SlicerRT: Radiation therapy research toolkit for 3D Slicer

In this paper, the highest level of inter-and intra-observer conformity achievable with different treatment planning systems (TPSs), contouring tools, shapes, and sites have been established for metrics including the Dice similarity coefficient (DICE) 2 AbstractIn this paper, metrics including the Dice similarity coefficient (DICE) and Hausdorff Distance determine the highest level of inter-and intra-observer conformity achievable with different treatment planning systems (TPSs), contouring tools, shapes, and sites. High conformity values, e.g. DICE Breast_Shape =0.99±0.01, are achieved with differing TPSs. Decreasing image resolution decreased contouring conformity.

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“…JI and DICE values from CERR were verified in 3D Slicer [24][25][26] and MILXview and were consistent to within 2 significant figures.…”

Section: Analysis Metricssupporting

confidence: 54%

A phantom assessment of achievable contouring concordance across multiple treatment planning systems

Pogson

Begg

Jameson

et al. 2015

Radiotherapy and Oncology

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“…DVH evaluation was performed with Slicer3D (21) . DVH metrics explained in the IMRT section were calculated.…”

Section: Methodsmentioning

confidence: 99%

Intensity‐modulated radiotherapy versus proton radiotherapy versus carbon ion radiotherapy for spinal bone metastases: a treatment planning study

Rief

Chaudhri

Tonndorf-Martini

et al. 2015

J Applied Clin Med Phys

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Outcomes for selected patients with spinal metastases may be improved by dose escalation using stereotactic body radiotherapy (SBRT). As target geometry is complex, we compared SBRT plans using step‐and‐shoot intensity‐modulated radiotherapy (IMRT), carbon ion RT, and proton RT. We prepared plans treating cervical, thoracic, and lumbar metastases for three different techniques — IMRT, carbon ion, and proton plans — to deliver a median single 24 Gy fraction such that at least 90% of the planning target volume (PTV) received more than 18 Gy and were compared for PTV coverage, normal organ sparing, and estimated delivery time. PTV coverage did not show significant differences for the techniques, spinal cord dose sparing was lowered with the particle techniques. For the cervical lesion spinal cord maximum dose, dose of 1% (D1), and percent volume receiving 10 Gy (normalV10Gy) were 11.9 Gy, 9.1 Gy, and 0.5% in IMRT. This could be lowered to 4.3 Gy, 2.5 Gy, and 0% in carbon ion planning and to 8.1 Gy, 6.1 Gy, and 0% in proton planning. Regarding the thoracic lesion no difference was found for the spinal cord. For the lumbar lesion maximum dose, D1 and percent volume receiving 5 Gy (normalV5Gy) were 13.4 Gy, 8.9 Gy, and 8.9% for IMRT; 1.8 Gy, 0.7 Gy, and 0% for carbon ions; and 0 Gy,<0.01 Gy, and 0% for protons. Estimated mean treatment times were shorter in particle techniques (6–7 min vs. 12–14 min with IMRT). This planning study indicates that carbon ion and proton RT can deliver high‐quality PTV coverage for complex treatment volumes that surround the spinal cord.PACS number: 87.55.dk

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“…Non-rigid registration: hippocampus A non-rigid transformation, ˚e x,in , is required to account for deformations of the hippocampi during and after surgery. Subsequent to the landmark-based similarity transform, we performed a deformable landmark-based registration for our hippocampal specimens using radial basis functions (RBF) for local corrections as implemented in the Plasti match plug-in (Pinter et al, 2012) in 3D Slicer. Two new sets of corresponding landmarks were placed, on I sim ex and I in , in coronal MR slices to match the coronally slice histology.…”

Section: Landmark-based Similarity Transformationmentioning

confidence: 99%

Registration of in-vivo to ex-vivo MRI of surgically resected specimens: A pipeline for histology to in-vivo registration

Goubran

Ribaupierre

Hammond

et al. 2015

Journal of Neuroscience Methods

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h i g h l i g h t s• We present a protocol for registration of in-vivo to ex-vivo brain specimens.• This protocol completes a registration pipeline for histology to in-vivo MRI.• A TRE of 1.35 ± 0.11 mm (neocortex) and 1.41 ± 0.33 mm (hippocampus) was found.• Deformable registration significantly improved the registration accuracy.• This pipeline allows for the assessment of pathological correlates in MRI. a r t i c l e i n f o t r a c tBackground: Advances in MRI have the potential to improve surgical treatment of epilepsy through improved identification and delineation of lesions. However, validation is currently needed to investigate histopathological correlates of these new imaging techniques. The purpose of this work is to develop and evaluate a protocol for deformable image registration of in-vivo to ex-vivo resected brain specimen MRI. This protocol, in conjunction with our previous work on ex-vivo to histology registration, completes a registration pipeline for histology to in-vivo MRI, enabling voxel-based validation of novel and existing MRI techniques with histopathology. New method: A combination of image-based and landmark-based 3D registration was used to register in-vivo MRI and the ex-vivo MRI from patients (N = 10) undergoing epilepsy surgery. Target registration error (TRE) was used to assess accuracy and the added benefit of deformable registration. Results: A mean TRE of 1.35 ± 0.11 and 1.41 ± 0.33 mm was found for neocortical and hippocampal specimens respectively. Statistical analysis confirmed that the deformable registration significantly improved the registration accuracy for both specimens.Comparison with existing methods: Image registration of surgically resected brain specimens is a unique application which presents numerous technical challenges and that have not been fully addressed in previous literature. Our computed TRE are comparable to previous attempts tackling similar applications, as registering in-vivo MRI to whole brain or serial histology. Conclusion: The presented registration pipeline finds dense and accurate spatial correspondence between in-vivo MRI and histology and allows for the spatially local and quantitative assessment of pathological correlates in MRI.

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SlicerRT: Radiation therapy research toolkit for 3D Slicer

Cited by 224 publications

References 15 publications

A phantom assessment of achievable contouring concordance across multiple treatment planning systems

A phantom assessment of achievable contouring concordance across multiple treatment planning systems

Intensity‐modulated radiotherapy versus proton radiotherapy versus carbon ion radiotherapy for spinal bone metastases: a treatment planning study

Registration of in-vivo to ex-vivo MRI of surgically resected specimens: A pipeline for histology to in-vivo registration

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