Overview

ZFrameRegistration is a 3D Slicer extension designed to support the workflow of the in-bore MRI-guided therapies (see references below for clinical context). ZFrameRegistration was developed and tested to support transperineal MRgBx and CryoAblation procedures in the Advanced Multimodality Image Guided Operating (AMIGO) at the Brigham and Women's Hospital, Boston. Its applicability to other types of procedures has not been evaluated. The registration of the intra-procedural image frame of reference with the transperineal biopsy or cryoablation templates.

Usage:

With 3D slicer main window.

1. After install the extension, the user need to switch to the module ZFrameRegistrationWithROI.
2. Select the desired zFrame model from the list. The module provides two zFrame model options:

• original (vertical) version
• modified (horizontal) version

3. Load a nrrd file into 3D Slicer by clicking the Slicer Add Data button.

4. Choose the volume in the Zframe template volume selector.

5. The ROI definition will be automatically triggered if the volume is selected or changed, user needs to define ROI by clicking two points in the slice widget.

6. Press the run algorithm button, the registration will be performed and the zframe model will be shown both in the slice widgets and the 3D view widget.

7. If the result is not good, click the "Reset" button or user the manual start/end indexes. If the "Reset" button is clicked, the user will be prompt to do the ROI definition as in step 3. Afterwards, press the run algorithm button again.

8. When the result looks good, the zframe will align very well with the fiducial artifacts on the slice widgets and the 3D view window.

Slicelet mode

The user have the option to run the module in a slicelet mode Type the following command in a terminal in Linux or Mac OS system.

$ cd ${Slicer_execution_path}
$ ./Slicer --no-main-window --python-script lib/Slicer-x.x/qt-scripted-modules/ZFrameRegistrationWithROI.py

For Windows system, see the link for more information Slicelet Mode

Disclaimer

ZFrameRegistration, same as 3D Slicer, is a research software. ZFrameRegistration is NOT an FDA-approved medical device. It is not intended for clinical use. The user assumes full responsibility to comply with the appropriate regulations.

Support

Please feel free to contact us for questions, feedback, suggestions, bugs, or you can create issues in the issue tracker: https://github.com/leochan2009/SlicerZframeRegistration/issues

• Junichi Tokuda tokuda@bwh.harvard.edu

• Longquan Chen lchen@bwh.harvard.edu

• Christian Herz cherz@bwh.harvard.edu

• Andrey Fedorov fedorov@bwh.harvard.edu

Acknowledgments

Development of ZFrameRegistration is supported in part by the following NIH grants:

• R01 EB020667 OpenIGTLink: a network communication interface for closed-loop image-guided interventions
• R01 CA111288 Enabling Technologies for MRI-guided prostate interventions
• P41 EB015898 National Center for Image Guided Therapy (NCIGT), http://ncigt.org

The source code was adopted from the open source projects as follows:

• ProstateNav module of 3D Slicer version 3 (see source code here, no revision history); although we do not have the precise record of contribution to that functionality in the ProstateNav module, we believe main contributors were Junichi Tokuda and Simon Di Maio (while at BWH, now at Intuitive Surgical)
• SliceTracker, courtesy Christian Herz @che85

References

The following publications led to the development of ZFrameRegistration.

1. Tokuda J., Tuncali K., Iordachita I., Song S-EE., Fedorov A., Oguro S., Lasso A., Fennessy FM., Tempany CM., Hata N. 2012. In-bore setup and software for 3T MRI-guided transperineal prostate biopsy. Physics in medicine and biology 57:5823–5840. DOI: 10.1088/0031-9155/57/18/5823: procedure technical setup.
2. DiMaio S, Samset E, Fischer G, Iordachita I, Fichtinger G, Jolesz F, et al. Dynamic MRI scan plane control for passive tracking of instruments and devices. MICCAI. 2007;10:50–8.