Saving and exchanging data with Slicer

Any dataset loaded into or derived from existing data (e.g., segmentation) becomes part of the Slicer ‘scene’. In an active project, where you might be doing segmentation, measurements, or landmarking, scene may get complex quickly. Saving (or rather forgetting to save) these different components is a typical point of frustration for the end user. Here, I will use one of the nightly builds (r27390) of Slicer to demonstrate the complex Save As dialog box.

First use the Sample Data module to obtain the MR head dataset, and visualize in 3D renderer using the Volume Rendering Preset MR-Default. Then, place some landmarks using the Fiducial tool, and finally take 3D distance measurement. This will generate enough components to create a semi-complex scene like this:

Now, go to the File->Save as to see the File Save Dialog box, which looks like this for my scene:

As you can see there is a volume (MR-head.nrrd), a volume rendering property (MR-Default.vp), a markups list that contain the four landmark (F.fcsv), and a measurement annotation file (M.acsv) that contain the 3D distance. Notice that all files, except the volume has a check mark next to it. That’s because they have not saved before. The reason MR-head does not have a check mark, because it hasn’t been changed by the user since the last time it is loaded. So, any file that’s previously saved in the session, and remain unchanged will be not have a check mark in the save as dialog box, next time you invoke the save command. You can manually change these. Every time you are saving your scene, make sure the files you care about have a check mark next to them.

A complex scene may have tens of components. If you find yourself in a situation that you need to share your scene and all of its component, or looking for a convenient option to move data from one computer to the next, consider trying the medical reality bundle:

It is the rightmost icon (the gift packaged one) on the top row. As you click, it grays out all the fields, and only lets you specify the name of the MRB file and its location. In essence, MRB is a self-contained zip-file with all the data loaded into the scene. Once it is saved, you can send the mrb file to your collaborator, or move it another computer without having to worry about where each of those component files are located on your hard drive. You can drag’n’drop MRB files into Slicer, and it will automatically load the scene.

The downside is you will have to unpack the MRB, if you need to access the components directly (e.g., you want to read your landmark coordinates into R directly).


Leave a Reply

Your email address will not be published. Required fields are marked *