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 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.
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.
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.
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.
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.
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
..\adac.d
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)
1
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