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| # Intro | ||
| This repository provides python scripts for head-and-neck photon and proton radiotherapy planning (in Raystation). It produces results for the paper - "Large-scale dose evaluation of deep learning organ contours in head-and-neck radiotherapy by leveraging existing plans" (under review). | ||
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| # Abstract | ||
| **Background and Purpose**: Retrospective dose evaluation for organ-at-risk auto-contours has previously used small cohorts due to additional manual effort required for treatment planning on auto-contours. We aim to do this at large scale, by a) proposing and assessing an automated plan optimization workflow that uses existing clinical plan parameters and b) using it for head-and-neck auto-contour dose evaluation. | ||
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| **Materials and Methods**: Our automated workflow emulates our clinics treatment planning protocol and reuses existing clinical plan optimization parameters. This workflow recreates the original clinical plan (P<sub>OG</sub>) with manual contours (Pmc) and evaluates the dose effect (P<sub>OG</sub> − P<sub>MC</sub>) on 70 photon and 30 proton plans of head-and-neck patients. As a use-case, the same workflow (and parameters) creates a plan using auto-contours (P<sub>AC</sub>) of eight head-and-neck organs-at-risk from a commercial tool and evaluates their dose effect (P<sub>MC</sub> − P<sub>AC</sub>). | ||
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| **Results**: For plan recreation (P<sub>OG</sub> − P<sub>MC</sub>), our workflow, has a median impact of 0.99% and 1.45%, across dose metrics of auto-contours, for photon and proton, respectively. Computer time of automated planning is 25% (photon) and 42% (proton) of manual | ||
| planning time. For auto-contour evaluation (P<sub>MC</sub> − P<sub>AC</sub>), we notice an impact of 2.01% and 2.58% for photon and proton radiotherapy. All evaluations have a median ∆NTCP less than 0.30%. | ||
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| **Conclusions**: The plan replication capability of our automated program provides a blueprint for other clinics to perform auto-contour dose evaluation with large patient cohorts and minimal skill and resource requirements. Finally, in spite of geometric differences, auto-contours, have a minimal mediandose impact, hence inspiring confidence in their utility and facilitating their clinical adoption. | ||
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| # Method | ||
| <img src='assets/graphical-abstract.jpg'> | ||
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| # Scripts | ||
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| ## Installation | ||
| Within the Raystation python 3.6 environment, run the following command to install the required packages. | ||
| ```bash | ||
| pip install pydicom | ||
| ``` | ||
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| 1. For photons | ||
| - [src/hnDosePhotons.py](src/hnDosePhotons.py) | ||
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| 2. For protons | ||
| - [src/hnDoseProtons.py](src/hnDoseProtons.py) | ||
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| 3. Other files | ||
| - [src/config.py](src/config.py) | ||
| - [src/helpers.py](src/helpers.py) |
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| PTV_DL1_DVH;V95%DL1 (%); | ||
| PTV_DL1_obj;D0.03cc (%DL1);Dmean (%DL1) | ||
| PTV_DL2_DVH;V95%DL2 (%); | ||
| PTV_DL2_obj;Dmean (%DL2);D0.03cc (%DL2) | ||
| SpinalCord;D0.03cc (cGy); | ||
| SpinalCord+3;D0.03cc (cGy); | ||
| Brainstem_Surf;D0.03cc (cGy); | ||
| Brainstem_Core;D0.03cc (cGy); | ||
| OpticChiasm;D0.03cc (cGy); | ||
| OpticNrv_L;D0.03cc (cGy); | ||
| OpticNrv_R;D0.03cc (cGy); | ||
| Eye_L;D0.03cc (cGy); | ||
| Eye_R;D0.03cc (cGy); | ||
| Brain;D0.03cc (cGy);D2% (cGy) | ||
| Pituitary;Dmean (cGy); | ||
| Lens_L;D0.03cc (cGy); | ||
| Lens_R;D0.03cc (cGy); | ||
| Cochlea_L;Dmean (cGy); | ||
| Cochlea_R;Dmean (cGy); | ||
| Parotid_L;Dmean (cGy); | ||
| Parotid_R;Dmean (cGy); | ||
| Glnd_Submand_L;Dmean (cGy); | ||
| Glnd_Submand_R;Dmean (cGy); | ||
| Oral_Cavity;Dmean (cGy); | ||
| Musc_Constrict_S;Dmean (cGy); | ||
| Musc_Constrict_M;Dmean (cGy); | ||
| Musc_Constrict_I;Dmean (cGy); | ||
| Cricopharyngeus;Dmean (cGy); | ||
| Larynx_SG;Dmean (cGy); | ||
| Esophagus;Dmean (cGy); | ||
| Glottic_Area;Dmean (cGy); | ||
| Bone_Mandible;D2% (cGy); | ||
| Bone_Mandible-PTV;D2% (cGy); | ||
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| { | ||
| "CTV_DL1 [D98%>95%]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "CTV_DL1 [D98%>94%]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "CTV_DL2 [D98%>95%]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "CTV_DL2 [D98%>94%]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "CTV_DL2 [D2%<107%]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "SpinalCord_Core [D0.03cc (cGy) < 5000]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "SpinalCord_Core [D0.03cc (cGy) < 5569]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "SpinalCord_Surf [D0.03cc (cGy) < 6000]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "SpinalCord_Surf [D0.03cc (cGy) < 6310]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Brainstem_Core [D0.03cc (cGy) < 5400]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Brainstem_Core [D0.03cc (cGy) < 5870]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Brainstem_Surf [D0.03cc (cGy) < 6000]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Brainstem_Surf [D0.03cc (cGy) < 6310]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Brain-CTV_DL2 [D0.03cc (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Brain-CTV_DL2 [D0.03cc (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Cochlea_L [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Cochlea_R [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Parotid_L [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Parotid_R [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Glnd_Submand_L [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Glnd_Submand_R [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Oral_Cavity [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Musc_Constrict_S [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Musc_Constrict_M [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Musc_Constrict_I [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Cricopharyngeus [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Larynx_SG [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Glottic_Area [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Esophagus [Dmean (cGy)]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| , "Bone_Mandible [D2%<100%]":{ | ||
| "Passed": -1, "Voxelwise-worst": -1, "NominalDose": -1, "Scenarios": [] | ||
| } | ||
| } |
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| <?xml version="1.0" encoding="ASCII" standalone="yes"?> | ||
| <RayStationScriptTemplates> | ||
| <IsodoseTemplate conditionalDoseLevels="DL1"> | ||
| <Isodose relativeToDoseLevel="DL1" color="64,0,0">115</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="128,0,0">110</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="255,0,0">107</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="255,128,0">105</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,128,0">100</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,255,0">95</Isodose> | ||
| </IsodoseTemplate> | ||
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| <IsodoseTemplate conditionalDoseLevels="DL1,DL2"> | ||
| <Isodose relativeToDoseLevel="DL2" color="255,0,0">107</Isodose> | ||
| <Isodose relativeToDoseLevel="DL2" color="255,192,0">100</Isodose> | ||
| <Isodose relativeToDoseLevel="DL2" color="255,255,128">95</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="255,255,255">107</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,128,0">100</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,255,0">95</Isodose> | ||
| </IsodoseTemplate> | ||
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| <IsodoseTemplate conditionalDoseLevels="DL1,DL2,DL3"> | ||
| <Isodose relativeToDoseLevel="DL3" color="255,0,0">107</Isodose> | ||
| <Isodose relativeToDoseLevel="DL3" color="192,0,96">100</Isodose> | ||
| <Isodose relativeToDoseLevel="DL3" color="255,128,192">95</Isodose> | ||
| <Isodose relativeToDoseLevel="DL2" color="255,255,255">107</Isodose> | ||
| <Isodose relativeToDoseLevel="DL2" color="255,192,0">100</Isodose> | ||
| <Isodose relativeToDoseLevel="DL2" color="255,255,128">95</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="255,255,255">107</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,128,0">100</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,255,0">95</Isodose> | ||
| </IsodoseTemplate> | ||
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| <IsodoseTemplate> | ||
| <Isodose relativeToDoseLevel="DL1" color="0,0,128">90</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="64,64,192">80</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="128,128,255">70</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="192,192,255">50</Isodose> | ||
| <Isodose relativeToDoseLevel="DL1" color="192,192,192">25</Isodose> | ||
| </IsodoseTemplate> | ||
| </RayStationScriptTemplates> |
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