Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain

Andreasen, Daniel; Van Leemput, Koen; Hansen, Rasmus H.; Andersen, Jon A. L.; Edmund, Jens M.

doi:10.1118/1.4914158

Title: Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain

Full Record
Other Related Research

Abstract

Purpose: In radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, the information on electron density must be derived from the MRI scan by creating a so-called pseudo computed tomography (pCT). This is a nontrivial task, since the voxel-intensities in an MRI scan are not uniquely related to electron density. To solve the task, voxel-based or atlas-based models have typically been used. The voxel-based models require a specialized dual ultrashort echo time MRI sequence for bone visualization and the atlas-based models require deformable registrations of conventional MRI scans. In this study, we investigate the potential of a patch-based method for creating a pCT based on conventional T{sub 1}-weighted MRI scans without using deformable registrations. We compare this method against two state-of-the-art methods within the voxel-based and atlas-based categories. Methods: The data consisted of CT and MRI scans of five cranial RT patients. To compare the performance of the different methods, a nested cross validation was done to find optimal model parameters for all the methods. Voxel-wise and geometric evaluations of the pCTs were done. Furthermore, a radiologic evaluation based on water equivalent path lengths was carried out, comparing the upper hemisphere of the head in the pCTmore »« less

Authors:

Andreasen, Daniel ^[1]; Van Leemput, Koen ^[2]; Hansen, Rasmus H. ^[3]; Andersen, Jon A. L.; Edmund, Jens M. ^[4]

Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby 2800, Denmark and Department of Oncology, Radiotherapy Research Unit, Copenhagen University Hospital, Herlev 2730 (Denmark)
Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby 2800, Denmark and A.A. Martinos Center for Biomedical Imaging, MGH, Harvard Medical School, Charlestown, Massachusetts 02129 (United States)
Department of Radiology, Copenhagen University Hospital, Herlev 2730 (Denmark)
Department of Oncology, Radiotherapy Research Unit, Copenhagen University Hospital, Herlev 2730 (Denmark)

Publication Date:: Wed Apr 15 00:00:00 EDT 2015

OSTI Identifier:: 22413494

Resource Type:: Journal Article

Journal Name:: Medical Physics

Additional Journal Information:: Journal Volume: 42; Journal Issue: 4; Other Information: (c) 2015 American Association of Physicists in Medicine; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0094-2405

Country of Publication:: United States

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES; ACCURACY; BRAIN; COMPARATIVE EVALUATIONS; COMPUTERIZED TOMOGRAPHY; ELECTRON DENSITY; GEOMETRY; HEAD; NMR IMAGING; PATIENTS; RADIOTHERAPY

Citation Formats


                    Andreasen, Daniel, Van Leemput, Koen, Hansen, Rasmus H., Andersen, Jon A. L., and Edmund, Jens M. Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain.  United States: N. p., 2015. 
        Web.  doi:10.1118/1.4914158.

Copy to clipboard


                    Andreasen, Daniel, Van Leemput, Koen, Hansen, Rasmus H., Andersen, Jon A. L., & Edmund, Jens M. Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain.  United States.  https://doi.org/10.1118/1.4914158

Copy to clipboard


                    Andreasen, Daniel, Van Leemput, Koen, Hansen, Rasmus H., Andersen, Jon A. L., and Edmund, Jens M. 2015.  
        "Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain".  United States.  https://doi.org/10.1118/1.4914158.

Copy to clipboard


                    
@article{osti_22413494,

  title        = {Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain},

  author       = {Andreasen, Daniel and Van Leemput, Koen and Hansen, Rasmus H. and Andersen, Jon A. L. and Edmund, Jens M.},

  abstractNote = {Purpose: In radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, the information on electron density must be derived from the MRI scan by creating a so-called pseudo computed tomography (pCT). This is a nontrivial task, since the voxel-intensities in an MRI scan are not uniquely related to electron density. To solve the task, voxel-based or atlas-based models have typically been used. The voxel-based models require a specialized dual ultrashort echo time MRI sequence for bone visualization and the atlas-based models require deformable registrations of conventional MRI scans. In this study, we investigate the potential of a patch-based method for creating a pCT based on conventional T{sub 1}-weighted MRI scans without using deformable registrations. We compare this method against two state-of-the-art methods within the voxel-based and atlas-based categories. Methods: The data consisted of CT and MRI scans of five cranial RT patients. To compare the performance of the different methods, a nested cross validation was done to find optimal model parameters for all the methods. Voxel-wise and geometric evaluations of the pCTs were done. Furthermore, a radiologic evaluation based on water equivalent path lengths was carried out, comparing the upper hemisphere of the head in the pCT and the real CT. Finally, the dosimetric accuracy was tested and compared for a photon treatment plan. Results: The pCTs produced with the patch-based method had the best voxel-wise, geometric, and radiologic agreement with the real CT, closely followed by the atlas-based method. In terms of the dosimetric accuracy, the patch-based method had average deviations of less than 0.5% in measures related to target coverage. Conclusions: We showed that a patch-based method could generate an accurate pCT based on conventional T{sub 1}-weighted MRI sequences and without deformable registrations. In our evaluations, the method performed better than existing voxel-based and atlas-based methods and showed a promising potential for RT of the brain based only on MRI.},

  doi          = {10.1118/1.4914158},

  url          = {https://www.osti.gov/biblio/22413494},
  journal      = {Medical Physics},

  issn         = {0094-2405},

  number       = 4,

  volume       = 42,

  place        = {United States},

  year         = {Wed Apr 15 00:00:00 EDT 2015},

  month        = {Wed Apr 15 00:00:00 EDT 2015}

}

Copy to clipboard

Journal Article:

https://doi.org/10.1118/1.4914158

Other availability

Find in Google Scholar

Search WorldCat to find libraries that may hold this journal

Save / Share:

Export Metadata

Save to My Library

Similar records in OSTI.GOV collections:

A patch-based pseudo-CT approach for MRI-only radiotherapy in the pelvis

Journal Article Andreasen, Daniel; Van Leemput, Koen; Edmund, Jens - Medical Physics

Purpose: In radiotherapy based only on magnetic resonance imaging (MRI), knowledge about tissue electron densities must be derived from the MRI. This can be achieved by converting the MRI scan to the so-called pseudo-computed tomography (pCT). An obstacle is that the voxel intensities in conventional MRI scans are not uniquely related to electron density. The authors previously demonstrated that a patch-based method could produce accurate pCTs of the brain using conventional T{sub 1}-weighted MRI scans. The method was driven mainly by local patch similarities and relied on simple affine registrations between an atlas database of the co-registered MRI/CT scan pairsmore »« less
https://doi.org/10.1118/1.4958676
TH-CD-206-09: Learning-Based MRI-CT Prostate Registration Using Spare Patch-Deformation Dictionary

Journal Article Yang, X; Jani, A; Rossi, P; ... - Medical Physics

Purpose: To enable MRI-guided prostate radiotherapy, MRI-CT deformable registration is required to map the MRI-defined tumor and key organ contours onto the CT images. Due to the intrinsic differences in grey-level intensity characteristics between MRI and CT images, the integration of MRI into CT-based radiotherapy is very challenging. We are developing a learning-based registration approach to address this technical challenge. Methods: We propose to estimate the deformation between MRI and CT images in a patch-wise fashion by using the sparse representation technique. Specifically, we assume that two image patches should follow the same deformation if their patch-wise appearance patterns aremore »« less
https://doi.org/10.1118/1.4958190
MRI-based treatment planning with pseudo CT generated through atlas registration

Journal Article Uh, Jinsoo; Merchant, Thomas; Hua, Chiaho; ... - Medical Physics

Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration ofmore »« less
https://doi.org/10.1118/1.4873315
SU-E-J-220: Assessment of MRI Geometric Distortion in Head and Neck Cancer Patients Scanned in Immobilized Radiation Treatment Position

Journal Article Hansen, C; Mohamed, A; Weygand, J; ... - Medical Physics

Purpose: Uncertainties about geometric distortion have somewhat hindered MRI simulation in radiation therapy. Most of the geometric distortion studies were performed with phantom measurements but another major aspect of MR distortion is patient related. We studied the geometric distortion in patient images by comparing their MRI scans with the corresponding CT, using CT as the non-distorted gold standard. Methods: Ten H&N cancer patients were imaged with MRI as part of a prospective IRB approved study. All patients had their treatment planning CT done on the same day or within one week of the MRI. MR Images were acquired with amore »« less
https://doi.org/10.1118/1.4924306
SU-F-J-104: Weekly MRI for Dose Assessment of Organs at Risk During Treatment of HN Cancer of the Oropharynx

Journal Article Ludwig, K; Li, J; Venigalla, P; ... - Medical Physics

Purpose: Investigate the feasibility of using weekly MRI to assess dose to organs at risk utilizing deformable image registration. Methods: Sixteen H&N patients with oropharyngeal cancer were imaged on a 3T MR scanner using T2W and mDIXON sequence. Patients were imaged on a weekly basis in treatment position. Parotids (LP & RP), submandibular glands (LS, RS), and oral cavity (OC) were delineated on the weekly MR and reviewed by a board certified radiation oncologist. The original planning CT (pCT), RT-Dose, and RT-Structures were deformed and registered to each weekly MRIs. The deformed CTs and RT-Structures were imported to the treatmentmore »« less
https://doi.org/10.1118/1.4956012

Similar Records