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Magnetic resonance imaging with ultrashort echo time as a substitute for X-ray computed tomography
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.ORCID iD: 0000-0001-9849-2143
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Radiotherapy dose calculations have evolved from simple factor based methods performed with pen and paper, into computationally intensive simulations based on Monte Carlo theory and energy deposition kernel convolution.

Similarly, in the field of positron emission tomography (PET), attenuation correction, which was originally omitted entirely, is now a crucial component of any PET reconstruction algorithm.

Today, both of these applications – radiotherapy and PET – derive their needed in-tissue radiation attenuation coefficients from images acquired with X-ray computed tomography (CT). Since X-ray images are themselves acquired using ionizing radiation, the intensity at a point in an image will reflect the radiation interaction properties of the tissue located at that point.

Magnetic resonance imaging (MRI), on the other hand, does not use ionizing radiation. Instead MRI make use of the net transverse magnetization resulting from the spin polarization of hydrogen nuclei. MR image contrast can be varied to a greater extent than CT and the soft tissue contrast is, for most MR sequences, superior to that of CT. Therefore, for many cases, MR images provide a considerable advantage over CT when identifying or delineating tumors or other diseased tissues.

For this reason, there is an interest to replace CT with MRI for a great number of diagnostic and therapeutic workflows. Also, replacing CT with MRI would reduce the exposure to ionizing radiation experienced by patients and, by extension, reduce the associated risk to induce cancer.

In part MRI has already replaced CT, but for radiotherapy dose calculations and PET attenuation correction, CT examinations are still necessary in clinical practice. One of the reasons is that the net transverse magnetization imaged in MRI cannot be converted into attenuation coefficients for ionizing radiation in a straightforward way. More specifically, regions with similar appearance in magnetic resonance (MR) images, such as bone and air pockets, are found at different ends of the spectrum of attenuation coefficients present in the human body. In a CT image, bone will appear bright white and air as black corresponding to high and no attenuation, respectively. In an MR image, bone and air both appear dark due to the lack of net transverse magnetization.

The weak net transverse magnetization of bone is a result of low hydrogen density and rapid transverse relaxation. A particular category of MRI sequences with so-called ultrashort echo time (UTE) can sample the MRI signal from bone before it is lost due to transverse relaxation. Thus, UTE sequences permit bone to be imaged with MRI albeit with weak intensity and poor resolution.

Imaging with UTE in combination with careful image analysis can permit ionizing-radiation attenuation-maps to be derived from MR images. This dissertation and appended articles present a procedure for this very purpose. However, as attenuation coefficients are radiation-quality dependent the output of the method is a Hounsfield unit map, i.e. a substitute for a CT image. It can be converted into an attenuation map using conventional clinical procedure.

Obviating the use of CT would reduce the number of examinations that patients have to endure during preparation for radiotherapy. It would also permit PET attenuation correction to be performed on images from the new imaging modality that combines PET and MRI in one scanner – PET/MR.

Place, publisher, year, edition, pages
Umeå: Umeå universitet , 2014. , 78 p.
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 1675
Keyword [en]
magnetic resonance imaging, computed tomography substitute, ultrashort echo time, parallel imaging, radial imaging
National Category
Physical Sciences
Research subject
radiofysik
Identifiers
URN: urn:nbn:se:umu:diva-93053ISBN: 978-91-7601-138-6 (print)OAI: oai:DiVA.org:umu-93053DiVA: diva2:760894
Public defence
2014-12-05, Hörsal Betula, Unod L 0, Byggnad 6M, Norrlands universitetssjukhus, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2014-11-14 Created: 2014-09-11 Last updated: 2014-11-13Bibliographically approved
List of papers
1. CT substitute derived from MRI sequences with ultrashort echo time
Open this publication in new window or tab >>CT substitute derived from MRI sequences with ultrashort echo time
2011 (English)In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 38, no 5, 2708-2714 p.Article in journal (Refereed) Published
Abstract [en]

Purpose: Methods for deriving computed tomography (CT) equivalent information from MRI are needed for attenuation correction in PET/MRI applications, as well as for patient positioning and dose planning in MRI based radiation therapy workflows. This study presents a method for generating a drop in substitute for a CT image from a set of magnetic resonance (MR)images.

Methods:A Gaussian mixture regression model was used to link the voxel values in CT images to the voxel values in images from three MRI sequences: one T2 weighted 3D spin echo based sequence and two dual echo ultrashort echo time MRI sequences with different echo times and flip angles. The method used a training set of matched MR and CT data that after training was able to predict a substitute CT (s-CT) based entirely on the MR information for a new patient. Method validation was achieved using datasets covering the heads of five patients and applying leave-one-out cross-validation (LOOCV). During LOOCV, the model was estimated from the MR and CT data of four patients (training set) and applied to the MR data of the remaining patient (validation set) to generate an s-CT image. This procedure was repeated for all five training and validation data combinations.

Results: The mean absolute error for the CT number in the s-CT images was 137 HU. No large differences in method accuracy were noted for the different patients, indicating a robust method. The largest errors in the s-CT images were found at air–tissue and bone–tissue interfaces. The model accurately discriminated between air and bone, as well as between soft tissues and nonsoft tissues.

Conclusions: The s-CT method has the potential to provide an accurate estimation of CT information without risk of geometrical inaccuracies as the model is voxel based. Therefore, s-CT images could be well suited as alternatives to CT images for dose planning in radiotherapy and attenuation correction in PET/MRI.

Place, publisher, year, edition, pages
American Association of Physicists in Medicine, 2011
Keyword
magnetic resonance imaging, computed tomography substitute, ultrashort echo time, Gaussian mixture, dose calculation
Identifiers
urn:nbn:se:umu:diva-44330 (URN)10.1118/1.3578928 (DOI)
Available from: 2011-05-31 Created: 2011-05-31 Last updated: 2017-12-11Bibliographically approved
2. Voxel-wise uncertainty in CT substitute derived from MRI
Open this publication in new window or tab >>Voxel-wise uncertainty in CT substitute derived from MRI
Show others...
2012 (English)In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 39, no 6, 3283-3290 p.Article in journal (Refereed) Published
Abstract [en]

Purpose: In an earlier work, we demonstrated that substitutes for CT images can be derived from MR images using ultrashort echo time (UTE) sequences, conventional T2 weighted sequences, and Gaussian mixture regression (GMR). In this study, we extend this work by analyzing the uncertainties associated with the GMR model and the information contributions from the individual imaging sequences.

Methods: An analytical expression for the voxel-wise conditional expected absolute deviation (EAD) in substitute CT (s-CT) images was derived. The expression depends only on MR images and can thus be calculated along with each s-CT image. The uncertainty measure was evaluated by comparing the EAD to the true mean absolute prediction deviation (MAPD) between the s-CT and CT images for 14 patients. Further, the influence of the different MR images included in the GMR model on the generated s-CTs was investigated by removing one or more images and evaluating the MAPD for a spectrum of predicted radiological densities.

Results: The largest EAD was predicted at air-soft tissue and bone-soft tissue interfaces. The EAD agreed with the MAPD in both these regions and in regions with lower EADs, such as the brain. Two of the MR images included in the GMR model were found to be mutually redundant for the purpose of s-CT generation.

Conclusions: The presented uncertainty estimation method accurately predicts the voxel-wise MAPD in s-CT images. Also, the non-UTE sequence previously used in the model was found to be redundant.

Place, publisher, year, edition, pages
American Association of Physicists in Medicine, 2012
Keyword
magnetic resonance imaging, computed tomography substitute, ultrashort echo time, quality assurance, Gaussian mixture, dose calculation, attenuation correction
National Category
Physical Sciences
Identifiers
urn:nbn:se:umu:diva-55694 (URN)10.1118/1.4711807 (DOI)
Available from: 2013-01-04 Created: 2012-05-28 Last updated: 2017-12-07Bibliographically approved
3. Improved quality of computed tomography substitute derived from magnetic resonance (MR) data by incorporation of spatial information: potential application for MR-only radiotherapy and attenuation correction in positron emission tomography
Open this publication in new window or tab >>Improved quality of computed tomography substitute derived from magnetic resonance (MR) data by incorporation of spatial information: potential application for MR-only radiotherapy and attenuation correction in positron emission tomography
Show others...
2013 (English)In: Acta Oncologica, ISSN 0284-186X, E-ISSN 1651-226X, Vol. 52, no 7, 1369-1373 p.Article in journal (Refereed) Published
Abstract [en]

Background: Estimation of computed tomography (CT) equivalent data, i.e. a substitute CT (s-CT), from magnetic resonance (MR) images is a prerequisite both for attenuation correction of positron emission tomography (PET) data acquired with a PET/MR scanner and for dose calculations in an MR-only radiotherapy workflow. It has previously been shown that it is possible to estimate Hounsfield numbers based on MR image intensities, using ultra short echo-time imaging and Gaussian mixture regression (GMR). In the present pilot study we investigate the possibility to also include spatial information in the GMR, with the aim to improve the quality of the s-CT. Material and methods: MR and CT data for nine patients were used in the present study. For each patient, GMR models were created from the other eight patients, including either both UTE image intensities and spatial information on a voxel by voxel level, or only UTE image intensities. The models were used to create s-CT images for each respective patient. Results: The inclusion of spatial information in the GMR model improved the accuracy of the estimated s-CT. The improvement was most pronounced in smaller, complicated anatomical regions as the inner ear and post-nasal cavities. Conclusions: This pilot study shows that inclusion of spatial information in GMR models to convert MR data to CT equivalent images is feasible. The accuracy of the s-CT is improved and the spatial information could make it possible to create a general model for the conversion applicable to the whole body.

National Category
Radiology, Nuclear Medicine and Medical Imaging Cancer and Oncology
Identifiers
urn:nbn:se:umu:diva-81537 (URN)10.3109/0284186X.2013.819119 (DOI)000324776100016 ()23984810 (PubMedID)
Available from: 2013-10-14 Created: 2013-10-14 Last updated: 2017-12-06Bibliographically approved
4. CT substitutes derived from MR images reconstructed with parallel imaging
Open this publication in new window or tab >>CT substitutes derived from MR images reconstructed with parallel imaging
2014 (English)In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 41, no 8, 474-480 p.Article in journal (Refereed) Published
Abstract [en]

Purpose: Computed tomography (CT) substitute images can be generated from ultrashort echo time (UTE) MRI sequences with radial k-space sampling. These CT substitutes can be used as ordinary CT images for PET attenuation correction and radiotherapy dose calculations. Parallel imaging allows faster acquisition of magnetic resonance (MR) images by exploiting differences in receiver coil element sensitivities. This study investigates whether non-Cartesian parallel imaging reconstruction can be used to improve CT substitutes generated from shorter examination times.

Methods: The authors used gridding as well as two non-Cartesian parallel imaging reconstruction methods, SPIRiT and CG-SENSE, to reconstruct radial UTE and gradient echo (GE) data into images of the head for 23 patients. For each patient, images were reconstructed from the full dataset and from a number of subsampled datasets. The subsampled datasets simulated shorter acquisition times by containing fewer radial k-space spokes (1000, 2000, 3000, 5000, and 10 000 spokes) than the full dataset (30 000 spokes). For each combination of patient, reconstruction method, and number of spokes, the reconstructed UTE and GE images were used to generate a CT substitute. Each CT substitute image was compared to a real CT image of the same patient.

Results: The mean absolute deviation between the CT number in CT substitute and CT decreased when using SPIRiT as compared to gridding reconstruction. However, the reduction was small and the CT substitute algorithm was insensitive to moderate subsampling (≥5000 spokes) regardless of reconstruction method. For more severe subsampling (≤3000 spokes), corresponding to acquisition times less than aminute long, the CT substitute quality was deteriorated for all reconstructionmethods but SPIRiT gave a reduction in the mean absolute deviation of down to 25 Hounsfield units compared to gridding.

Conclusions: SPIRiT marginally improved the CT substitute quality for a given number of radial spokes as compared to gridding. However, the increased reconstruction time of non-Cartesian parallel imaging reconstruction is difficult to motivate from this improvement. Because the CT substitute algorithm was insensitive to moderate subsampling, data for a CT substitute could be collected in as little as minute and reconstructed with gridding without deteriorating the CT substitute quality.

Keyword
magnetic resonance imaging, computed tomography substitute, ultrashort echo time, parallel imaging, radial imaging
National Category
Physical Sciences
Research subject
radiofysik
Identifiers
urn:nbn:se:umu:diva-93051 (URN)10.1118/1.4886766 (DOI)000341068100043 ()
Available from: 2014-09-11 Created: 2014-09-11 Last updated: 2017-12-05Bibliographically approved

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