ReadDicomCheck. 1

Coordinate Systems. 2

Patient 2

Warning Selecting Patient: 2

Auto Read Case. 3

Stacked Image Set 4

CT number to Density Conversion. 4

Regions of Interest (ROI) 4

Options. 4

Plan. 4

Beams. 5

Contouring. 5

Auto Report 5

Saving of Dicom Files. 5

Dosimetry Check. 5





Run the program ReadDicomCheck to import plans in Dicom RT format to Dosimetry Check.You can select this program from DosimetryCheckTasks, or you can run the program from the current directory by typing:


in a command prompt window.


Below is a picture of the main window for this program:



This program will read in Dicom RT files and write out the patient directory with the plan for Dosimetry Check to pick up.The planning system should write out the plan into Dicom RT files, which are then read.Either navigate to the directory where these files are, or copy them into some convenient directory.†† By default, the file selection box starts in the directory where it expects to find image files as defined in the file NewDicomRTDirectory.loc in the program resources directory, or if that file is not present, then the file NewImagesDirectory.loc.†† The CT scans will be each in a separate file.The outlined region of interest structures, plan, and 3D dose matrix are assumed to be in different files.These files may or may not start with convenient prefixes, such as the structure file starting with the letters RS, the beam geometry in a file starting with the letters RP, and the 3D dose matrix in a file starting with the letters RD.After reading in the Dicom RT files, run Dosimetry Check and select the patient directory created here, and then the plan created here.Below are comments on running the program ReadDicomCheck.

Coordinate Systems

The Dicom standard is that the coordinate system is to be Dicom, and everything, CT images, isocenter, points, region of interest contours, must be in the same coordinate system (otherwise how would one know where isocenter is relative to the CT scans, etc.).  Further, the Dicom standard states that the medical accelerator coordinates (referring to gantry angle, couch angle, collimator angle, etc.) must be in IEC coordinates.Internally Dosimetry Check is IEC, so no transformations are needed upon reading in accelerator coordinates.The Geometry file (see beam data section) is only referred to in presenting a machine coordinate to the user (see Beam below).


Therefore, after passing through the Dicom filter,


all information about the coordinate system used in the treatment planning system is lost and unrecoverable.


The coordinate system used by Dosimetry Check is IEC, not Dicom.IEC is positive Y axis toward the patient's head, positive Z axis posterior to anterior. Only the X axis agrees with Dicom. The origin is at the center of the box that holds all the CT scans, hence is dead center in the patient model.


You have to first create a patient or select an existing patient in your present system unless you are going to use the Auto Read Case option below.


Warning Selecting Patient:

Once you have selected a patient, the program will continue to use the same patient.You have to back out of the program to select or create a different patient.Be sure you are putting files into the correct patient directory.


The current patientís name is shown on the title bar of the main application window.


If you don't know the patient's name you can get it from any CT scan file using program DicomDump in the tools.dir directory respectively.This program is an ASCII program.Invoke with the program name followed by the name of the CT scan file to read.You might want to pipe to the more function, for example:

DicomDumpfile_name | more

Youcan also access the program from DosimetryCheckTasks or MarkRT tasks, in which case you will get a file selection box where you can navigate to the file and select it.

Look for Dicom (10,10).


Other Dicom display functions can be found on the internet.


Create the patient if a new patient or select an existing patient.It is your responsibility to guarantee that the images and plan belong to the correct patient, and that the plan is for the stacked image set selected.


Auto Read Case

You may use this feature to read in a case.You do not have to first create or select a patient.The program will do so from the patientís name in the Dicom plan file.But you must back out of the program to create or use a different patient.By selecting a patient, you can over ride which patient where the data goes.


You must navigate to the top of a directory tree that will contain all the files for the case:CT scans, structure file, plan file, and dose file.There can be more than one patient and case in the directory tree.The program will present you the list of patient-plans that it finds, and you are to pick one.Selecting this option the program will do the rest but you should review the messages when it finishes. You might have to select the accelerator for instance if the machine name in the plan is not in the list of machines for Dosimetry Check or MarkRT.


This auto feature will also accept MRI scans.


If these conditions are not met, you can select individual components as described below.


But this function has the limitation that you can only use it once, there after you will have to back out of the program (hit Exit) and then select to run the program again. The limitation is that only one stacked image set can be supported per run.However, you can manually select a second plan (and then dose) to read in for the same stacked image set and patient (see below)


If you have a second plan for the same stacked image set, then select the stacked image set and manually select the plan and dose file below.†† If you use the Auto Read Case feature, you will end up with a duplicate stacked image set.However, if your contours for the second plan are different, you might want a duplicate stacked image set for the plan. Each plan is associated with a stacked image set, but a stacked image set can be used by more than one plan.ROI contours belong to the stacked image set in Dosimetry Check and MarkRT, not the plan.


Stacked Image Set

You next have to select an existing stacked image set or read in a new one.The plan to be read has to be for the stacked image set.If creating a new stacked image set, use the filter on the file selection box to read in only scan files, for example, by setting the filter to CT*.Then select all files to read in.This program will here allow you to only select or read in one stacked image set.Back out of the program if you have to read in a second one.This stacked image set is the primary image set for the plan which supplies the external body outline and the CT number to density conversion function.



CT number to Density Conversion

There is no mechanism in Dicom RT for specifying how CT numbers are converted to density.†† Therefore you will still have to provide a conversion for Dosimetry Check.Go under StackedImageSet to Options to Density.You can read in a scan of a phantom with biological materials (by creating a stacked image set out of the scan) and run a curve.You can also type in numbers if you have values.Water density for most CT scanners have a pixel value of 1024 in Dosimetry Check.Dosimetry Check does not use Hounsfield numbers.A Houndsfield number of -1000 would be a pixel value of 24, 0 1024, and 1000 2024.


Regions of Interest (ROI)

Once you have read in the stacked image set you should read in outlined regions of interest (ROI).There is a mechanism for identifying which ROI is the external body outline.However, if that fails or is absent, you will have to select the body outline or create it in Dosimetry Check.To create a body outline, use the tool for that purpose under Contouring.To select an existing body outline, go under StackedImageSets to Options to Skin.You might want to check the choice as a matter of routine.There is a check to see if the ROI came from the selected stacked image set.


Generally the Dicom RT ROI file starts with the letters RS.


You can push the Stacked Image Set options toolbar to make selections for the CT number to density curve, and the ROI volume that is to be the body contour.


Once you have the stacked image set, you can read in a plan.Here we only pick up the beam positions (gantry, collimator, and couch angles, and isocenter location) and 3D dose matrix.First select to read in the beams by reading in the plan file.You must read in the beams first and then select to read in the dose matrix second.You cannot read in the dose matrix without having read the beam file first in the same session.This is because there is information about the plan in the beam file that is needed by the dose matrix function that is not provided in the dose file.There is a check that the dose file is for the selected beam file.


Generally the Dicom RT beam file starts with the letters RP and the dose file with the letters RD.



If the accelerator machine name is not one that exist in the treatment machine directory, you will be prompt to select the accelerator that the beams are to use.This choice will apply to all the beams.Naturally the selected machine must have the required energy.Dicom RT specifies the accelerator coordinates in IEC coordinates, which is also the system for Dosimetry Check, so no conversion is needed here.The Geometry file in each machine directory simply specifies how the coordinates are presented to the user.For example, for a non-IEC accelerator, the gantry angle will be converted from IEC to the system specified in the Geometry file when presented to the user.Changing the Geometry file will therefore not change the actual angle of a beam, only the angle reported to the user.This will not apply of course if the user types in an angle.


If the machine name in the plan read above is not found in the list of machines in Dosimetry Check, then you will be prompted to select an accelerator.You will always have the option of picking a different machine afterwards.The machine list in Dosimetry Check is the list of directory names in bd.d.The option menu will show the accelerator that was picked.


You can push the contouring toolbar to complete any needed contouring, assignments of densities to region of interest volumes, and creation of a couch model.

Auto Report

For automatic processing of EPID images to occur you must make selections for the auto report, input the dose for gamma analysis and the gamma criteria.If this section is incomplete the auto report cannot be produced automatically.

Saving of Dicom Files

All the imported files are saved under the sub-directory Imports.d in the patientís directory.

Dosimetry Check

After reading in the plan, exit the program and run Dosimetry Check (or MarkRT).Select the patient, stacked image set, and then the plan.For each beam you must read in a fluence file (in rmu units).Dosimetry Check shows the dose in the resolution selected under Evaluate.For example, if Dosimetry Check has the default value of 0.5 cm, then a matrix of that spacing is provided for any selected plane.Doses are interpolated out of the 3D dose matrix read above.If the imported 3D dose matrix has a spacing of 0.1 cm and the above is set to 0.5 cm, you will see the isodose curves plotted on a 0.5 cm matrix.There is an option under Evaluate on the Plan toolbar to show just the dose from the treatment planning system.Dosimetry Check could thus be used as a tool to display plans from other systems.