Changeset 1337 for trunk/examples/extended/medical/DICOM/README

Timestamp:

Sep 30, 2010, 2:47:17 PM (14 years ago)

Author:

garnier

Message:

tag geant4.9.4 beta 1 + modifs locales

File:

• trunk/examples/extended/medical/DICOM/README (modified) (6 diffs)

trunk/examples/extended/medical/DICOM/README

@@ -18 +18 @@
 
 And it has been deeply reviewed by Pedro Arce in December 2007.
+Very small changes by Stephane Chauvie in January 2008.
+Stephane Chauvie, Oct 2009: changed Physics list; changes in DICOM read. 
+Stephane Chauvie and Andrea Armando; June 2010 adapted for reading  whatever DICOM file
 
 
@@ -30 +33 @@
 
  - A standard Geant4 example GNUmakefile is provided            
- - Compile it with 'make' 
+ - Compile it with 'make'/'gmake' 
 
 ---> 3) Run the example:
 
- - To run the environment variable G4LEDATA needs to be set, pointing to the low energy data base, G4EMLOW4.3      
+ - To run the environment variabmore le G4LEDATA needs to be set, pointing to the low energy data base
 
  - batch mode:
@@ -41 +44 @@
  - interactive mode:
    - $G4INSTALL/bin/Linux-g++/dicom
-   the file vis.mac is read in order to visualise the phantom with OpenGL
+   the file vis.mac is read in order to visualise the phantom with OpenGL, DAWN or VRML
 
 --->4) Metadata:
 
  The file Data.dat has the following information
-  - A line with the compression value (used only to create the .g4dcm, not to read it)
+  - A line with the compression value (used only to create the .g4dcm and .g4dcmb, not to read it)
   - A line with the number of files 
   - A line for each file name (to these names it will be added the suffix .dcm to read the DICOM files in their original format, and the suffix .g4dcm to read the text files that contain the DICOM information where the Hounsfield numbers have been converted to material and densities)
@@ -94 +97 @@
 The file Colormap.dat defines the colour that will be assigned to the voxels of each material.
 
---->8) DICOM text file format:
+--->8) DICOM file formats:
 
 The DICOM files are converted to a simple text format. You may create your own file with the following format (see e.g. 14196616.g4dcm):
@@ -109 +112 @@
 As commented before the DICOM files (.dcm) are assumed to describe one Z slice per file, and therefore the GEANT4 text files (.g4dcm) created from them have also one unique Z slice per file. Nevertheless if you create your own .g4dcm file you may include as many Z slices as desired. In any case you have to respect the rule that the Z slices must be contiguous.
 
+The same information is also used to fill a file in binary format, that contains the same information as the text format. Its name ends in .g4dcmb, instead of .g4dcm .
+
 --->9) Choosing different parameterisation/navigation options:
 
 There are four possible ways in GEANT4 to treat the navigation in regular voxelised volumes:
 
-- The non-optimised way. It will be very slow because each time a track exits a voxel it has to loop to all other voxels to know which one it may enter
-- The optimisation with G4SmartVoxel: a 3D grid is built, so that the location of voxels is fast, but it requires a lot of memory
+- The 1D optimisation . It will be very slow because each time a track exits a voxel it has to loop to all other voxels to know which one it may enter
+- The 3D optimisation with G4SmartVoxel: a 3D grid is built, so that the location of voxels is fast, but it requires a lot of memory
 - Using G4NestedParameterisation. The search is done hierarchically in X, Y and Z. It is fast and does not require big memory
-- Using G4PhantomParameterisation/G4RegularNavigation: an special algorithm to navigate in regular voxelised geometries (see GEANT4 doc). This is the fastest way without any extra memory requirement (and it is the default in this example). It includes an option (default) to skip frontiers between voxels when they have the same material
+- Using G4PhantomParameterisation/G4RegularNavigation: an special algorithm to navigate in regular voxelised geometries (see GEANT4 doc). This is the fastest way without any extra memory requirement (and it is the default in this example). It includes an option (default) to skip frontiers between voxels when they have the same material. When using this option at each step the energy is all deposited in the last voxel; for properly distribution of the dose (=energy/volume) the G4PSDoseDeposit_RegNav scorer can be used (see below)
 
 You can select amont the four options in the following way:
@@ -138 +143 @@
 - To use the third option you have to set the enviromental variable DICOM_NESTED_PARAM to 1
 
+
+--->10) Calculating dose in phantom voxels for regular navigation
+
+As mentioned above the regular navigation has the option to keip voxel frontiers when two voxels share the same material, what can make the CPU time several times smaller. But this option makes that all energy deposited is computed in the last voxel, instead of distributing it along the voxels traversed. To properly calculate the dose in each voxel the G4PSDoseDeposit_RegNav scorer can be used.
+It takes into account the fact that,  when the particle travels through the voxels it looses energy and therefore the energy lost per length (dEdx) is bigger and also the effect of the multiple scattering is bigger. 
+The algorithm to make this correction is an iterative one, as the step length increase due multiple scattering (that converts the geometrical step length in what we will call the true step length) and the energy loss are correlated.
+It works in the folloing way: first the total true step length is distributed among the voxels proportionally to their geometrical step length; with these values it is calculated one voxel after another the value of dEdx and then the value of the kinetic energy at the entrance of each voxel; with these values it is calculated the geometrical to true step corrections due to multiple scattering for each voxel; finally these new values are used to recalculate the energy lost in each voxel. It has been demonstrated for dose in a water phantom and in a real phantom that the two-step iteration described is enough to reproduce the dose calcualted when no skipping of voxel frontiers is done.
+
+This scorer is implemented in this examples if the regular navigation option is 
+chosen. It is triggered at the method RegularDicomDetectorConstruction::ConstructPatient() by the call
+
+SetScorer(voxel_logic);
+
+--->11) Output
+dicom.out is produced running th macro file run.mac. It has 2 columns: the first is the number of 
+voxel (ordered in x,y,z) and the second the dose there deposited (in Gy)
+It is produced, as an example, with a compression value of 32