dvf

Dose warping implementation using deformation vector field (DICOM)

Class design

Class to represent a type of 3D rectangles, CT, RTDOSE, and DVF is written.

Among interpolation algorithms such as Trilinear, Prismatic, Pyramid, Tetrahedra, Nearest neighbor, etc., Trilinear is implemented.

How to compile

Library dependencies: gdcm (2.6.x)
compiler:
- For Mac, Apple LLVM version 10.0.1 (clang-1001.0.46.3).
- For Linux, never tested


$ cmake .
$ make 
$ ./dvf --ctdir <your_ct_dir_path> --dosefile <your_rtdose_file> --dvffile <your_dvf_file>

Getting DVF from MIM

Load Two image series using MIM

Click fuse icon
Then MIM will show at bottom (be careful which one is moving or fixed) The seriese you click first will be the reference.

Click DIR button
Then there will be a new CT that is deformed (top row).
Click Save DIR

Then a DICOM file is created. For the detail of the file see:

http://dicom.nema.org/MEDICAL/dicom/2017b/output/chtml/part03/sect_C.20.3.html

Example code (dvf_smc.cpp)

//ctdir
std::string dname = cl_opts["--ctdir"][0];
rti::ct<float> myct(dname);
myct.load_data();

//rtdose
std::string fname = cl_opts["--dosefile"][0];
rti::rtdose<float> mydose(fname);
mydose.load_data();

//dvf file
std::string dvfname = cl_opts["--dvffile"][0];
rti::dvf<float, float> mydvf(dvfname);
mydvf.load_data();

//Create empty grids
rti::rect3d<float,float>  dose_grid;
rti::rect3d<float,float>  ct_grid;
rti::rect3d<float,float>  dvf_grid;

//Copy various grid structures to empty grids
rti::clone_structure(mydose, dose_grid);
rti::clone_structure(myct, ct_grid);
rti::clone_structure(mydvf, dvf_grid);

float fill_value = 0.0;

//Write dose to various grid
rti::interpolate(mydose, dose_grid, fill_value); //interpolate dose on DOSE grid
rti::interpolate(mydose, ct_grid,   fill_value); //interpolate dose on CT grid
rti::interpolate(mydose, dvf_grid,  fill_value); //interpolate dose on DVF grid

CT (nx,ny,nz): (512, 512, 200)
CT (dx,dy,dz): (1.26953, 1.26953, 2.5)
CT (x,y,z): (-325, -325, -317.5)
RTDOSE (nx,ny,nz): (100, 100, 60)
RTDOSE (dx,dy,dz): (2, 2, 2.5)
RTDOSE (x,y,z): (-181.1, 7.4, -47.55)
DVF (nx,ny,nz): (144, 101, 161)
DVF (dx,dy,dz): (2.9975, 2.99157, 2.99689)
DVF (x,y,z): (-211.148, -104.51, 162.252)

It took < 1 sec to load CT, RTDOSE, and DVF on mac i5 3.5 Ghz and 3.5 secs to perform all interpolation.

CT grid and DOSE grid (small)	Doses interpolated to CT grid and DOSE grid

Grid (CT, DVF, DOSE) alignment with CT	Grid (CT, DVF, DOSE) alignment with DVF and dose

Here are the conversion result (including interpolation step)

source	destination	success/fail	comment
CT	CT	FAIL	needs fix (not high priority), interpolation with int?
CT	RTDOSE	FAIL
CT	DVF	FAIL
DOSE	CT	SUCCESS
DOSE	RTDOSE	SUCCESS
DOSE	DVF	SUCCESS
DVF	CT	SUCCESS
DVF	RTDOSE	SUCCESS
DVF	DVF	SUCCESS

Dose warping

The dose warping is implemented. Dose of source (moving phase) is pulled from the destination grid.

Based on the point calculated from vector field, 8 points enclosing the translated point are found, and then dose is interpolated.

Plastimatch uses its own implementation or uses itk::WarpImageFilter

https://itk.org/Doxygen/html/classitk_1_1WarpImageFilter.html

ncidosimetry/dvf

dvf

Class design

How to compile

Getting DVF from MIM

Example code (dvf_smc.cpp)

Dose warping