Transform'.

This list can also be used to delete and reorder data loaded into 3D Slicer. To do so, click on any list entry with the right mouse button, and use the menu opening to edit the list item.

Go to the 'Alignments' panel to edit the matrix, and select the 'Props' tab. Use the 'Active Matrix' selector in case you are using several transformations at the same time. The 3x3 matrix in the upper left corner can be used to scale and rotate the axes. The right column controls shifting of the data.

Transformation matrixes are presently not reliably saved. This is due to a bug within Slicer that is not under immediate control by AM. While the data will be read in reliably, the data might be significantly displaced within the volume. We recommend to keep notes on used transformations.

The example data is well fit into the display using the following transformation:

1   0   0   0
0   5   0 -800
0   0   1   0
0   0   0   1

The factor of 5 on the main diagonal is used to enlarge the velocity axis. A shift of -800 units is necessary to move the data into the display box.

Saving Scenes

Complex bundles of volumes, models, and transformatons can be saved in scenes. Scene files do not contain actual data, but store XML-encoded information which data was displayed using which parameters. See the tour on iso-intensity surfaces in L1448 to learn how to read scenes.

For the example case we assume that models have been saved, as suggested before. Unnecessary data not used in future analysis of a scene should be removed from memory before saving the scene. Therefore, go to the 'Data' panel, and delete the volumes 'LowIntensityLabel', 'MidIntensityLabel', and 'HighIntensityLabel'. Do so by clicking on the related list entries with the right mouse button, and selecting the 'Delete' entry in the menu opening.

Finally, select 'Save Scene As...' from the 'File' submenu. Use a filename of your choice. Then select 'Save Scene with Options' to also write information on viewing perspectives into the scene file.

Slicer writes scene files using absolute path names. This can lead to problems when transfering data to other positions in the directory tree. In these cases try to edit the scene file using a simple ASCII editor. Replace absolute paths starting with "/" by relative paths starting with "./".