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Dunås, Tora
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Dunås, T., Wåhlin, A., Zarrinkoob, L., Malm, J. & Eklund, A. (2019). 4D flow MRI: automatic assessment of blood flow in cerebral arteries. Biomedical Physics & Engineering Express, 5(1), Article ID 015003.
Open this publication in new window or tab >>4D flow MRI: automatic assessment of blood flow in cerebral arteries
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2019 (English)In: Biomedical Physics & Engineering Express, ISSN 2057-1976, Vol. 5, no 1, article id 015003Article in journal (Refereed) Published
Abstract [en]

Objective: With a 10-minute 4D flow MRI scan, the distribution of blood flow to individual arteries throughout the brain can be analyzed. This technique has potential to become a biomarker for treatment decisions, and to predict prognosis after stroke. To efficiently analyze and model the large dataset in clinical practice, automatization is needed. We hypothesized that identification of selected arterial regions using an atlas with a priori probability information on their spatial distribution can provide standardized measurements of blood flow in the main cerebral arteries.

Approach: A new method for automatic placement of measurement locations in 4D flow MRI was developed based on an existing atlas-based method for arterial labeling, by defining specific regions of interest within the corresponding arterial atlas. The suggested method was evaluated on 38 subjects with carotid artery stenosis, by comparing measurements of blood flow rate at automatically selected locations to reference measurements at manually selected locations.

Main results: Automatic and reference measurement ranged from 10 to 580 ml min−1 and were highly correlated (r = 0.99) with a mean flow difference of 0.61 ± 10.7 ml min−1 (p = 0.21). Out of the 559 arterial segments in the manual reference, 489 were correctly labeled, yielding a sensitivity of 88%, a specificity of 85%, and a labeling accuracy of 87%.

Significance: This study confirms that atlas-based labeling of 4D flow MRI data is suitable for efficient flow quantification in the major cerebral arteries. The suggested method improves the feasibility of analyzing cerebral 4D flow data, and fills a gap necessary for implementation in clinical use.

Place, publisher, year, edition, pages
Institute of Physics Publishing (IOPP), 2019
Keywords
cerebral arteries, hemodynamics, carotid stenosis, magnetic resonance imaging, circle of willis, cerebrovascular circulation
National Category
Medical Image Processing
Identifiers
urn:nbn:se:umu:diva-147254 (URN)10.1088/2057-1976/aae8d1 (DOI)000457627700003 ()
Funder
Swedish Research Council, 2015-05616Swedish Heart Lung Foundation, 20110383, 20140592
Note

Originally included in thesis in manuscript form

Available from: 2018-04-30 Created: 2018-04-30 Last updated: 2019-03-04Bibliographically approved
Dunås, T., Holmgren, M., Wåhlin, A., Malm, J. & Eklund, A. (2019). Accuracy of blood flow assessment in cerebral arteries with 4D flow MRI: Evaluation with three segmentation methods. Journal of Magnetic Resonance Imaging, 50(2), 511-518
Open this publication in new window or tab >>Accuracy of blood flow assessment in cerebral arteries with 4D flow MRI: Evaluation with three segmentation methods
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2019 (English)In: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 50, no 2, p. 511-518Article in journal (Refereed) Published
Abstract [en]

Background: Accelerated 4D flow MRI allows for high‐resolution velocity measurements with whole‐brain coverage. Such scans are increasingly used to calculate flow rates of individual arteries in the vascular tree, but detailed information about the accuracy and precision in relation to different postprocessing options is lacking.

Purpose: To evaluate and optimize three proposed segmentation methods and determine the accuracy of in vivo 4D flow MRI blood flow rate assessments in major cerebral arteries, with high‐resolution 2D PCMRI as a reference.

Study Type: Prospective.

Subjects: Thirty‐five subjects (20 women, 79 ± 5 years, range 70–91 years).

Field Strength/Sequence: 4D flow MRI with PC‐VIPR and 2D PCMRI acquired with a 3 T scanner.

Assessment: We compared blood flow rates measured with 4D flow MRI, to the reference, in nine main cerebral arteries. Lumen segmentation in the 4D flow MRI was performed with k‐means clustering using four different input datasets, and with two types of thresholding methods. The threshold was defined as a percentage of the maximum intensity value in the complex difference image. Local and global thresholding approaches were used, with evaluated thresholds from 6–26%.

Statistical Tests: Paired t‐test, F‐test, linear correlation (P < 0.05 was considered significant) along with intraclass correlation (ICC).

Results: With the thresholding methods, the lowest average flow difference was obtained for 20% local (0.02 ± 15.0 ml/min, ICC = 0.97, n = 310) or 10% global (0.08 ± 17.3 ml/min, ICC = 0.97, n = 310) thresholding with a significant lower standard deviation for local (F‐test, P = 0.01). For all clustering methods, we found a large systematic underestimation of flow compared with 2D PCMRI (16.1–22.3 ml/min).

Data Conclusion: A locally adapted threshold value gives a more stable result compared with a globally fixed threshold. 4D flow with the proposed segmentation method has the potential to become a useful reliable clinical tool for assessment of blood flow in the major cerebral arteries.

Level of Evidence: 2

Technical Efficacy: Stage 2

Keywords
magnetic resonance imaging, cerebral arteries, phase‐contrast MRI, 4D flow MRI, cerebral blood flow, Circle of Willis
National Category
Medical Image Processing
Identifiers
urn:nbn:se:umu:diva-147255 (URN)10.1002/jmri.26641 (DOI)000475681600017 ()30637846 (PubMedID)2-s2.0-85059966858 (Scopus ID)
Funder
Swedish Research Council, 2015–05616; 2017-04949Swedish Heart Lung Foundation, 20140592
Note

Originally included in thesis in manuscript form with title "Blood flow assessment in cerebral arteries with 4D flow MRI, concordance with 2D PCMRI"

Available from: 2018-04-30 Created: 2018-04-30 Last updated: 2019-08-12Bibliographically approved
Dunås, T. (2018). Blood flow assessment in cerebral arteries with 4D flow magnetic resonance imaging: an automatic atlas-based approach. (Doctoral dissertation). Umeå: Umeå universitet
Open this publication in new window or tab >>Blood flow assessment in cerebral arteries with 4D flow magnetic resonance imaging: an automatic atlas-based approach
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Blodflödesmätning i cerebrala artärer med 4D flödes magnetresonanstomografi : en automatisk atlasbaserad metod
Abstract [en]

Background: Disturbed blood flow to the brain has been associated with several neurological diseases, from stroke and vascular diseases to Alzheimer’s and cognitive decline. To determine the cerebral arterial blood flow distribution, measurements are needed in both distal and proximal arteries.

4D flow MRI makes it possible to obtain blood flow velocities from a volume covering the entire brain in one single scan. This facilitates more extensive flow investigations, since flow rate assessment in specific arteries can be done during post-processing. The flow rate assessment is still rather laborious and time consuming, especially if the number of arteries of interest is high. In addition, the quality of the measurements relies heavily on the expertise of the investigator.

The aim of this thesis was to develop and evaluate an automatic post-processing tool for 4D flow MRI that identifies the main cerebral arteries and calculates their blood flow rate with minimal manual input. Atlas-based labeling of brain tissue is common in toolboxes for analysis of neuroimaging-data, and we hypothesized that a similar approach would be suitable for arterial labeling. We also wanted to investigate how to best separate the arterial lumen from background for calculation of blood flow.

Methods: An automatic atlas-based arterial identification method (AAIM) for flow assessment was developed. With atlas-based labeling, voxels are labeled based on their spatial location in MNI-space, a stereotactic coordinate system commonly used for neuroimaging analysis. To evaluate the feasibility of this approach, a probabilistic atlas was created from a set of angiographic images derived from 4D flow MRI. Included arteries were the anterior (ACA), middle (MCA) and posterior (PCA) cerebral arteries, as well as the internal carotid (ICA), vertebral (VA), basilar (BA) and posterior communicating (PCoA) arteries. To identify the arteries in an angiographic image, a vascular skeleton where each branch represented an arterial segment was extracted and labeled according to the atlas. Labeling accuracy of the AAIM was evaluated by visual inspection.

Next, the labeling method was adapted for flow measurements by pre-defining desired regions within the atlas. Automatic flow measurements were then compared to measurements at manually identified locations. During the development process, arterial identification was evaluated on four patient cohorts, with and without vascular disease. Finally, three methods for flow quantification using 4D flow MRI: k-means clustering; global thresholding; and local thresholding, were evaluated against a standard reference method.

Results: The labeling accuracy on group level was between 96% and 87% for all studies, and close to 100% for ICA and BA. Short arteries (PCoA) and arteries with large individual anatomical variation (VA) were the most challenging. Blood flow measurements at automatically identified locations were highly correlated (r=0.99) with manually positioned measurements, and difference in mean flow was negligible.

Both global and local thresholding out-performed k-means clustering, since the threshold value could be optimized to produce a mean difference of zero compared to reference. The local thresholding had the best concordance with the reference method (p=0.009, F-test) and was the only method that did not have a significant correlation between flow difference and flow rate. In summary, with a local threshold of 20%, ICC was 0.97 and the flow rate difference was -0.04 ± 15.1 ml/min, n=308.

Conclusion: This thesis work demonstrated that atlas-based labeling was suitable for identification of cerebral arteries, enabling automated processing and flow assessment in 4D flow MRI. Furthermore, the proposed flow rate quantification algorithm reduced some of the most important shortcomings associated with previous methods. This new platform for automatic 4D flow MRI data analysis fills a gap needed for efficient in vivo investigations of arterial blood flow distribution to the entire vascular tree of the brain, and should have important applications to practical use in neurological diseases.

Place, publisher, year, edition, pages
Umeå: Umeå universitet, 2018. p. 60
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 1965
Keywords
Circle of Willis, 4D flow MRI, Cerebral arteries, Vascular disease, Stroke, Automatic labeling, Probabilistic atlas, Cerebral blood flow, Neuroimaging, Magnetic Resonance Imaging
National Category
Medical Engineering
Identifiers
urn:nbn:se:umu:diva-147256 (URN)978-91-7601-889-7 (ISBN)
Public defence
2018-05-25, Betula, NUS, Umeå, 13:00 (Swedish)
Opponent
Supervisors
Funder
Swedish Research Council, 2015–05616Swedish Heart Lung Foundation, 20110383Swedish Heart Lung Foundation, 20140592The Swedish Brain Foundation
Available from: 2018-05-04 Created: 2018-04-30 Last updated: 2018-06-09Bibliographically approved
Dunås, T., Wåhlin, A., Ambarki, K., Zarrinkoob, L., Malm, J. & Eklund, A. (2017). A Stereotactic Probabilistic Atlas for the Major Cerebral Arteries. Neuroinformatics, 15(1), 101-110
Open this publication in new window or tab >>A Stereotactic Probabilistic Atlas for the Major Cerebral Arteries
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2017 (English)In: Neuroinformatics, ISSN 1539-2791, E-ISSN 1559-0089, Vol. 15, no 1, p. 101-110Article in journal (Refereed) Published
Abstract [en]

Improved whole brain angiographic and velocity-sensitive MRI is pushing the boundaries of noninvasively obtained cerebral vascular flow information. The complexity of the information contained in such datasets calls for automated algorithms and pipelines, thus reducing the need of manual analyses by trained radiologists. The objective of this work was to lay the foundation for such automated pipelining by constructing and evaluating a probabilistic atlas describing the shape and location of the major cerebral arteries. Specifically, we investigated how the implementation of a non-linear normalization into Montreal Neurological Institute (MNI) space improved the alignment of individual arterial branches. In a population-based cohort of 167 subjects, age 64-68 years, we performed 4D flow MRI with whole brain volumetric coverage, yielding both angiographic and anatomical data. For each subject, sixteen cerebral arteries were manually labeled to construct the atlas. Angiographic data were normalized to MNI space using both rigid-body and non-linear transformations obtained from anatomical images. The alignment of arterial branches was significantly improved by the non-linear normalization (p < 0.001). Validation of the atlas was based on its applicability in automatic arterial labeling. A leave-one-out validation scheme revealed a labeling accuracy of 96 %. Arterial labeling was also performed in a separate clinical sample (n = 10) with an accuracy of 92.5 %. In conclusion, using non-linear spatial normalization we constructed an artery-specific probabilistic atlas, useful for cerebral arterial labeling.

Keywords
Cerebral arteries, Probabilistic atlas, 4D flow MRI, Automatic labeling, Spatial normalization
National Category
Clinical Medicine
Identifiers
urn:nbn:se:umu:diva-131144 (URN)10.1007/s12021-016-9320-y (DOI)000394260000009 ()27873151 (PubMedID)2-s2.0-84996542654 (Scopus ID)
Available from: 2017-02-06 Created: 2017-02-06 Last updated: 2018-06-09Bibliographically approved
Dunås, T., Wåhlin, A., Ambarki, K., Zarrinkoob, L., Birgander, R., Malm, J. & Eklund, A. (2016). Automatic labeling of cerebral arteries in magnetic resonance angiography. Magnetic Resonance Materials in Physics, Biology and Medicine, 29(1), 39-47
Open this publication in new window or tab >>Automatic labeling of cerebral arteries in magnetic resonance angiography
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2016 (English)In: Magnetic Resonance Materials in Physics, Biology and Medicine, ISSN 0968-5243, E-ISSN 1352-8661, Vol. 29, no 1, p. 39-47Article in journal (Refereed) Published
Abstract [en]

In order to introduce 4D flow magnetic resonance imaging (MRI) as a standard clinical instrument for studying the cerebrovascular system, new and faster postprocessing tools are necessary. The objective of this study was to construct and evaluate a method for automatic identification of individual cerebral arteries in a 4D flow MRI angiogram. Forty-six elderly individuals were investigated with 4D flow MRI. Fourteen main cerebral arteries were manually labeled and used to create a probabilistic atlas. An automatic atlas-based artery identification method (AAIM) was developed based on vascular-branch extraction and the atlas was used for identification. The method was evaluated by comparing automatic with manual identification in 4D flow MRI angiograms from 67 additional elderly individuals. Overall accuracy was 93 %, and internal carotid artery and middle cerebral artery labeling was 100 % accurate. Smaller and more distal arteries had lower accuracy; for posterior communicating arteries and vertebral arteries, accuracy was 70 and 89 %, respectively. The AAIM enabled fast and fully automatic labeling of the main cerebral arteries. AAIM functionality provides the basis for creating an automatic and powerful method to analyze arterial cerebral blood flow in clinical routine.

Keywords
Magnetic resonance angiography, Cerebral angiography, Circle of Willis, Atlases as topic, Automatic data processing
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-117830 (URN)10.1007/s10334-015-0512-5 (DOI)000370159800005 ()
Available from: 2016-04-05 Created: 2016-03-04 Last updated: 2018-06-07Bibliographically approved
Dunås, T., Wåhlin, A., Zarrinkoob, L., Ambarki, K., Malm, J. & Eklund, A. (2015). Towards Automatic Identification of Cerebral Arteries in 4D Flow MRI. In: Henrik Mindedal, Mikael Persson (Ed.), 16th Nordic-Baltic Conference on Biomedical Engineering: . Paper presented at 16th Nordic-Baltic Conference on Biomedical Engineering, October 14-16, 2014, Gothenburg, Sweden (pp. 40-43). , 48
Open this publication in new window or tab >>Towards Automatic Identification of Cerebral Arteries in 4D Flow MRI
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2015 (English)In: 16th Nordic-Baltic Conference on Biomedical Engineering / [ed] Henrik Mindedal, Mikael Persson, 2015, Vol. 48, p. 40-43Conference paper, Published paper (Refereed)
Abstract [en]

4D flow MRI is a powerful imaging technique which provides an angiographic image with information about blood flow in a large volume, time resolved over the cardiac cycle, in a short imaging time. This study aims to develop an automatic method for identification of cerebral arteries. The proposed method is based on an atlas of twelve arteries, developed from 4D flow MRI of 25 subjects. The atlas was constructed by normalizing all images to MNI-space, manually identifying the arteries and creating an average over the volume. The identification is done by extracting a vascular skeleton from the image, transforming it to MNI-space, labeling it with the atlas and transforming it back to subject space. The method was evaluated on a pilot cohort of 8 subjects. The rate of correctly identified arteries was 97%.

Series
IFMBE Proceedings, ISSN 1680-0737 ; 48
Keywords
Cerebral arteries, automatic labeling, 4D flow MRI, cerebrovascular atlas
National Category
Neurosciences
Identifiers
urn:nbn:se:umu:diva-100149 (URN)10.1007/978-3-319-12967-9_11 (DOI)000347893000011 ()978-3-319-12966-2 (ISBN)978-3-319-12967-9 (ISBN)
Conference
16th Nordic-Baltic Conference on Biomedical Engineering, October 14-16, 2014, Gothenburg, Sweden
Available from: 2015-02-26 Created: 2015-02-24 Last updated: 2018-06-07Bibliographically approved
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