Computed tomography

== <span style="color:#000080"> Introduction </span> ==

This tutorial is based on the GEANT4 DICOM example originally developed by Louis Archambault, Luc Beaulieu and Vincent Hubert-Tremblay. In this example a list of DICOM files (.dcm) are converted to ASCII files (.g4dcm) and binary (.g4bin) that can be read by GEANT4. Each of these files corresponds to a Z slice. Then, the .g4dcm (.g4bin) files are merged into one unique volume and used by GEANT4 to construct patient geometry and materials.  

The geometry is constructed by voxelizing the volume. There are four navigation algorithms used to create the voxel geometry: '''G4RegularNavigation''', '''G4VNestedParameterisation''', '''G4SmartVoxel'''/'''G4VoxelNavigation''' and '''G4PVReplica'''.   

The material is constructed by converting the pixel values (Hounsfield numbers) from the DICOM images to densities using   
the [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/CT2Density.dat Hounsfield scale]. Then, the densities are converted to material types according to this [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/Materials.txt table].

A simple monenergetic electron beam is simulated using '''G4ParticleGun''' class. The output of the tutorial is a text file with dose deposition in several voxels. The dose is scored using classes '''G4VSensitiveDetector''' and '''G4THitsMap'''. 

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/dicom.png

This is one of the DICOM files that is used in the tutorial.

== <span style="color:#000080"> How to run the tutorial </span> ==

; Connect to the HEP cluster and create folder DICOMFolder in your area

<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk 

username@plus1.hep.ucl.ac.uk's password: type your password here

[username@plus1 ~]$ mkdir DICOMFolder 

[username@plus1 ~]$ cd DICOMFolder  
</pre>

; Setup your environment

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh  
</pre>

; Copy the code to your working directory and rename it

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ cp -r /unix/pbt/tutorials/advanced/DICOM .
  
[username@plus1 DICOMFolder]$ mv DICOM DICOM_source
</pre>

; Inside /home/username/DICOMFolder/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ mkdir DICOM_build  
</pre>

; To compile the code enter this directory and run cmake and make 

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOMFolder]$ cd DICOM_build 

[username@plus1 DICOM_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/DICOMFolder/DICOM_source 

[username@plus1 DICOM_build]$ make  
</pre>

; Before running the code you can chose among several voxelization algorithms.  

* Using <span style="color:#ff0000"> G4RegularNavigation </span>:

It is a special algorithm to navigate in a regular voxelised geometry. It includes an option to skip frontiers between voxels when they have the same material i.e. "replacing group of voxels with a smaller number of larger voxels". '''G4RegularNavigation''' class is the default setup for this tutorial. To run with the default settings simply run macro run.mac.

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

* Using <span style="color:#ff0000"> G4NestedParameterization </span>:

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ export DICOM_NESTED_PARAM=1
</pre>

You can check if you set this environment variable correctly by typing in the command line

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ env
</pre>

Then, run the code:

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

* Usinging <span style="color:#ff0000"> G4SmartVoxel / G4VoxelNavigation </span>:

Using smart voxels required a huge amount of memory. At /home/username/DICOMFolder/DICOM_source/src/DicomRegularDetectorConstruction.cc set
 
<pre style="color: #800000; background-color: #dcdcdc">
patient_phys->SetRegularStructureId(0);
</pre>

compile and run the code:

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ make

[username@plus1 DICOM_build]$ ./DICOM run.mac
</pre>

== <span style="color:#000080"> How to analyze data </span> ==

This is a [http://geant4.web.cern.ch/geant4/UserDocumentation/Doxygen/examples_doc/html/ExampleDICOM.html link] to the official DICOM explanation notes. We recommend to read it before proceeding with this tutorial.

=== <span style="color:#000080"> Text files </span> ===

The macro run.mac produces a text file which includes the dose deposition in several voxels.

=== <span style="color:#000080"> Visualisation </span> ===

Run the visualisation macro vis.mac

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ ./DICOM vis.mac
</pre>

which will produce .prim file. You can open this file in DAWN

<pre style="color: #800000; background-color: #dcdcdc">
[username@plus1 DICOM_build]$ dawn g4_00.prim
</pre> 

This will create 3D image showing the patient geometry and the incident electron beam. The image is big and it takes time to open:

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DICOM/g4_03.eps