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results
When the script has finished running, the results are stored on disk in the folder specified by 'output_path' in the YAML file. Most of the results are DICOM files. These can be opened in any DICOM viewer, such as for example openREGGUI. There are some additional files which are not DICOM files as described in the tables below.
The root folder containing all the results is defined by the field 'output_path' in the YAML file. The folder contains the following results files:
| File name | Description |
|---|---|
| CT.mhd, info.mat , w.mat, CT.raw, ipopt_output_file.txt, NLPsolver_options.mat, ROI.mat, warm_start_out.mat, config.txt, dvh_data.mat ,log.txt | Temporary files created at the end of the weight optimization by MIROPT. By keeping these files on disk, MIROPT will not run again an optimization of the weight when the script is restarted. |
| Plan_ridge_tmp1.mat | Temporary files at MATLAB binary format. There is one file per beam. The file is created after optimization of the CEM of the corresponding beam. |
| planRidge.mat | Temporary file at MATLAB binary format. This file is created after having computed the CEM for all the beams. |
This folder contains the main results of the computation. This is where the most interesting information is located.
| Folder name | File name | Description |
|---|---|---|
| Plan_IMPT.dcm | Multi energy layer IMPT plan (mother plan) at DICOM format. This is the IMPT plan, with range shifter, range compensator and the aperture block but without the CEM. The weights in this plan are the result of the MIROPT optimization. | |
| MCsquare_Dose_IMPT.dcm | Dose map (at DICOM format) for the complete treatment (all beams and all fractions). This is the dose map of the mother IMPT plan with multiple energy layers, the range shifter and the aperture but no CEM. |
For each beam in the plan, there is a sub-folder with the output generate for that beam. The folder is name with the beam number.
| Folder name | File name | Description |
|---|---|---|
| Plan_CEM.dcm | Single energy layer plan at DICOM format. This is the plan, with range shifter, aperture and with CEM. The weight are the sum of the weight of all the PBS spots from different energy layers contributing to the single energy layer. | |
| *.stl | 3D representation of the CEM. The file is at the STL format. There is one STL file per treatment beam. The name of the file is defined by the field AccessoryCode for the corresponding beam. | |
| DRprct_beam_1_in_ct_OAR.dcm | Percentile dose rate map (at DICOM format) in the specified RT struct and for the specified beam. There is one such file per beam and per RT-struct defined in a term in the optFunction module. A DICOM editor will open this file as if it was a dose map. The unit is Gy/s. | |
| DADR_beam_1_in_ct_OAR.dcm | Dose averaged dose rate map (at DICOM format) in the specified RT struct and for the specified beam. There is one such file per beam and per RT-struct defined in a term in the optFunction module. A DICOM editor will open this file as if it was a dose map. The unit is Gy/s. | |
| Dose_withCEF.dcm | Dose map (at DICOM format) for one of the beam. There is one such file per beam. This is the dose map at the original resolution with the size of the CT scan with apertures saved in the folder Folder 'output_path'/Outputs/reggui_ct/. It is computed with the CEM, the range shifter and the aperture block and using the single energy layer plan. This dose map is downsampled from the dose maps at resolution CEFDoseGrid |
This folder contains the temporary files created by MCsquare when computing the dose influence matrix of each individual beamlets of the IMPT plan with range shifter and aperture and no CEM. The content of this folder is used by MIROPT to create the dose influence matrix for the IMPT plan witrh all the spots of all energy layers.
| Folder name | File name | Description |
|---|---|---|
| ./Beamlets/, ../ Materials/ | Folder created by MCsquare with temporary file used during dose computation. |
This folders is created only when the field SpotSpacing=0. In order to compute the spot sigma at isocentre, FLASH-MIRTOP computes the dose distribution in the patient CT scan (with the range shifter) for one single PBS spot on the optical axis and with maximum energy. The temporary files for this computation are stored in this folder. See section Folder 'output_path'/Beamlets/ for more information on the content of the folder.
This folder contains a CT scan with the pixel resolution of the original CT scan. The aperture block, range shifter and the range compensator are added in the CT scan. This is the expanded CT scan used to optimize the mother plan (IMPT multi-layers). The range compensator is added directly upstream to the aperture block. The dose map of the mother plan (IMPT multi-layer) should be overlaid to this CT scan.
| Folder name | File name | Description |
|---|---|---|
| ct_IMPT_0001.dcm | CT scan (at DICOM format) with the same spatial resolution as the original planning CT. The aperture block, range shifter and the range compensator are added to the CT scan by setting the HU of the relevant voxel to the HU of relevant material. If the original CT scan was to small to fit the aperture and range compensator, the CT was expanded before adding the aperture. The range shifter is added upstream to the range compensator. | |
| rtstructs_withAperture.dcm | RT struct set (at DICOM format) with the same spatial resolution as the original planning CT. If the CT scan was expanded, the RT-struct have the size of the expanded CT scan. The set contains all the RT struct used by MIROPT to optimize the treatment plan. |
This folder contains a CT scan with the pixel resolution of the original CT scan. The aperture block is included inthe CT scan. This is the expanded CT scan used to optimize the mono-layer plan with CEM. The dose map of mono-layer plan with CEM should be overlaid to this CT scan.
| Folder name | File name | Description |
|---|---|---|
| ct_CEM_0001.dcm | CT scan (at DICOM format) with the same spatial resolution as the original planning CT. The aperture block is added to the CT scan by setting the HU of the relevant voxel to the HU of brass. If the original CT scan was to small to fit the aperture, the CT was expanded before adding the aperture. |
The RT structs stored in 'output_path'/Outputs/ct_IMPT/rtstructs_withAperture.dcm cna be overlaid on this Ct scan.
This folder contains the temporary data to compute the high resolution CT scan and the high resolution dose maps. The original CT scan is divided into sub-volumes. Each sub-volume is centered around one PBS spot. The sub-volume is re-sampled at the spatial resolution specified in intrpCTpxlSize. The CEM, range shifter and the aperture block are added to this high resolution CT scan. A Monte Carlo simulation for one PBS spot is run into this high resolution CT scan and the dose is tallied at a resolution specified by CEFDoseGrid. The global dose map at resolution CEFDoseGrid is computed by adding the dose maps computed in each sub-volume. The dose map is then re-sampled at the resolution of the original CT scan and with the same size as the CT scan in 'output_path'/Outputs/reggui_ct/.
This folder contains the high resolution CT of a sub-volume centered on one PBS spot. There is one folder per PBS spot. The name of the folder describes the X and Y coordinates of the PBS spot (in mm in the IEC gantry coordinate system).
| Folder name | File name | Description |
|---|---|---|
| CT_with_CEM_spt_X_0_Y_15 | CT scan (at DICOM format) around one of the PBS spot at a high spatial resolution defined by the parameter intrpCTpxlSize. The folder name indicates the spot position (mm) in IEC gantry coordinate system. The CT scan contains the CEM (defined by setting the HU of the relevant voxel to the HU of the CEM material), the range shifter and the aperture. The high resolution dose map of the corresponding PBS spot can be overlaid onto this CT scan. |
This folder contains the high resolution dose map of one PBS spot.
| Folder name | File name | Description |
|---|---|---|
| dose_HighRes_spt6_spt_X_0_Y_15.dcm | Dose map (at DICOM format) for one of the PBS spot. The file name indicates the spot position (mm) in IEC gantry coordinate system. This is the dose map computed at resolution CEFDoseGrid, with the CEM, the range shifter and the aperture block and using the single energy layer plan. There is one file per PBS spot. The dose map can be overlaid on the high resolution CT scan 'output_path'/Outputs/CEM_beam1/CT_with_CEM_spt_X_0_Y_15/. |
To allow the researcher to have access to the dose influence matrix of each individual beamlets in the coordinate system of the original CT scan and to have access to the timing of the beamlets, some information is stored in the /Outputs/SpotDoseInCT folder. This allows researchers to develop algorithm to compute dose rate using different definitions.
| Folder name | File name | Description |
|---|---|---|
| dose_UserGrid_spt1_spt_X_-20_Y_0.dcm | Dose map at DICOM format for the beamlet number indicated in the file name. The X,Y position of the bemalet in the IEC gantry CS is indicated in the file name. The coordinate system of the dose map is the same as the low resolution CT scan 'output_path'/Outputs/ct_CEM/. The beamlet can be overlaid onto this CT scan. There is one dose map per beamlet. | |
| SpotTiming.txt | Text file with timing information for each beamlet. |
Each line of the SpotTiming.txt file corresponds to the delivery of one PBS beamlet.
- Column 1 : number of the beamlet (as indicated in the dose map of the beamlet)
- Column 2 and 3 : X and Y position (mm) of the beamlet axis in the IEC gantry coordinate system
- Column 4: Time stamp (ms) at the beginning of the delivery of the beamlet
- Column 5 : Time stamp (ms) at the end of the delivery of the beamlet
Spot Nb , X(mm) , Y(mm) , Tstart (ms) , Tend (ms)
3 , -20.00 , 0.00 , 0.00 , 25.68
2 , 0.00 , 0.00 , 28.18 , 49.04
1 , 20.00 , 0.00 , 51.54 , 74.31
Sometime one wants to restart the simulation but does not wish to restart from scratch because that would take to much time. ConformalFLASH saves the partial results on disk. When restarting the computation, if some partial results are found on disk, the computation of these intermediate results is skipped and the previous results are loaded from disk. The parameter PlanExistentFile must contain the name of the folder containing the intermediate results.
In this section, we describe how to restart the computation from different steps in the process.
| Step | Folder name and File name | Description |
|---|---|---|
| Compute dose influence matrix | ./Beamlets/, ../ Materials/ | If these 2 folder are present in the output path, then the dose influence matrix will not be computed again with MCsaure. The previously saved dose influence matrix will be reloaded from disk. |
| Optimize spot weights | /Outputs/ CT.mhd, info.mat , w.mat, CT.raw, ipopt_output_file.txt, NLPsolver_options.mat, ROI.mat, warm_start_out.mat, config.txt, dvh_data.mat ,log.txt | If these files are present on disk, then the spot weight will not be optimised again by MIROPT. The previouslty optimised wieghts will be reloaded from disk. |
| Optimize spot weights | /Outputs/MCsquare_Dose_IMPT.dcm | If the IMPT dose map has already been computed by MCsquare, it will not be computed again. |
| Optimize CEM shape | /Outputs/Plan_ridge_tmp1.mat | When restarting the simulation, if the CEM will not be re-optimised for all the beams for which this temporary file is present on disk. |
| Optimize CEM shape | /Outputs/planRidge.mat | When restarting the simulation, if the CEM will not be re-optimised for any of the beams if this temporary file is present on disk (NB: all Plan_ridge_tmp1.mat files must be present on disk as well ). |
| Compute high resolution dose maps | /Outputs/CEM_beam1/CT_with_CEM_spt_X_0_Y_15/ ,/Outputs/CEM_beam1/Outputs/dose_HighRes_spt6_spt_X_0_Y_15.dcm | If the high resolution dose map and the high resolution CT scan of a speciifc sub-volume is already present on disk, then the simulation will not recompute the high resolution dose map with MCsaure. It will reload the dose map from disk. |
If you want the simulation to recompute one of the intermediate results (for exmaple because a parameter has changed in the YAML), then you need to delete the files listed in the table at the step you wish to re-start the simulation. You also need to delete all the file of the following steps in the table. Indeed, if a partial result has change at one step in the table, this will impact the following computation and the partial results of these steps cannot be reloaded from disk.