Loading Custom Data

This tutorial will show you how to prepare your own data for use with AutoscoperM. This tutorial assumes that you have some familiarity with tracking data using AutoscoperM. If you are new to AutoscoperM, please see the Loading and Tracking Data tutorial for information on how to track data with AutoscoperM.

Note

This tutorial is intended for users who wish to use their own data with AutoscoperM. However, for learning purposes, it can still be followed using the sample data provided with AutoscoperM. The sample data is downloaded into the cache directory of 3D Slicer. To locate your cache directory open 3D Slicer and go to Edit -> Application Settings -> Cache. You can then click on the button next to Cache location: to open the cache directory.

Preparing the Data

AutoscoperM requires the following data to track a skeletal structure:

One or more radiograph series
A 3D volume of each bone in the skeletal structure you wish to track
A camera calibration file for each radiograph series

Recommended File Structure

Below is the recommended file structure for a trial that tracks k bones over n cameras consisting of m frames each

trial name
├── radiographs
│   ├── camera 1
│   │   ├── 0001.tif
│   │   ├── 0002.tif
│   │   ├── ...
│   │   └── m.tif
│   └── camera 2
│   |   ├── 0001.tif
│   |   ├── 0002.tif
│   |   ├── ...
│   |   └── m.tif
|   ...
|   └── camera n
│       ├── 0001.tif
│       ├── 0002.tif
│       ├── ...
│       └── m.tif
├── volumes
│   ├── bone1.tif
│   ├── bone2.tif
│   ├── ...
│   └── bonek.tif
├── calibration
|   ├── camera 1.csv
|   ├── camera 2.csv
|   ├── ...
|   └── camera n.csv
└── trial name.cfg

Automatic filter and tracking data loading

AutoscoperM can automatically load filter and tracking data from a trial. To do this, the filter and tracking data must be in the following format:

trial name
├── radiographs
|   └── ...
├── volumes
|   └── ...
├── calibration
|   └── ...
├── xParamters
|   └── control_settings.vie
├── Tracking
|   ├── {trial name}_bone1.tra
|   ├── {trial name}_bone2.tra
|   ├── ...
|   └── {trial name}_bonek.tra
└── trial name.cfg

Camera Calibration File

For information on how to create a camera calibration file, see the Camera Calibration File Format page.

Creating a Configuration File

Note

If you have any unsaved changes to your current trial, you will be prompted to save them before creating a new trial.

AutoscoperM uses a .cfg file to specify the location of the radiographs, volumes, and camera calibration files. You can create a .cfg file by going to File -> New. This will open up the configuration dialog:

From the dialog you can create as many cameras as needed. Where the Calibration File points the the camera calibration file and the Video Path points to the folder containing the radiographs for each camera.

You can also create as many volumes as needed. Where the File points to the volume file. and the Scale XYZ is the scale of the volume in the x, y, and z directions. The Scale XYZ is used to scale the volume to match the size of the radiographs. The Flip XYZ indicates whether the volume should be flipped in the x, y, and z directions. The Flip XYZ is used to match the orientation of the volume to the radiographs.

Once everything is set in the dialog you can press OK to automatically load the trial into AutoscoperM. In order to save the configuration file, you can go to File -> Save Trial as. This will save the configuration file to the specified location. You can also press Crtl + Shift + S to save the configuration file.