RTOG Download. 1

Planning system download. 1

Program ReadRtogCheck. 1

Patient and Plans. 2

CT images. 2

Additional plans. 2

Beams. 3

Limitations. 3

Skin outline. 3

Example run. 3



RTOG Download


Planning system download

Down load the plan to include the beam positions, the CT scans, the outlined regions of interest including the body outline, and the 3D dose matrix, from the planning system.  If you don’t get the beam positions, you will have to manually locate isocenter and beam angles of each beam.   If no skin boundary, you will have to create one.  Note however, that RTOG does not include the conversion of CT numbers to density.   Dosimetry Check could be used with this program as a means for displaying plans from other systems.


Program ReadRtogCheck

Program ReadRtogCheck is provided to read in treatment plans written in RTOG format.  This is an ASCII program (runs in a winterm or xterm window with a keyboard interface and commands, in Windows a command prompt window) and is invoked with the flag -d followed by the directory where the RTOG files are for the particular patient.  For example:  


ReadRtogCheck  -d  rtog.dir


Where rtog.dir is the directory where the files are.   You must specify the path to this directory if not a subdirectory of the directory you are in.  For Windows, change directory to c:\mathresolutions (use the cd command to change directories for Windows and unix).


This program was created from read_x_tape provided by the RTOG center for the purpose of building a routine to read files in the RTOG format, in case you are familiar with those templates.  That template program makes calls to write information out which we provided to create a patient and plan entry for Dosimetry Check.  The nature of the program as an ASCII program was kept in tact, but we did not support writing all generated messages shown on the screen to a log file.  If any error occurs, note carefully the error message written out and left on the screen.  Some errors are reported which do not effect the read in of the plan.


The program will first list the contents of the directory (our addition) indicated on the command line with the -d flag.  You must specify the characters that form the root of the names of the files.  The files names are typically “aapm0000”, “aapm0001”, etc..  The 0000 file contains a list and specification for the remaining files.  Simply hit the enter key to default (again our addition) to “aapm”.  You may next specify any postfix should there be one following the numbers used in the file names.  Simply hit the enter key to default to none.  Again hit the enter key to select the default number of digits that follow the above root name, or enter a number if different from four.


Patient and Plans

All plans for Dosimetry Check are written under the directory of a particular patient.  The current patient directory is next listed on the screen for convenience.  You will then be prompted to either select an existing patient or to create a new patient directory.  Select an existing patient directory if you all ready have a directory for the particular patient.  Otherwise create a new directory.  When creating a new patient, you can either specify the patient’s name or let the program build the name from the contents of the RTOG file.  Note that the program is limited to downloading only one patient case per run of the program.


CT images

Normally you should be downloading the CT images with the plan and the program is limited to downloading only one set of such images per program run.  These images must by definition be stackable and are specified that way by the RTOG format.  The program will create a new directory under the patient’s directory to hold the image set.  These images are converted to DICOM format when saved.  At this time only CT images are supported.  The RTOG format does not include sufficient information for MRI images to locate the images relative to a coordinate system of the patient, a requirement of DICOM.  Patient supine or prone, head first or feet first is not specified with MRI images.  For CT images the patient will be assumed to be head first supine if that information is otherwise missing.  Upon reading in and displaying the images it is important that you check that the orientation labels, among right, left, anterior, posterior, superior, and inferior, are correct.


Additional plans

You may down load another plan later without including the images.  If not downloading an image set, you will be prompted to select an existing stacked image set.  Generally you should download the CT images with the beam position data, outlined regions of interest, and a 3d dose matrix.  Plans are stored also under the patient’s directory and are associated with a particular stacked image set.



For each beam that is encountered, you will be prompted to select the machine that the beam is on.  The RTOG format is not going to include the name of the directory you have assigned to each treatment machine.  Once you have selected a machine for the first beam, you have the option of defaulting all further beams to that same machine.



There are limitations.  RTOG is limited to transverse only images.  And the outlined regions of interest are limited to contours being coplanar with the transverse image planes.


There is no provision in RTOG for specifying the conversion of CT numbers to density.  You will have to generate a curve to do that.  This function is also found under the Options toolbar under the Stacked Image Sets pulldown and is described in a separate section of this manual under the Primary Stacked Image Set.  If you are able to down load CT images with the pixel values converted to some linear scale relative to density, you will have to specify a conversion of pixel value to density so that the correct density values will result.


Skin outline

If you have downloaded a skin outline, you may later specify this volume as representing the skin boundary.  The selection is made after running Dosimetry Check and is under the Options toolbar under the Stacked Image Sets pulldown.  Otherwise you will have to use the contouring tools to produce a skin outline.  Note that there is an automatic function for that purpose.


Example run

An example run of ReadRtogCheck follows.  The RTOG files in this example are up a directory and in subdirectory adac.d from where ReadRtogCheck is run.   Below “…” indicates where we have left out the reporting of files written.   We want to show the conversation the user has with the program and we have also inserted comments below in a different font from the log.


$ ./ReadRtogCheck -d ../adac.d


ReadRtogCheck, Version 1 Release 2

Depth for motif interface = 24 planes.

Made new color map for Motif.

Can't create overlay visual of depth 8 for Motif popup interface.

For drawing areas, use Open GL and X

For images depth = 24 planes, for 3d displays depth = 24 planes.


Directory of ..\adac.d:

 Volume in drive C has no label.

 Volume Serial Number is 403E-53C4


 Directory of c:\home\adac.d


[.]            [..]           foredose       foredose.gif   RTOG0000

RTOG0001       RTOG0002       RTOG0003       RTOG0004       RTOG0005

RTOG0006       RTOG0007       RTOG0008       RTOG0009       RTOG0010

RTOG0011       RTOG0012       RTOG0013       RTOG0014       RTOG0015

RTOG0016       RTOG0017       RTOG0018       RTOG0019       RTOG0020

RTOG0021       RTOG0022       RTOG0023       RTOG0024       RTOG0025

RTOG0026       RTOG0027       RTOG0028       RTOG0029       RTOG0030

RTOG0031       RTOG0032       RTOG0033       RTOG0034       RTOG0035

RTOG0036       RTOG0037       RTOG0038       RTOG0039       RTOG0040

RTOG0041       RTOG0042       RTOG0043       RTOG0044       RTOG0045

RTOG0046       RTOG0047       RTOG0048       RTOG0049       RTOG0050

RTOG0051       RTOG0052       RTOG0053       RTOG0054       RTOG0055

RTOG0056       RTOG0057       RTOG0058       RTOG0059       RTOG0060

RTOG0061       RTOG0062       RTOG0063       RTOG0064       RTOG0065

RTOG0066       RTOG0067       RTOG0068       RTOG0069       RTOG0070

RTOG0071       RTOG0072       RTOG0073       RTOG0074       RTOG0075

RTOG0076       RTOG0077

              80 File(s)     24,088,152 bytes

               2 Dir(s)  32,553,619,456 bytes free


Note above that the contents of the directory are listed out.   If you don’t see any files than you specified the path incorrectly after the –d flag.  Below the user or prompted to enter the prefix for the files, which typically is either RTOG as in this case, or aapm.  Only the files of the form “RTOGnnnn” are RTOG files in this example.  The form is generally four letters followed by four numbers.  0000 is the file that list the rest of the files.


Enter prefix for file names to be read (usually 'aapm'):RTOG

prefix = RTOG


Enter postfix for file names to be read (usually ''):


# of digits for file name #'s to be read (usually '4'):

# of digits = 4


prefix = RTOG

           Program: read_x_tape.c,v $ - Version: 1.3 $ - Date: 2000/01/19 17:2

52 $

           Started on: 01/26/2004 at: 15:53 PM by NO_USER_NAME

           Source directory for processing


           Date of directory file creation: Thu Mar 20 16:41:12 2003


Patient Directory pat.d:



Is patient ADAC CASE a new patient? (1=Yes, 0=No) 1

Patient directory name = ADACCASE

Is this right? (1=Yes, 0=No)


           patient directory = ADACCASE


The reading program was downloaded from the RTOG center and may indicate some errors which evidently do not effect the read in of the plan.  Just select to continue processing.


ERROR!: [CT IMAGE] Scan type entry missing

ERROR!: Parsing CT directory entries FILE: 1

           Tape standard for this data set = 3.00

ERROR!: Initializing the tape directory structure


Continue (1=Yes, 0=No): 1

        Processing CTSCAN file (1)

           wrote file pat.d\ADACCASE\SIS.d\CT_26-Jan-2004\CT_001

        Processing CTSCAN file (2)

           wrote file pat.d\ADACCASE\SIS.d\CT_26-Jan-2004\CT_002

        Processing CTSCAN file (3)

           wrote file pat.d\ADACCASE\SIS.d\CT_26-Jan-2004\CT_003

        Processing CTSCAN file (4)

           wrote file pat.d\ADACCASE\SIS.d\CT_26-Jan-2004\CT_004



. . .  Here all the CT scans are read in.


wrote file pat.d\ADACCASE\ckpn.d\0\PrimarySIS

wrote file pat.d\ADACCASE\ckpn.d\0\PlanType


Next, the program prompts the user to select the accelerator that the first beam uses, since the Dosimetry Check accelerator name will not be in the RTOG file.


For plan 0, select treatment machine

for beam number 0, LAO, energy= 6 MeV

1  GeneralAccel

2  SL20B

Select machine directory: 1


. . .


wrote file pat.d\ADACCASE\ckpn.d\0\b.d\RPO_03\IsocenterLoc

wrote file pat.d\ADACCASE\ckpn.d\0\b.d\RPO_03\Angles

           beam RPO_03 is done.

        Processing BEAMGEOM file (59)

           Plan name: 0


Next the user selects to continue to associate the rest of the beams with the first choice made for an accelerator for the first beam encountered above.


For plan 0,

for beam number 1, L Lat, energy= 6 MeV

  1   Use machine GeneralAccel for this and all remaining beams.

  2   Continue to choose the machine for each beam.For plan 0, 1


. . .


        Processing BEAMGEOM file (61)

           Plan name: 0

wrote file pat.d\ADACCASE\ckpn.d\0\b.d\L_Lat_ref_06\MachineName

wrote file pat.d\ADACCASE\ckpn.d\0\b.d\L_Lat_ref_06\BeamEnergy

wrote file pat.d\ADACCASE\ckpn.d\0\b.d\L_Lat_ref_06\BeamType

wrote file pat.d\ADACCASE\ckpn.d\0\b.d\L_Lat_ref_06\IsocenterLoc

wrote file pat.d\ADACCASE\ckpn.d\0\b.d\L_Lat_ref_06\Angles

           beam L_Lat_ref_06 is done.

        Processing DOSEDIST file (62)

3D dose matrix size is 47 horizontal by 59 vertical by 53 depth

           Plan name: 0

           wrote file: pat.d\ADACCASE\ckpn.d\0\Foreign3dDoseLattice

        Processing DOSEVOLUMEHISTOGRAM file (63)

           'save_dvh' not supported

        Processing DOSEVOLUMEHISTOGRAM file (64)

           'save_dvh' not supported


. . .


We do not use the dose volume histogram files.   Dose volume histograms are recomputed from the 3D dose matrix read in and compared to that computed by Dosimetry Check.


        Processing DOSEVOLUMEHISTOGRAM file (77)

           'save_dvh' not supported

           Finished on: 01/26/2004 at: 16:00 PM


Finished on: 01/26/2004 at: 16:00 PM