Introduction

In the present, radiation therapy (RT) research is constantly developing, but software tools that
available for researchers are mostly either expensive, closed proprietary applications, or free open-
source packages with limited scope, extensibility, reliability, or user support. Based on this
problem in 2012 C. Pinter et al [1] have developed a radiation therapy research toolkit for 3DSlicer
namely SlicerRT to address these limitations, customizable, free, and open-source radiation
therapy research toolkit. SlicerRT provides specific measurement tools such as contour
comparison, dose volume histograms and dose comparison[2].

In radiation therapy (RT) treatment, modalities have increased the complexity of radiation
therapy treatments, and producing advanced patient dose deliveries. Due to this complexity,
verification of dose delivery and quality assurance of new treatment techniques to validate that the
dose delivery to the patient is accurate and precise is crucial. Gel dosimeters have been shown to
be promising tools for measuring and verifying radiation dose deliveries. Typically, gel dosimeters
are read out using modalities such as magnetic resonance imaging, x-ray computed tomography
(CT), or optical CT. Optical CT is becoming more frequently used as it is a simple and convenient
method of acquiring dose distribution information[3]. Summary from tutorials SlicerRT and Gel
dosimetry which used in 3DSlicer for analyze dose distribution through medical imaging would
discussed in this work.

Part I :
Summary from tutorial of SlicerRT
This tutorial demonstrates how to perform a radiation therapy research workflow using the
SlicerRT extension in 3DSlicer[4]. In this tutorial is divided into several stage as follows:

1. Install SlicerRT extension.

2. Load data from DICOM and nrrd.
3. Create isodose lines and surfaces.
4. Perform rigid registration on CT images.
5. Resample day 2 dose volume.
6. Compare dose distributions.
7. Accumulate doses and Compute dose volume histogram
1. How to install SlicerRT extension
Before install SlicerRT extension, You must to Install 3DSlicer software from Slicer download
page https://download.slicer.org Download it according to your OS (Windows, Mac OS X, or
Linux). Open Slicer.exe and choose view in bar menu. Figure 1 shows simple step to install
SlicerRT extension.

Figure 1. Step to install SlicerRT extension

If slicerRT has been successfully installed it will display as in Figure 2

Figure 2. SlicerRT extension has been successfully installed

2. Load DICOM and nrrd data

Datasets downloaded from http://slicer.kitware.com/midas3/download/folder/1345/Slice
rRtTutorial_Namic2013June.zip. After extracted dataset, we obtain 2 folder namely
EclipseEntPhantomRtData and EclipseEntComputedDay2Data. EclipseEntPhantomRtData
contains CT data from patient’s head while EclipseEntComputedDay2Data contains dose radiation
therapy treatment in day 2.
Loading DICOM data and nrrd to Slicer.exe produced medical imaging as illustrated in Figure
3. DICOM is radiation therapy reference data and nrrd is radiation therapy data in day 2. It will
compare soon in the next step.
Figure 3. Medical imaging after load a) DICOM data, b) nrrd data

3. Isodose line and Surface

After applied isodose module in 3DSlicer, isodose line and surface mapping was illustrated In
figure 4. Isodose line indicates the difference of radiation dose level in the process of radiation
therapy with variation color. From dose scalar bar the highest dose represented with red while the
lowest dose was represented with green.

Figure 4. Medical imaging using isodose module represented isodose line and surface with
viewpoint of a) Axial, b) Sagittal, and c) Coronal
4. Perform rigid registration on CT images
General Registration (BRAINS) module was used in this registration stage. Input and output
image data was arranged as well as registration phase. Planning CT (ENT IMRT) was used as
reference imaging and day 2 CT (ENT IMRT Day 2) as second imaging. The output from this
registration is linear transform namely Transform_Day2ToDay1_Rigid and registration phase
Rigid (6 DOF) was used.

5. Resample day 2 dose volume

At this stage, the module used is Resample Image (BRAINS) with image to warp and reference
image as parameters. The output parameters are output image, pixel type and warping in the form
of transform file and interpolation mode. RTDOSE Day 2 was used as image to warp and
RTDOSE: BRAI1 as reference image. The output parameter is an image named 5_RTDOSE
_Day2Registered_Rigid with a flat pixel type. In warping parameter use Transform_Day2
ToDay1_Rigid as transform file with linear interpolation mode.

6. Compare dose distribution

Figure 5. Dose comparison between RTDOSE: BRAI1 and 5_RTDOSE

_Day2Registered_Rigid

After dose from RTDOSE: BRAI1 and 5_RTDOSE _Day2Registered_Rigid were compared,
gamma volume indicated difference dose between them. The “warmer gamma volume, the bigger
difference. From this result there is a little difference from RTDOSE: BRAI1 and 5_RTDOSE
_Day2Registered_Rigid.

7. Accumulate doses and Compute dose volume histogram

Final stage for this work are accumulate doses unregistered and compute dose volume
histogram. Dose accumulate module was used with input data RTDOSE: BRAI1, RTDOSE_Day2
and output is Accumulated_5: RTDOSE: BRAI15 RTDOSE Day2 to obtain accumulate doses
unregistered. Input data RTDOSE: BRAI1, 5_RTDOSE _Day2Registered_Rigid and output is
Accumulated_5 RTDOSE Day25: RTDOSE: BRAI1 to obtain accumulate doses registered.
Furthermore, this accumulation could use to obtain dose volume histogram that illustrated in
Figure 6.

Figure 6. Dose Volume Histogram

Part II :
Summary from tutorial of Gel Dosimetry
This tutorial demonstrates how to perform Analysis of a gel dosimetry, imaged using an optical
CT scanner. In this tutorial is divided into several step as follows:

1. Preparation
2. Gel Dosimetry Analysis Slicelet
a. Import Data
b. Registration
c. Calibration
d. Dose Comparison
1. Preparation
In this stage, all materials which needed in this work were prepared. Materials needed are as
follows:

1. 3DSlicer software
2. SlicerRT extension
3. Gel Dosimetry extension
4. Gel Dosimetry data

3DSlicer and SlicerRT were installed as a previous work. For Gel Dosimetry installation
process almost same as installation process for SlicerRT extension. Figure 7 shows simple step to
install Gel Dosimetry extension.

Figure 7. Step to install Gel Dosimetry extension

If Gel Dosimetry has been successfully installed it will display as in Figure 8

Figure 8. Gel Dosimetry extension has been successfully installed

Dataset in this work could downloaded from http://slicer.kitware.com/midas3/item/205391 .

Data was obtained from Gel dosimeter that positioned inside a phantom (Figure 9), and CT
simulation images were acquired (Planning CT volume). Treatment planning using Eclipse with
single arc delivery using fixed field size. Finally, gel jar was contoured and dose distribution was
calculated. So, output that obtained are dose volume planning, and structures. There are two
treatment for gel jar. Gel 1 was scanned using an optical CT scanner, then fiducial markings were
made with a marker, and metal BBs were taped to those markings. While for Gel 2 also optically
scanned with no markings. Irradiated in Gel 1 was planned delivery and for Gel 2, irradiated with
an electron beam. Both gels are scanned post-irradiation, and are reconstructed to create 3D digital
volumes (Measured gel dosimeter volume, calibration gel volume).
Figure 9. Gel dosimeter that positioned Figure 10. irradiated a) Gel 1 with planned delivery b)
inside a phantom Gel 2 with an electron beam

2. Gel Dosimetry Analysis Slicelet

a. Import Data
At this stage, the module used is Gel Dosimetry Analysis. In module menu choose slicelets
and click Gel Dosimetry Analysis. Data that used in this work are DICOM and non-DICOM
data. DICOM data consist of CT from OBI volume and planning data while non-DICOM data
consist of energy from electron beam, measured, and calibration data. After data DICOM and
non-DICOM were imported to 3DSlicer, results obtained the medical imaging that illustrated
in figure 11.

Figure 11. medical imaging from DICOM and non-DICOM data after imported process
b. Registration
At this stage registration was done from planning CT volume and measured gel volume to
CBCT or OBI volume. Registration of data planning CT volume was done in auto mode or
manual mode by doing translation and rotation arrangement. Based in figure 11, CT volume
marked as green color and CBCT or OBI volume marked as grey color. In process, Registration
was determined OBI fiducial points and measured gel dosimeter fiducial points by shifting the
medical imaging. Results from this process is illustrate in figure 12.

Figure 12. a) OBI fiducial points, and b) measured gel dosimeter fiducial points

Final step in this stage is register gel volume to OBI. The accuracy of the registered data
depends on the value of Fiducial Registration Error.

c. Calibration

Figure 13. Calibration process Figure 14. graph of optical attenuation

comparison with dose
This calibration stage is performed to determine the optical density in the gel that indicate
the dose from radiation. Data that used in dose calibration were data reference data of percent
depth-dose (PDD), relative dose factor, energy from electron beam, delivered monitor unit
(MUs) and averaging radius. Furthermore, data were plotted to obtain graph comparison of
PDD data and measured calibration data. Finally, measured calibration data adjusted manually
to PDD data (Figure 13). A comparison graph of PDD data with calibration data can be used
to obtain a graph of optical attenuation comparison with dose by limiting the line graph in a
particular region and obtain the value of its polynomial residue (Figure 14).

d. Dose Comparison
In this stage, plan dose volume and calibrate gel volume were compared to obtains new
volume gamma in the form of jar. From the comparison result in figure 15, we can measure
the profile of CT simulation image. Measurements can be made by measuring the gel region.
From the measurement will be obtained graph line profile in the form of correlation intensity
with the distance in the gel jar.

Figure 15. Dose comparison from line profile

Part III :
Variation 2D and 3D view of Volume Maximum Dose in Gel
Dosimetry
Variation in this work were 10%, 40%, 60%, 80%, 90%, and 100% of volume percent maximum
dose. Each variation produced dose distribution that could be identification from 3D jar and profile
line. Results from this work are illustration in figure 16.
Figure 16. 3D and 2D view of variation volume maximum dose

From figure 16, in 3DSlicer with Gel Dosimetry Analysis extension we can variation volume
maximum dose in jar. This features could increase accuracy for measurement at some point due to
more narrowed area.
Profile line can measure the profile of CT simulation image. Measurements can be made
by measuring the gel region. From the measurement will be obtained graph line profile in the form
of correlation intensity with the distance in the gel jar. In figure 17 we can conclude high dose
distribution identification by warmer the gamma volume.

Figure 17 dose distribution in 2D measurement with profile line

Reference
[1] C. Pinter, A. Lasso, A. Wang, D. Jaffray, and G. Fichtinger, “SlicerRT: radiation therapy
research toolkit for 3D Slicer,” Med. Phys., vol. 39, no. 10, pp. 6332–6338, 2012.
[2] C. Pinter et al., “Performing radiation therapy research using the open-source SlicerRT
toolkit,” in World Congress on Medical Physics and Biomedical Engineering, June 7-12,
2015, Toronto, Canada, 2015, pp. 622–625.
[3] K. M. Alexander, C. Pinter, J. Andrea, G. Fichtinger, and L. J. Schreiner, “Implementation of
an efficient workflow process for gel dosimetry using 3D Slicer,” in Journal of Physics:
Conference Series, 2015, vol. 573, p. 012042.
[4] C. Pinter, A. Lasso, and K. Wang, “Tutorial: SlicerRT Extension.” NA-MIC National Alliance
for Medical Image Computing http://www.na-mic.org, 2013.