This is the page with all the transform theoretical explanation

Main transform tree.

All the transforms are centered on the OptiTracker (tracker) which is fixed.

As you have tools with markers, and you also have defined them in the config file, the tools's transforms are going to appear automatically and you don't need to change them. These transforms are named “ToolToTracker”. They are moving transforms (green color in the picture), that means that they are changing all the time because you are moving the tools. This type of transform can't be saved and needs to be monitored during the whole process.

The blue ones are static transforms. That means they can be saved once you did the calibration right. This is necesary in order to have every single model in the right position, so when you move the tools in the real life the movement of the 3D models in the slicer scene is the same.

For the calibration, you have to follow the tree ways. Here you will find the explanation for the three tools we use. There are some tips you have to tke in to account before doing each calibration:

• The model of the tool you are calibrating must be under the scene and not inside othe transform.
• The transform you are calibrating must be under the scene and not inside other transform.
• For the patient, probe or other tool calibration (not stylus or needle), you will have to include NeedleToTracker under (TrackerToTool), so you will be using the same reference system.

First of all, we started with the stylus/needle because it is necessary to calibrate the rest of the tools.

After doing the needle calibatrion by following the steps in the calibration section, we followed the tree way and took the tracker as scene, so we colocated the transforms like this: Scene –> NeedleToTracker–>NeedleTipToNeedle–>NeedleModel(which is immediately NeedleModelToNeedleTip).

For the patient calibration we used this hierarchy: (Remember to have the 3d models under the scene)

During the fiducials calibration you have to follow that tree way including the NeedleToTracker (with all inside) under the TrackerToPatient (red). Doing this you are taking the points in the same reference system (tracker) that you did for the stylus.After this, you can move de phantom model under PhantomModelToPatient calibration.

Following the same explanation that the patient calibration and also the tips of the begining, you must include the NeedleToTracker under TrackerToProbe during this calibration.

Same for this because it is a part of the probe so you use TrackerToProbe.

After the calibration, you have to organize the hierarchy again. We followed this diagram: