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  • 1.
    Andersson, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. Antaros Med, Mölndal, Sweden.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. Antaros Med, Mölndal, Sweden.
    Separation of water and fat signal in whole-body gradient echo scans using convolutional neural networks2019In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 82, no 3, p. 1177-1186Article in journal (Refereed)
    Abstract [en]

    Purpose: To perform and evaluate water–fat signal separation of whole‐body gradient echo scans using convolutional neural networks.

    Methods: Whole‐body gradient echo scans of 240 subjects, each consisting of 5 bipolar echoes, were used. Reference fat fraction maps were created using a conventional method. Convolutional neural networks, more specifically 2D U‐nets, were trained using 5‐fold cross‐validation with 1 or several echoes as input, using the squared difference between the output and the reference fat fraction maps as the loss function. The outputs of the networks were assessed by the loss function, measured liver fat fractions, and visually. Training was performed using a graphics processing unit (GPU). Inference was performed using the GPU as well as a central processing unit (CPU).

    Results: The loss curves indicated convergence, and the final loss of the validation data decreased when using more echoes as input. The liver fat fractions could be estimated using only 1 echo, but results were improved by use of more echoes. Visual assessment found the quality of the outputs of the networks to be similar to the reference even when using only 1 echo, with slight improvements when using more echoes. Training a network took at most 28.6 h. Inference time of a whole‐body scan took at most 3.7 s using the GPU and 5.8 min using the CPU.

    Conclusion: It is possible to perform water–fat signal separation of whole‐body gradient echo scans using convolutional neural networks. Separation was possible using only 1 echo, although using more echoes improved the results.

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  • 2. Avventi, Enrico
    et al.
    Ryden, Henric
    Norbeck, Ola
    Berglund, Johan
    Sprenger, Tim
    Skare, Stefan
    Projection-based 3D/2D registration for prospective motion correction.2020In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 84, no 3, p. 1534-1542Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To develop a registration method that is capable of estimating the full range of rigid body motion from three orthogonal collapsed images of the head. These images can be obtained using the collapsed FatNav, a previously introduced navigator for prospective motion correction. It combines a short duration with wide compatibility with different main sequences due to its robustness against spin history effects.

    THEORY AND METHODS: A projection-based 3D/2D registration method is presented and then modified to take into account the peculiarities of the collapsed FatNav. Water/fat separated volumes were used in simulations to assess the accuracy of the proposed method at different resolutions by comparison with high-resolution 3D registration. The sensitivity with respect to masking strategies and starting motion parameters was investigated. Finally, prospective experiments with a healthy volunteer were performed with different types of motion patterns. A PROPELLER main sequence was chosen to compare the prospective correction with PROPELLER's own retrospective correction.

    RESULTS: In the simulations the proposed method has shown comparable performance to 3D registration. Furthermore, evidence of its robustness with respect to masking strategies and starting motion parameters was presented. The combination with collapsed FatNav has performed well in correcting most of the motion artifacts prospectively with improved image quality compared to only using PROPELLER's retrospective motion correction.

    CONCLUSIONS: The proposed 3D/2D registration together with collapsed FatNav is characterized by a good balance between navigator duration and estimate accuracy. Further work is needed to validate the method across a wider variety of subject anatomies.

  • 3. Barral, Joëlle K.
    et al.
    Gudmundson, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Stikov, Nikola
    Etezadi-Amoli, Maryam
    Stoica, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Nishimura, Dwight G.
    A Robust Methodology for In Vivo T1 Mapping2010In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 64, no 4, p. 1057-1067Article in journal (Refereed)
  • 4.
    Berglund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Two-point dixon method with flexible echo times2011In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 65, no 4, p. 994-1004Article in journal (Refereed)
    Abstract [en]

    The two-point Dixon method is a proton chemical shift imaging technique that produces separated water-only and fat-only images from a dual-echo acquisition. It is shown how this can be achieved without the usual constraints on the echo times. A signal model considering spectral broadening of the fat peak is proposed for improved water/fat separation. Phase errors, mostly due to static field inhomogeneity, must be removed prior to least-squares estimation of water and fat. To resolve ambiguity of the phase errors, a corresponding global optimization problem is formulated and solved using a message-passing algorithm. It is shown that the noise in the water and fat estimates matches the Cramér-Rao bounds, and feasibility is demonstrated for in vivo abdominal breath-hold imaging. The water-only images were found to offer superior fat suppression compared with conventional spectrally fat suppressed images.

  • 5.
    Berglund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Model-based mapping of fat unsaturation and chain length by chemical shift imaging: phantom validation and in vivo feasibility2012In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 68, no 6, p. 1815-1827Article in journal (Refereed)
    Abstract [en]

    Knowledge about the triglyceride (fat) 1H spectrum enables quantitative determination of several triglyceride characteristics. This work describes a model-based chemical shift imaging method that separates water and fat signal and provides maps of three triglyceride quantities: fatty acid carbon chain length (CL), number of double bond pairs (ndb), and number of methylene-interrupted double bonds (nmidb). The method was validated by imaging a phantom containing ten different oils using 1.5 T and 3.0 T clinical scanners, with gas-liquid chromatography (GLC) as reference. Repeated acquisitions demonstrated high reproducibility of the method. Statistical tests of correlation and linear regression were performed to examine the accuracy of the method. Significant correlation was found at both field strengths for all three quantities, and high correlation (r2 > 0.96) was found for measuring ndb and nmidb. Feasibility of the method for in vivo imaging of the thigh was demonstrated at both field strengths. The estimates of ndb and nmidb in subcutaneous adipose tisse were in agreement with literature values, while CL appears overestimated. The method has potential use in large-scale cross-sectional and longitudinal studies of triglyceride composition, and its relation to diet and various diseases.

  • 6.
    Berglund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Three-point Dixon method enables whole-body water and fat imaging of obese subjects2010In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 63, no 6, p. 1659-1668Article in journal (Refereed)
    Abstract [en]

    Dixon imaging techniques derive chemical shift-separated water and fat images, enabling the quantification of fat content and forming an alternative to fat suppression. Whole-body Dixon imaging is of interest in studies of obesity and the metabolic syndrome, and possibly in oncology. A three-point Dixon method is proposed where two solutions are found analytically in each voxel. The true solution is identified by a multiseed three-dimensional region-growing scheme with a dynamic path, allowing confident regions to be solved before unconfident regions, such as background noise. 2 pi-Phase unwrapping is not required. Whole-body datasets (256 x 184 x 252 voxels) were collected from 39 subjects (body mass index 19.8-45.4 kg/m(2)), in a mean scan time of 5 min 15 sec. Water and fat images were reconstructed offline, using the proposed method and two reference methods. The resulting images were subjectively graded on a four-grade scale by two radiologists, blinded to the method used. The proposed method was found superior to the reference methods. It exclusively received the two highest grades, implying that only mild reconstruction failures were found. The computation time for a whole-body dataset was 1 min 51.5 sec +/- 3.0 sec. It was concluded that whole-body water and fat imaging is feasible even for obese subjects, using the proposed method.

  • 7.
    Berglund, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Three-dimensional water/fat separation and T2* estimation based on whole-image optimization: application in breathhold liver imaging at 1.5 T2012In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 67, no 6, p. 1684-1693Article in journal (Refereed)
    Abstract [en]

    The chemical shift of water and fat resonances in proton MRI allows separation of water and fat signal from chemical shift encoded data. This work describes an automatic method that produces separate water and fat images as well as quantitative maps of fat signal fraction and T2* from complex multi-echo gradient recalled datasets. Accurate water and fat separation is challenging due to signal ambiguity at the voxel level. Whole-image optimization can resolve this ambiguity, but might be computationally demanding, especially for three-dimensional (3D) data. In this work, periodicity of the model fit residual as a function of the off-resonance was utilized to modify a previously proposed formulation of the problem. This gives a smaller solution space and allows rapid optimization. Feasibility and accurate separation of water and fat signal was demonstrated in breathhold 3D liver imaging of ten volunteer subjects, with both acquisition and reconstruction times below 20 seconds.

  • 8. Berglund, Johan
    et al.
    Rydén, Henric
    Avventi, Enrico
    Norbeck, Ola
    Sprenger, Tim
    Skare, Stefan
    Fat/water separation in k-space with real-valued estimates and its combination with POCS.2020In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 83, no 2, p. 653-661Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To develop reconstruction methods for improved image quality of chemical shift displacement-corrected fat/water imaging combined with partial Fourier acquisition.

    THEORY: Fat/water separation in k-space enables correction of chemical shift displacement. Modeling fat and water as real-valued rather than complex improves the conditionality of the inverse problem. This advantage becomes essential for k-space separation. In this work, it was described how to perform regularized fat/water imaging with real estimates in k-space, and how fat/water imaging can be combined with partial Fourier reconstruction using Projection Onto Convex Sets (POCS).

    METHODS: The reconstruction methods were demonstrated on chemical shift encoded gradient echo and fast spin echo data from volunteers, acquired at 1.5 T and 3 T. Both fully sampled and partial Fourier acquisitions were made. Data was retrospectively rejected from the fully sampled dataset to evaluate POCS and homodyne reconstruction.

    RESULTS: Fat/water separation in k-space eliminated chemical shift displacement, while real-valued estimates considerably reduced the noise amplification compared to complex estimates. POCS reconstruction could recover high spatial frequency information in the fat and water images with lower reconstruction error than homodyne. Partial Fourier in the readout direction enabled more flexible choice of gradient echo imaging parameters, in particular image resolution.

    CONCLUSION: Chemical shift displacement-corrected fat/water imaging can be performed with regularization and real-valued estimates to improve image quality by reducing ill-conditioning of the inverse problem in k-space. Fat/water imaging can be combined with POCS, which offers improved image quality over homodyne reconstruction.

  • 9.
    Berglund, Johan
    et al.
    Karolinska Univ Hosp, Dept Med Radiat Phys, P9 02, SE-17176 Stockholm, Sweden.;Karolinska Inst, Dept Clin Sci Intervent & Technol, Stockholm, Sweden..
    Skorpil, Mikael
    Umeå Univ, Dept Radiat Sci, Umeå, Sweden..
    Multi-scale graph-cut algorithm for efficient water-fat separation2017In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 78, no 3, p. 941-949Article in journal (Refereed)
    Abstract [en]

    Purpose

    To improve the accuracy and robustness to noise in water-fat separation by unifying the multiscale and graph cut based approaches to B-0-correction.

    Methods

    A previously proposed water-fat separation algorithm that corrects for B-0 field inhomogeneity in 3D by a single quadratic pseudo-Boolean optimization (QPBO) graph cut was incorporated into a multi-scale framework, where field map solutions are propagated from coarse to fine scales for voxels that are not resolved by the graph cut. The accuracy of the single-scale and multi-scale QPBO algorithms was evaluated against benchmark reference datasets. The robustness to noise was evaluated by adding noise to the input data prior to water-fat separation.

    Results

    Both algorithms achieved the highest accuracy when compared with seven previously published methods, while computation times were acceptable for implementation in clinical routine. The multi-scale algorithm was more robust to noise than the single-scale algorithm, while causing only a small increase (+10%) of the reconstruction time.

    Conclusion

    The proposed 3D multi-scale QPBO algorithm offers accurate water-fat separation, robustness to noise, and fast reconstruction. The software implementation is freely available to the research community. Magn Reson Med 78:941-949, 2017.

  • 10. Berglund, Johan
    et al.
    Sprenger, Tim
    van Niekerk, Adam
    Rydén, Henric
    Avventi, Enrico
    Norbeck, Ola
    Skare, Stefan
    Motion-insensitive susceptibility weighted imaging.2021In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 86, no 4, p. 1970-1982Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To enable SWI that is robust to severe head movement.

    METHODS: Prospective motion correction using a markerless optical tracker was applied to all pulse sequences. Three-dimensional gradient-echo and 3D EPI were used as reference sequences, but were expected to be sensitive to motion-induced B0 changes, as the long TE required for SWI allows phase discrepancies to accumulate between shots. Therefore, 2D interleaved snapshot EPI was investigated for motion-robust SWI and compared with conventional 2D EPI. Repeated signal averages were retrospectively corrected for motion. The sequences were evaluated at 3 T through controlled motion experiments involving two cooperative volunteers and SWI of a tumor patient.

    RESULTS: The performed continuous head motion was in the range of 5-8° rotations. The image quality of the 3D sequences and conventional 2D EPI was poor unless the rotational motion axis was parallel to B0 . Interleaved snapshot EPI had minimal intraslice phase discrepancies due to its small temporal footprint. Phase inconsistency between signal averages was well tolerated due to the high-pass filter effect of the SWI processing. Interleaved snapshot EPI with prospective and retrospective motion correction demonstrated similar image quality, regardless of whether motion was present. Lesion depiction was equal to 3D EPI with matching resolution.

    CONCLUSION: Susceptibility-based imaging can be severely corrupted by head movement despite accurate prospective motion correction. Interleaved snapshot EPI is a superior alternative for patients who are prone to move and offers SWI which is insensitive to motion when combined with prospective and retrospective motion correction.

  • 11. Berglund, Johan
    et al.
    van Niekerk, Adam
    Rydén, Henric
    Sprenger, Tim
    Avventi, Enrico
    Norbeck, Ola
    Glimberg, Stefan L
    Olesen, Oline V
    Skare, Stefan
    Prospective motion correction for diffusion weighted EPI of the brain using an optical markerless tracker.2021In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 85, no 3, p. 1427-1440Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To enable motion-robust diffusion weighted imaging of the brain using well-established imaging techniques.

    METHODS: An optical markerless tracking system was used to estimate and correct for rigid body motion of the head in real time during scanning. The imaging coordinate system was updated before each excitation pulse in a single-shot EPI sequence accelerated by GRAPPA with motion-robust calibration. Full Fourier imaging was used to reduce effects of motion during diffusion encoding. Subjects were imaged while performing prescribed motion patterns, each repeated with prospective motion correction on and off.

    RESULTS: Prospective motion correction with dynamic ghost correction enabled high quality DWI in the presence of fast and continuous motion within a 10° range. Images acquired without motion were not degraded by the prospective correction. Calculated diffusion tensors tolerated the motion well, but ADC values were slightly increased.

    CONCLUSIONS: Prospective correction by markerless optical tracking minimizes patient interaction and appears to be well suited for EPI-based DWI of patient groups unable to remain still including those who are not compliant with markers.

  • 12.
    Björk, Marcus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Ingle, R. Reeve
    Gudmundson, Erik
    Stoica, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Nishimura, Dwight G.
    Barral, Joëlle K.
    Parameter estimation approach to banding artifact reduction in balanced steady-state free precession2014In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 72, no 3, p. 880-892Article in journal (Refereed)
    Abstract [en]

    Purpose: The balanced steady-state free precession (bSSFP) pulse sequence has shown to be of great interest due to its high signal-to-noise ratio efficiency. However, bSSFP images often suffer from banding artifacts due to off-resonance effects, which we aim to minimize in this article. Methods: We present a general and fast two-step algorithm for 1) estimating the unknowns in the bSSFP signal model from multiple phase-cycled acquisitions, and 2) reconstructing band-free images. The first step, linearization for off-resonance estimation (LORE), solves the nonlinear problem approximately by a robust linear approach. The second step applies a Gauss-Newton algorithm, initialized by LORE, to minimize the nonlinear least squares criterion. We name the full algorithm LORE-GN. Results: We derive the Cramer-Rao bound, a theoretical lower bound of the variance for any unbiased estimator, and show that LORE-GN is statistically efficient. Furthermore, we show that simultaneous estimation of T-1 and T-2 from phase-cycled bSSFP is difficult, since the Cramer-Rao bound is high at common signal-to-noise ratio. Using simulated, phantom, and in vivo data, we illustrate the band-reduction capabilities of LORE-GN compared to other techniques, such as sum-of-squares. Conclusion: Using LORE-GN we can successfully minimize banding artifacts in bSSFP.

  • 13.
    Björk, Marcus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Zachariah, Dave
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology.
    Stoica, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    A multicomponent T2 relaxometry algorithm for myelin water imaging of the brain2016In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 75, no 1, p. 390-402Article in journal (Refereed)
  • 14.
    Björnerud, Atle
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Bjerner, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Assessment of myocardial blood volume and water exchange: theoretical considerations and in vivo results.2003In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 49, no 5, p. 828-837Article in journal (Refereed)
  • 15.
    Bjørnerud, Atle
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Johansson, Lars O.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Ahlström, Håkan K.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Renal T(*)(2) perfusion using an iron oxide nanoparticle contrast agent: influence of T(1) relaxation on the first-pass response2002In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 47, no 2, p. 298-304Article in journal (Refereed)
    Abstract [en]

    Quantitative perfusion measurements require accurate knowledge of the correlation between first-pass signal changes and the corresponding tracer concentration in tissue. In the present study, a detailed analysis of first-pass renal cortical changes in T(1) and T(*)(2) following bolus injection of the iron oxide nanoparticle NC100150 Injection was investigated in a pig model using a double-echo gradient-echo sequence. The estimated change in 1/T(*)(2) during first pass calculated from single-echo sequences was compared to the true double-echo-derived 1/T(*)(2) curves. Using a single-echo (TE = 6 ms) spoiled gradient-echo sequence, the first-pass 1/T(*)(2) response following a bolus injection of 1 mg Fe/kg of NC100150 Injection was significantly underestimated due to counteracting T(1) effects. Signal response simulations showed that the relative error in the first-pass response decreased with increasing TE and contrast agent dose. However, both the maximum TE and the maximum dose are limited by excessive cortical signal loss, and the maximum TE is further limited by high temporal resolution requirements. The problem of T(1) contamination can effectively be overcome by using a double-echo gradient-echo sequence. This yields a first-pass response that truly reflects the tissue tracer concentration, which is a critical requirement for quantitative renal perfusion assessment.

  • 16.
    Bjørnerud, Atle
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology. Radiologi.
    Johansson, Lars O.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Briley-Sæbø, Karen
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology. Radiologi.
    Ahlström, Håkan K.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Assessment of T1 and T2* effects in vivo and ex vivo using iron oxide nanoparticles in steady state: dependence on blood volume and water exchange2002In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 47, no 3, p. 461-471Article in journal (Refereed)
    Abstract [en]

    Accurate knowledge of the relationship between contrast agent concentration and tissue relaxation is a critical requirement for quantitative assessment of tissue perfusion using contrast-enhanced MRI. In the present study, using a pig model, the relationship between steady-state blood concentration levels of an iron oxide nanoparticle with a hydrated diameter of 12 nm (NC100150 Injection) and changes in the transverse and longitudinal relaxation rates (1/T2* and 1/T1, respectively) in blood, muscle, and renal cortex was investigated at 1.5 T. Ex vivo measurements of 1/T2* and 1/T1 were additionally performed in whole pig blood spiked with different concentrations of the iron oxide nanoparticle. In renal cortex and muscle, 1/T2* increased linearly with contrast agent concentration with slopes of 101 +/-22 s(-1)mM(-1) and 6.5 +/-0.9 s(-1)mM(-1) (mean +/- SD), respectively. In blood, 1/T2* increased as a quadratic function of contrast agent concentration, with different quadratic terms in the ex vivo vs. the in vivo experiments. In vivo, 1/T1 in blood increased linearly with contrast agent concentration, with a slope (T1-relaxivity) of 13.9 +/- 0.9 s(-1)mM(-1). The achievable increase in 1/T1 in renal cortex and muscle was limited by the rate of water exchange between the intra- and extravascular compartments and the 1/T1-curves were well described by a two-compartment water exchange limited relaxation model.

  • 17. Ericsson, A
    et al.
    Weis, J
    Hemmingsson, A
    Wikström, M
    Sperber, G O
    Measurements of magnetic field variations in the human brain using a 3D-FT multiple gradient echo technique.1995In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 33, no 2, p. 171-7Article in journal (Refereed)
    Abstract [en]

    A magnetic resonance 3DFT multiple gradient-echo technique was used for measurements of the proton spectrum for each voxel in the measured slice. Water, fat, magnetic field and T2 distributions in the head of a normal volunteer and a patient with intracerebral hematoma were computed. Magnetic field variations caused by the head were calculated after correction for the static magnetic field inhomogeneity. Large local magnetic field variations up to 3 ppm were found in the human brain near interfaces between air or bone and brain tissues and 0.5 ppm between hematoma and brain tissue. Information about magnetic field variations could be useful for shimming procedures in vivo and for correcting artifacts in imaging and spectroscopy.

  • 18.
    Juul, Troels
    et al.
    Aarhus Univ, Dept Clin Med, MR Res Ctr, Aarhus, Denmark.
    Palm, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology, Integrative Physiology.
    Nielsen, Per Mose
    Aarhus Univ, Dept Clin Med, MR Res Ctr, Aarhus, Denmark.
    Bertelsen, Lotte Bonde
    Aarhus Univ, Dept Clin Med, MR Res Ctr, Aarhus, Denmark.
    Laustsen, Christoffer
    Aarhus Univ, Dept Clin Med, MR Res Ctr, Aarhus, Denmark.
    Ex vivo hyperpolarized MR spectroscopy on isolated renal tubular cells: A novel technique for cell energy phenotyping.2017In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 78, no 2, p. 457-461Article in journal (Refereed)
    Abstract [en]

    PURPOSE: It has been demonstrated that hyperpolarized (13) C MR is a useful tool to study cultured cells. However, cells in culture can alter phenotype, which raises concerns regarding the in vivo significance of such findings. Here we investigate if metabolic phenotyping using hyperpolarized (13) C MR is suitable for cells isolated from kidney tissue, without prior cell culture.

    METHODS: Isolation of tubular cells from freshly excised kidney tissue and treatment with either ouabain or antimycin A was investigated with hyperpolarized MR spectroscopy on a 9.4 Tesla preclinical imaging system.

    RESULTS: Isolation of tubular cells from less than 2 g of kidney tissue generally resulted in more than 10 million live tubular cells. This amount of cells was enough to yield robust signals from the conversion of (13) C-pyruvate to lactate, bicarbonate and alanine, demonstrating that metabolic flux by means of both anaerobic and aerobic pathways can be quantified using this technique.

    CONCLUSION: Ex vivo metabolic phenotyping using hyperpolarized (13) C MR in a preclinical system is a useful technique to study energy metabolism in freshly isolated renal tubular cells. This technique has the potential to advance our understanding of both normal cell physiology as well as pathological processes contributing to kidney disease.

  • 19.
    Langner, Taro
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology.
    Hedström, Anders
    BioVenture Hub, Antaros Med, Molndal, Sweden.
    Mörwald, Katharina
    Paracelsus Med Univ, Dept Pediat, Salzburg, Austria; Paracelsus Med Univ, Obes Res Unit, Salzburg, Austria.
    Weghuber, Daniel
    Paracelsus Med Univ, Dept Pediat, Salzburg, Austria; Paracelsus Med Univ, Obes Res Unit, Salzburg, Austria.
    Forslund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Paediatric Inflammation Research.
    Bergsten, Peter
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Paediatric Inflammation Research.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. BioVenture Hub, Antaros Med, Mölndal, Sweden.
    Kullberg, Joel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. BioVenture Hub, Antaros Med, Mölndal, Sweden.
    Fully convolutional networks for automated segmentation of abdominal adipose tissue depots in multicenter water–fat MRI2019In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 81, no 4, p. 2736-2745Article in journal (Refereed)
    Abstract [en]

    Purpose: An approach for the automated segmentation of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) in multicenter water–fat MRI scans of the abdomen was investigated, using 2 different neural network architectures.

    Methods: The 2 fully convolutional network architectures U‐Net and V‐Net were trained, evaluated, and compared using the water–fat MRI data. Data of the study Tellus with 90 scans from a single center was used for a 10‐fold cross‐validation in which the most successful configuration for both networks was determined. These configurations were then tested on 20 scans of the multicenter study beta‐cell function in JUvenile Diabetes and Obesity (BetaJudo), which involved a different study population and scanning device.

    Results: The U‐Net outperformed the used implementation of the V‐Net in both cross‐validation and testing. In cross‐validation, the U‐Net reached average dice scores of 0.988 (VAT) and 0.992 (SAT). The average of the absolute quantification errors amount to 0.67% (VAT) and 0.39% (SAT). On the multicenter test data, the U‐Net performs only slightly worse, with average dice scores of 0.970 (VAT) and 0.987 (SAT) and quantification errors of 2.80% (VAT) and 1.65% (SAT).

    Conclusion: The segmentations generated by the U‐Net allow for reliable quantification and could therefore be viable for high‐quality automated measurements of VAT and SAT in large‐scale studies with minimal need for human intervention. The high performance on the multicenter test data furthermore shows the robustness of this approach for data of different patient demographics and imaging centers, as long as a consistent imaging protocol is used.

  • 20. Lindner, Thomas
    et al.
    Bolar, Divya S
    Achten, Eric
    Barkhof, Frederik
    Bastos-Leite, António J
    Detre, John A
    Golay, Xavier
    Günther, Matthias
    Wang, Danny J J
    Haller, Sven
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology.
    Ingala, Silvia
    Jäger, Hans R
    Jahng, Geon-Ho
    Juttukonda, Meher R
    Keil, Vera C
    Kimura, Hirohiko
    Ho, Mai-Lan
    Lequin, Maarten
    Lou, Xin
    Petr, Jan
    Pinter, Nandor
    Pizzini, Francesca B
    Smits, Marion
    Sokolska, Magdalena
    Zaharchuk, Greg
    Mutsaerts, Henk J M M
    Current state and guidance on arterial spin labeling perfusion MRI in clinical neuroimaging.2023In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 89, no 5, p. 2024-2047Article in journal (Refereed)
    Abstract [en]

    This article focuses on clinical applications of arterial spin labeling (ASL) and is part of a wider effort from the International Society for Magnetic Resonance in Medicine (ISMRM) Perfusion Study Group to update and expand on the recommendations provided in the 2015 ASL consensus paper. Although the 2015 consensus paper provided general guidelines for clinical applications of ASL MRI, there was a lack of guidance on disease-specific parameters. Since that time, the clinical availability and clinical demand for ASL MRI has increased. This position paper provides guidance on using ASL in specific clinical scenarios, including acute ischemic stroke and steno-occlusive disease, arteriovenous malformations and fistulas, brain tumors, neurodegenerative disease, seizures/epilepsy, and pediatric neuroradiology applications, focusing on disease-specific considerations for sequence optimization and interpretation. We present several neuroradiological applications in which ASL provides unique information essential for making the diagnosis. This guidance is intended for anyone interested in using ASL in a routine clinical setting (i.e., on a single-subject basis rather than in cohort studies) building on the previous ASL consensus review.

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    fulltext
  • 21. Norbeck, Ola
    et al.
    Sprenger, Tim
    Avventi, Enrico
    Rydén, Henric
    Kits, Annika
    Berglund, Johan
    Skare, Stefan
    Optimizing 3D EPI for rapid T1 -weighted imaging.2020In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 84, no 3, p. 1441-1455Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To investigate the use of 3D EPI for rapid T1 -weighted brain imaging, focusing on the RF pulse's influence on the contrast between gray and white matter.

    METHODS: An interleaved 3D EPI sequence use partial Fourier and CAIPIRINHA sampling was used to acquire T1 -weighted brain volumes with isotropic resolution, low echo times, and low geometric distortions. Five different RF pulses were evaluated in terms of fat suppression performance and gray-white matter contrast. Two binomial RF pulses were compared to a single rectangular (WE-rect) RF pulse exciting only water, and two new RF pulses developed in this work, where one was an extension of the WE-rect, and the other was an SLR pulse. The technique was demonstrated in three clinical cases, where brain tumor patients were imaged before and after gadolinium administration.

    RESULTS: A fat-suppressed 3D EPI sequence with a phase encoding bandwidth of around 100 Hz was found to exhibit a good trade-off between geometrical distortions and scan duration. Whole-brain T1 -weighted 3D EPI images with 1.2 mm isotropic voxel size could be acquired in 24 seconds. The WE-rect, its extension, and the SLR RF pulses resulted in reduced magnetization transfer effects and provided a 20% mean increase in gray-white matter contrast.

    CONCLUSION: Using a high phase encoding bandwidth and RF pulses that reduce magnetization transfer effects, a fat-suppressed multi-shot 3D EPI sequence can be used to rapidly acquire isotropic T1 -weighted volumes.

  • 22. Norbeck, Ola
    et al.
    van Niekerk, Adam
    Avventi, Enrico
    Rydén, Henric
    Berglund, Johan
    Sprenger, Tim
    Skare, Stefan
    T1 -FLAIR imaging during continuous head motion: Combining PROPELLER with an intelligent marker.2021In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 85, no 2, p. 868-882Article in journal (Refereed)
    Abstract [en]

    PURPOSE: The purpose of this work is to describe a T1 -weighted fluid-attenuated inversion recovery (FLAIR) sequence that is able to produce sharp magnetic resonance images even if the subject is moving their head throughout the acquisition.

    METHODS: The robustness to motion artifacts and retrospective motion correction capabilities of the PROPELLER (periodically rotated overlapping parallel lines with enhanced reconstruction) trajectory were combined with prospective motion correction. The prospective correction was done using an intelligent marker attached to the subject. This marker wirelessly synchronizes to the pulse sequence to measure the directionality and magnitude of the magnetic fields present in the MRI machine during a short navigator, thus enabling it to determine its position and orientation in the scanner coordinate frame. Three approaches to incorporating the marker-navigator into the PROPELLER sequence were evaluated. The specific absorption rate, and subsequent scan time, of the T1 -weighted FLAIR PROPELLER sequence, was reduced using a variable refocusing flip-angle scheme. Evaluations of motion correction performance were done with 4 volunteers and 3 types of head motion.

    RESULTS: During minimal out-of-plane movement, retrospective PROPELLER correction performed similarly to the prospective correction. However, the prospective clearly outperformed the retrospective correction when there was out-of-plane motion. Finally, the combination of retrospective and prospective correction produced the sharpest images even during large continuous motion.

    CONCLUSION: Prospective motion correction of a PROPELLER sequence makes it possible to handle continuous, large, and high-speed head motions with only minor reductions in image quality.

  • 23. Rydén, Henric
    et al.
    Berglund, Johan
    Norbeck, Ola
    Avventi, Enrico
    Skare, Stefan
    T1 weighted fat/water separated PROPELLER acquired with dual bandwidths.2018In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 80, no 6, p. 2501-2513Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To describe a fat/water separated dual receiver bandwidth (rBW) spin echo PROPELLER sequence that eliminates the dead time associated with single rBW sequences. A nonuniform noise whitening by regularization of the fat/water inverse problem is proposed, to enable dual rBW reconstructions.

    METHODS: Bipolar, flyback, and dual spin echo sequences were developed. All sequences acquire two echoes with different rBW without dead time. Chemical shift displacement was corrected by performing the fat/water separation in k-space, prior to gridding. The proposed sequences were compared to fat saturation, and single rBW sequences, in terms of SNR and CNR efficiency, using clinically relevant acquisition parameters. The impact of motion was investigated.

    RESULTS: Chemical shift correction greatly improved the image quality, especially at high resolution acquired with low rBW, and also improved motion estimates. SNR efficiency of the dual spin echo sequence was up to 20% higher than the single rBW acquisition, while CNR efficiency was 50% higher for the bipolar acquisition. Noise whitening was deemed necessary for all dual rBW acquisitions, rendering high image quality with strong and homogenous fat suppression.

    CONCLUSION: Dual rBW sequences eliminate the dead time present in single rBW sequences, which improves SNR efficiency. In combination with the proposed regularization, this enables highly efficient T1-weighted PROPELLER images without chemical shift displacement.

  • 24. Rydén, Henric
    et al.
    Berglund, Johan
    Norbeck, Ola
    Avventi, Enrico
    Sprenger, Tim
    van Niekerk, Adam
    Skare, Stefan
    RARE two-point Dixon with dual bandwidths.2020In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 84, no 5, p. 2456-2468Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To investigate the impact of dual readout bandwidths (dBW) in a dual echo fat/water acquisition and describe a dBW-rapid acquisition relaxation enhanced, or turbo spin echo sequence where the concept is used to improve SNR by removing dead times between refocusing pulses and avoiding redundant Chemical-shift encoded.

    METHODS: Cramér-Rao bounds and Monte Carlo simulations were used to investigate a two-point fat/water model where the difference in bandwidths is incorporated. In vivo images were acquired at 1.5 and 3 T with the dBW-rapid acquisition relaxation enhanced, or turbo spin echo sequence. Typical bandwidth ratios were 1:2. SNR was compared with a single bandwidth sequence under identical scan parameters at 3T.

    RESULTS: Monte Carlo simulations and Cramér-Rao analysis demonstrate that number of signal averages can be improved with dual bandwidths compared to conventional single bandwidth acquisitions. The dBW-rapid acquisition relaxation enhanced, or turbo spin echo sequence can acquire images with high readout resolutions with well-conditioned sampling. An SNR improvement of 52% was measured, in line with the theoretical gain of 54%.

    CONCLUSIONS: The proposed dBW-rapid acquisition relaxation enhanced, or turbo spin echo sequence is a highly SNR-efficient two-point rapid acquisition relaxation enhanced, or turbo spin echo sequence without dead times, and can acquire images at higher resolutions than current vendor-supplied alternatives.

  • 25. Rydén, Henric
    et al.
    Norbeck, Ola
    Avventi, Enrico
    Skorpil, Mikael
    van Niekerk, Adam
    Skare, Stefan
    Berglund, Johan
    Chemical shift encoding using asymmetric readout waveforms.2021In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 85, no 3, p. 1468-1480Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To describe a new method for encoding chemical shift using asymmetric readout waveforms that enables more SNR-efficient fat/water imaging.

    METHODS: Chemical shift was encoded using asymmetric readout waveforms, rather than conventional shifted trapezoid readouts. Two asymmetric waveforms are described: a triangle and a spline. The concept was applied to a fat/water separated RARE sequence to increase sampling efficiency. The benefits were investigated through comparisons to shifted trapezoid readouts. Using asymmetric readout waveforms, the scan time was either shortened or maintained to increase SNR. A matched in-phase waveform is also described that aims to improve the SNR transfer function of the fat and water estimates. The sequence was demonstrated for cervical spine, musculoskeletal (MSK), and optic nerve applications at 3T and compared with conventional shifted readouts.

    RESULTS: blurring. Maintaining the scan times and using asymmetric readout waveforms achieved an SNR improvement in agreement with the prolonged sampling duration.

    CONCLUSIONS: Asymmetric readout waveforms offer an additional degree of freedom in pulse sequence designs where chemical shift encoding is desired. This can be used to significantly shorten scan times or to increase SNR with maintained scan time.

  • 26. Schoenberg, Stefan O
    et al.
    Aumann, Silke
    Just, Armin
    Bock, Michael
    Knopp, Michael V
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Quantification of renal perfusion abnormalities using an intravascular contrast agent (part 2): results in animals and humans with renal artery stenosis2003In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 49, no 2, p. 288-298Article in journal (Refereed)
    Abstract [en]

    The interrelation between the morphologic degree of renal artery stenosis and changes in parenchymal perfusion is assessed using an intravascular contrast agent. In seven adult foxhounds, different degrees of renal artery stenosis were created with an inflatable clamp implanted around the renal artery. Dynamic susceptibility-weighted gradient-echo imaging was used to measure signal-time curves in the renal artery and the renal parenchyma during administration of 1.5 mg/kg BW of an intravascular ultrasmall particle iron oxide (USPIO) contrast agent. From the dynamic series, regional renal blood volume (rRBV), regional renal blood flow (rRBF), and mean transit time (MTT) were calculated. The morphologic degree of stenosis was measured in the steady state using a high-resolution 3D contrast-enhanced (CE) MR angiography (MRA) sequence (voxel size = 0.7 x 0.7 x 1 mm(3)). Five patients with renoparenchymal damage due to long-standing renal artery stenosis were evaluated. In the animal stenosis model, cortical perfusion remained unchanged for degrees of renal artery stenosis up to 80%. With degrees of stenoses > 80%, cortical perfusion dropped to 151 +/- 54 ml/100 g of tissue per minute as compared to a baseline of 513 +/- 76 ml/100 g/min. In the patients, a substantial difference in the cortical perfusion of more than 200 +/- 40 ml/100 g/min between the normal and the ischemic kidneys was found. The results show that quantitative renal perfusion measurements in combination with 3D-CE-MRA allow the functional significance of a renal artery stenosis to be determined in a single MR exam. Differentiation between renovascular and renoparenchymal disease thus becomes feasible.

  • 27. Sprenger, Tim
    et al.
    Kits, Annika
    Norbeck, Ola
    van Niekerk, Adam
    Berglund, Johan
    Karolinska Univ Hosp, Dept Neuroradiol, Stockholm, Sweden..
    Rydén, Henric
    Avventi, Enrico
    Skare, Stefan
    NeuroMix-A single-scan brain exam2022In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 87, no 5, p. 2178-2193Article in journal (Refereed)
    Abstract [en]

    PURPOSE: Implement a fast, motion-robust pulse sequence that acquires T1 -weighted, T2 -weighted, T2 * -weighted, T2 fluid-attenuated inversion recovery, and DWI data in one run with only one prescription and one prescan.

    METHODS: A software framework was developed that configures and runs several sequences in one main sequence. Based on that framework, the NeuroMix sequence was implemented, containing motion robust single-shot sequences using EPI and fast spin echo (FSE) readouts (without EPI distortions). Optional multi-shot sequences that provide better contrast, higher resolution, or isotropic resolution could also be run within the NeuroMix sequence. An optimized acquisition order was implemented that minimizes times where no data is acquired.

    RESULTS: NeuroMix is customizable and takes between 1:20 and 4 min for a full brain scan. A comparison with the predecessor EPIMix revealed significant improvements for T2 -weighted and T2 fluid-attenuated inversion recovery, while taking only 8 s longer for a similar configuration. The optional contrasts were less motion robust but offered a significant increase in quality, detail, and contrast. Initial clinical scans on 1 pediatric and 1 adult patient showed encouraging image quality.

    CONCLUSION: The single-shot FSE readouts for T2 -weighted and T2 fluid-attenuated inversion recovery and the optional multishot FSE and 3D-EPI contrasts significantly increased diagnostic value compared with EPIMix, allowing NeuroMix to be considered as a standalone brain MRI application.

  • 28.
    Szczepankiewicz, Filip
    et al.
    Harvard Med Sch, Boston, MA 02115 USA.;Brigham & Womens Hosp, Radiol, 75 Francis St, Boston, MA 02115 USA.;Lund Univ, Clin Sci Lund, Diagnost Radiol, Lund, Sweden..
    Sjölund, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Artificial Intelligence. Elekta Instrument AB, Stockholm, Sweden..
    Dall'Armellina, Erica
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Leeds, W Yorkshire, England..
    Plein, Sven
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Leeds, W Yorkshire, England..
    Schneider, Jürgen E.
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Leeds, W Yorkshire, England..
    Teh, Irvin
    Univ Leeds, Leeds Inst Cardiovasc & Metab Med, Leeds, W Yorkshire, England..
    Westin, Carl-Fredrik
    Harvard Med Sch, Boston, MA 02115 USA.;Brigham & Womens Hosp, Radiol, 75 Francis St, Boston, MA 02115 USA..
    Motion-compensated gradient waveforms for tensor-valued diffusion encoding by constrained numerical optimization2021In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 85, no 4, p. 2117-2126Article in journal (Refereed)
    Abstract [en]

    Purpose Diffusion-weighted MRI is sensitive to incoherent tissue motion, which may confound the measured signal and subsequent analysis. We propose a "motion-compensated" gradient waveform design for tensor-valued diffusion encoding that negates the effects bulk motion and incoherent motion in the ballistic regime. Methods Motion compensation was achieved by constraining the magnitude of gradient waveform moment vectors. The constraint was incorporated into a numerical optimization framework, along with existing constraints that account for b-tensor shape, hardware restrictions, and concomitant field gradients. We evaluated the efficacy of encoding and motion compensation in simulations, and we demonstrated the approach by linear and planar b-tensor encoding in a healthy heart in vivo. Results The optimization framework produced asymmetric motion-compensated waveforms that yielded b-tensors of arbitrary shape with improved efficiency compared with previous designs for tensor-valued encoding, and equivalent efficiency to previous designs for linear (conventional) encoding. Technical feasibility was demonstrated in the heart in vivo, showing vastly improved data quality when using motion compensation. The optimization framework is available online in open source. Conclusion Our gradient waveform design is both more flexible and efficient than previous methods, facilitating tensor-valued diffusion encoding in tissues in which motion would otherwise confound the signal. The proposed design exploits asymmetric encoding times, a single refocusing pulse or multiple refocusing pulses, and integrates compensation for concomitant gradient effects throughout the imaging volume.

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  • 29. van Niekerk, Adam
    et al.
    Berglund, Johan
    Sprenger, Tim
    Norbeck, Ola
    Avventi, Enrico
    Rydén, Henric
    Skare, Stefan
    Control of a wireless sensor using the pulse sequence for prospective motion correction in brain MRI.2022In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 87, no 2, p. 1046-1061Article in journal (Refereed)
    Abstract [en]

    PURPOSE: To synchronize and pass information between a wireless motion-tracking device and a pulse sequence and show how this can be used to implement customizable navigator interleaving schemes that are part of the pulse sequence design.

    METHODS: The device tracks motion by sampling the voltages induced in 3 orthogonal pickup coils by the changing gradient fields. These coils were modified to also detect RF-transmit events using a 3D RF-detection circuit. The device could then detect and decode a set RF signatures while ignoring excitations in the parent pulse sequence. A set of unique RF signatures were then paired with a collection of navigators and used to trigger readouts on the wireless device synchronous to the pulse sequence execution. Navigator interleaving schemes were then demonstrated in 3D RF-spoiled gradient echo, T1 -FLAIR (fluid-attenuated inversion recovery) PROPELLER (periodically rotated overlapping parallel lines with enhanced reconstruction), and T2 -FLAIR PROPELLER pulse sequences.

    RESULTS: Excitations in the parent pulse sequences were successfully rejected and the RF signatures successfully decoded. For the 3D gradient echo sequence, distortions were removed by interleaving flipped polarity navigators and taking the difference between consecutive readouts. The impact on scan duration was reduced by 54% by breaking up the navigators into smaller parts. Successful motion correction was performed using the PROPELLER pulse sequences in 3 Tesla and 1.5 Tesla MRI scanners without modifications to the device hardware or software.

    CONCLUSION: The proposed RF signature-based triggering scheme enables complex interactions between the pulse sequence and a wireless device. Thus, enabling prospective motion correction that is repeatable, versatile, and minimally invasive with respect to hardware setup.

  • 30. Weis, J
    et al.
    Ericsson, A
    Hemmingsson, A
    Chemical shift artifact-free microscopy: spectroscopic microimaging of the human skin.1999In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 41, no 5, p. 904-8Article in journal (Refereed)
    Abstract [en]

    A spectroscopic imaging technique with high spatial resolution was used for the study of human skin in vivo. The measurements were performed using a whole-body magnetic resonance system (1.5 T) with standard gradients and a standard 8-cm diameter circular surface coil. A decisive gain in signal-to-noise ratio was achieved by reducing the receiver bandwidth of the imaging system to values less than +/-5 kHz. The chemical shift misregistration was eliminated by post-detection data processing. The method was tested on different kinds of skin, on the foot sole and head. Water, fat, and chemical shift artifact-free images were obtained with resolution 0.107 x 0.143 mm in plane and slice thickness 1 mm. A major advantage of the spectroscopic imaging procedure is that the pulse sequence can be optimized for the maximum signal-to-noise ratio. There is no need for special modification of the sequence to circumvent the chemical shift artifacts (water, fat suppression, etc.).

  • 31.
    Weis, Jan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Courivaud, Frederic
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Hansen, Michael Schacht
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Ribe, Lars Riisgaard
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Radiology, Oncology and Radiation Science, Radiology.
    Lipid content in the musculature of the lower leg: evaluation with high-resolution spectroscopic imaging2005In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 54, no 1, p. 152-158Article in journal (Refereed)
    Abstract [en]

    A novel spectroscopic imaging method with high spectral and spatial resolution was developed for the specific goal of assessing muscle fat. Sensitivity to the methylene and methyl protons of fatty acids was improved by the use of a binomial 1 excitation pulse instead of the standard radiofrequency (RF) pulse. Acceptable measurement time is achieved by using a narrow spectral bandwidth (6 ppm). The spectral resolution is sufficient to resolve extramyocellular (EMCL) and intramyocellular (IMCL) lipids. A post-detection data processing scheme that permits correction of spectral artifacts caused by chemical shifts, spectral line aliasing, and magnetic field inhomogeneities is suggested. The lipid content in different lower leg muscles was evaluated. Muscle fiber orientation was taken into account in assessing quantities of EMCL and IMCL. The proposed technique allows small amounts of inhomogeneously distributed muscle lipids to be quantified.

  • 32. Weis, Jan
    et al.
    Ericsson, Anders
    Hemmingsson, Anders
    Chemical shift artifact-free microscopy: spectroscopic microimaging of the human skin1999In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 41, no 5, p. 904-908Article in journal (Refereed)
  • 33.
    Weis, Jan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Biomedical Informatics and Engineering.
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Courivaud, Frederic
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Karlsson, F. Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Quantification of intramyocellular lipids in obese subjects using spectroscopic imaging with high spatial resolution2007In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 57, no 1, p. 22-28Article in journal (Refereed)
    Abstract [en]

    Quantification of intramyocellular lipids (IMCL) in obese subjects by single-voxel spectroscopy (SVS) or conventional spectroscopic imaging (SI) often fails due to overlap of IMCL spectral lines by extramyocellular lipids (EMCL), and signal contamination from subcutaneous fat and bone marrow. This study demonstrates that these problems can be solved by high-resolution SI with 128 phase-encoding steps and a read gradient during acquisition. The small voxels obtained in this way facilitated differentiation between EMCL and IMCL. This method offers the possibility of studying different muscle groups and the variation of lipids within one muscle.

  • 34.
    Weis, Jan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Johansson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Ortiz-Nieto, Francisco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Ahlström, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Radiology.
    Assessment of lipids in skeletal muscle by high-resolution spectroscopic imaging using fat as the internal standard: comparison with water referenced spectroscopy2008In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 59, no 6, p. 1259-1265Article in journal (Refereed)
    Abstract [en]

    The main purpose of the study was to compare proton (1H) single-voxel MR spectroscopy (MRS) with high-spatial-resolution spectroscopic imaging (MRSI) to determine the lipid content in human skeletal muscle. Unsuppressed water line was used as a concentration reference in the processing of single-voxel spectra. The spectrum from yellow bone marrow with a 100% fat content and probe with the vegetable oil served as internal and external reference for high-spatial-resolution MRSI, respectively. Very good correlation was found between lipid concentrations measured by water referenced single-voxel MRS and high-spatial-resolution MRSI with yellow bone marrow as the internal standard. Excellent correlation was found between total lipid concentrations estimated by high-spatial-resolution MRSI with vegetable oil as the external fat standard and yellow bone marrow as the internal reference. From comparison of single-voxel MRS and MRSI approaches, it follows that relaxation correction of the reference water and methylene fat line is inevitable in processing the standard single-voxel spectra. The high-resolution MRSI approach is recommended to avoid the problem of relaxation corrections and enables using vegetable oil as the external fat standard.

  • 35.
    Wiesinger, Florian
    et al.
    GE Healthcare, Freisinger Landstr 50, D-85748 Munich, Germany.
    Bylund, Mikael
    Umea Univ, Umea, Sweden.
    Yang, Jaewon
    UCSF, San Francisco, CA USA.
    Kaushik, Sandeep
    GE Global Res, Bangalore, Karnataka, India.
    Shanbhag, Dattesh
    GE Global Res, Bangalore, Karnataka, India.
    Ahn, Sangtae
    GE Global Res, Niskayuna, NY USA.
    Jonsson, Joakim H.
    Umea Univ, Umea, Sweden.
    Lundman, Josef A.
    Umea Univ, Umea, Sweden.
    Hope, Thomas
    UCSF, San Francisco, CA USA.
    Nyholm, Tufve
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medical Radiation Science. Umea Univ, Umea, Sweden.
    Larson, Peder
    UCSF, San Francisco, CA USA.
    Cozzini, Cristina
    GE Healthcare, Freisinger Landstr 50, D-85748 Munich, Germany.
    Zero TE-based pseudo-CT image conversion in the head and its application in PET/MR attenuation correction and MR-guided radiation therapy planning2018In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 80, no 4, p. 1440-1451Article in journal (Refereed)
    Abstract [en]

    Purpose: To describe a method for converting Zero TE (ZTE) MR images into Xray attenuation information in the form of pseudo-CT images and demonstrate its performance for (1) attenuation correction (AC) in PET/MR and (2) dose planning in MR-guided radiation therapy planning (RTP). Methods: Proton density-weighted ZTE images were acquired as input for MRbased pseudo-CT conversion, providing (1) efficient capture of short-lived bone signals, (2) flat soft-tissue contrast, and (3) fast and robust 3D MR imaging. After bias correction and normalization, the images were segmented into bone, soft-tissue, and air by means of thresholding and morphological refinements. Fixed Hounsfield replacement values were assigned for air (-1000 HU) and soft-tissue (142 HU), whereas continuous linear mapping was used for bone. Results: The obtained ZTE-derived pseudo-CT images accurately resembled the true CT images (i. e., Dice coefficient for bone overlap of 0.73 +/- 0.08 and mean absolute error of 123 +/- 25 HU evaluated over the whole head, including errors from residual registration mismatches in the neck and mouth regions). The linear bone mapping accounted for bone density variations. Averaged across five patients, ZTE-based AC demonstrated a PET error of -0.04 +/- 1.68% relative to CT-based AC. Similarly, for RTP assessed in eight patients, the absolute dose difference over the target volume was found to be 0.23 +/- 0.42%. Conclusion: The described method enables MR to pseudo-CT image conversion for the head in an accurate, robust, and fast manner without relying on anatomical prior knowledge. Potential applications include PET/MR-AC, and MR-guided RTP.

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