647 results on '"Hutter, Jana"'
Search Results
202. Comprehensive CG-SENSE reconstruction of SMS-EPI
- Author
-
Cordero Grande, Lucilio, Price, Anthony, Hutter, Jana Maria, Hughes, Emer, and Hajnal, Joseph Vilmos
- Published
- 2016
203. Quantifying Placental Microcirculation and Microstructure with Anisotropic IVIM Models
- Author
-
Slator, Paddy J., primary, Hutter, Jana, additional, McCabe, Laura, additional, Santos Gomes, Ana Dos, additional, Price, Anthony N., additional, Panagiotaki, Eleftheria, additional, Rutherford, Mary A., additional, Hajnal, Joseph V., additional, and Alexander, Daniel C., additional
- Published
- 2017
- Full Text
- View/download PDF
204. Multimodal Surface Matching with Higher-Order Smoothness Constraints☆
- Author
-
Robinson, Emma C., primary, Garcia, Kara, additional, Glasser, Matthew F., additional, Chen, Zhengdao, additional, Coalson, Timothy S., additional, Makropoulos, Antonios, additional, Bozek, Jelena, additional, Wright, Robert, additional, Schuh, Andreas, additional, Webster, Matthew, additional, Hutter, Jana, additional, Price, Anthony, additional, Grande, Lucilio Cordero, additional, Hughes, Emer, additional, Tusor, Nora, additional, Bayly, Philip V., additional, Van Essen, David C., additional, Smith, Stephen M., additional, David Edwards, A., additional, Hajnal, Joseph, additional, Jenkinson, Mark, additional, Glocker, Ben, additional, and Rueckert, Daniel, additional
- Published
- 2017
- Full Text
- View/download PDF
205. A dedicated neonatal brain imaging system
- Author
-
Hughes, Emer J., primary, Winchman, Tobias, additional, Padormo, Francesco, additional, Teixeira, Rui, additional, Wurie, Julia, additional, Sharma, Maryanne, additional, Fox, Matthew, additional, Hutter, Jana, additional, Cordero-Grande, Lucilio, additional, Price, Anthony N., additional, Allsop, Joanna, additional, Bueno-Conde, Jose, additional, Tusor, Nora, additional, Arichi, Tomoki, additional, Edwards, A. D., additional, Rutherford, Mary A., additional, Counsell, Serena J., additional, and Hajnal, Joseph V., additional
- Published
- 2017
- Full Text
- View/download PDF
206. Three‐dimensional motion corrected sensitivity encoding reconstruction for multi‐shot multi‐slice MRI: Application to neonatal brain imaging
- Author
-
Cordero‐Grande, Lucilio, primary, Hughes, Emer J., additional, Hutter, Jana, additional, Price, Anthony N., additional, and Hajnal, Joseph V., additional
- Published
- 2017
- Full Text
- View/download PDF
207. Placenta Maps: In Utero Placental Health Assessment of the Human Fetus
- Author
-
Miao, Haichao, primary, Mistelbauer, Gabriel, additional, Karimov, Alexey, additional, Alansary, Amir, additional, Davidson, Alice, additional, Lloyd, David F. A., additional, Damodaram, Mellisa, additional, Story, Lisa, additional, Hutter, Jana, additional, Hajnal, Joseph V., additional, Rutherford, Mary, additional, Preim, Bernhard, additional, Kainz, Bernhard, additional, and Groller, M. Eduard, additional
- Published
- 2017
- Full Text
- View/download PDF
208. Time-efficient and flexible design of optimized multishell HARDI diffusion
- Author
-
Hutter, Jana, primary, Tournier, J. Donald, additional, Price, Anthony N., additional, Cordero-Grande, Lucilio, additional, Hughes, Emer J., additional, Malik, Shaihan, additional, Steinweg, Johannes, additional, Bastiani, Matteo, additional, Sotiropoulos, Stamatios N., additional, Jbabdi, Saad, additional, Andersson, Jesper, additional, Edwards, A. David, additional, and Hajnal, Joseph V., additional
- Published
- 2017
- Full Text
- View/download PDF
209. The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction
- Author
-
Makropoulos, Antonios, primary, Robinson, Emma C., additional, Schuh, Andreas, additional, Wright, Robert, additional, Fitzgibbon, Sean, additional, Bozek, Jelena, additional, Counsell, Serena J., additional, Steinweg, Johannes, additional, Vecchiato, Katy, additional, Passerat-Palmbach, Jonathan, additional, Lenz, Gregor, additional, Mortari, Filippo, additional, Tenev, Tencho, additional, Duff, Eugene P., additional, Bastiani, Matteo, additional, Cordero-Grande, Lucilio, additional, Hughes, Emer, additional, Tusor, Nora, additional, Tournier, Jacques-Donald, additional, Hutter, Jana, additional, Price, Anthony N., additional, Teixeira, Rui Pedro A. G., additional, Murgasova, Maria, additional, Victor, Suresh, additional, Kelly, Christopher, additional, Rutherford, Mary A., additional, Smith, Stephen M., additional, Edwards, A. David, additional, Hajnal, Joseph V., additional, Jenkinson, Mark, additional, and Rueckert, Daniel, additional
- Published
- 2017
- Full Text
- View/download PDF
210. A deformable model for the reconstruction of the neonatal cortex
- Author
-
Schuh, Andreas, primary, Makropoulos, Antonios, additional, Wright, Robert, additional, Robinson, Emma C., additional, Tusor, Nora, additional, Steinweg, Johannes, additional, Hughes, Emer, additional, Cordero Grande, Lucilio, additional, Price, Anthony, additional, Hutter, Jana, additional, Hajnal, Joseph V., additional, and Rueckert, Daniel, additional
- Published
- 2017
- Full Text
- View/download PDF
211. Learning Compact ${q}$ -Space Representations for Multi-Shell Diffusion-Weighted MRI.
- Author
-
Christiaens, Daan, Cordero-Grande, Lucilio, Hutter, Jana, Price, Anthony N., Deprez, Maria, Hajnal, Joseph V., and Tournier, J-Donald
- Subjects
MACHINE learning ,DIFFUSION magnetic resonance imaging ,MEDICAL imaging systems ,MICROSTRUCTURE ,OUTLIERS (Statistics) - Abstract
Diffusion-weighted MRI measures the direction and scale of the local diffusion process in every voxel through its spectrum in ${q}$ -space, typically acquired in one or more shells. Recent developments in microstructure imaging and multi-tissue decomposition have sparked renewed attention in the radial ${b}$ -value dependence of the signal. Applications in motion correction and outlier rejection, therefore, require a compact linear signal representation that extends over the radial as well as angular domain. Here, we introduce SHARD, a data-driven representation of the ${q}$ -space signal based on spherical harmonics and a radial decomposition into orthonormal components. This representation provides a complete, orthogonal signal basis, tailored to the spherical geometry of ${q}$ -space, and calibrated to the data at hand. We demonstrate that the rank-reduced decomposition outperforms model-based alternatives in human brain data, while faithfully capturing the micro- and meso-structural information in the signal. Furthermore, we validate the potential of joint radial-spherical as compared with single-shell representations. As such, SHARD is optimally suited for applications that require low-rank signal predictions, such as motion correction and outlier rejection. Finally, we illustrate its application for the latter using outlier robust regression. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
212. Optimizing maternal fat suppression with constrained image‐based shimming in fetal MR.
- Author
-
Gaspar, Andreia S., Nunes, Rita G., Ferrazzi, Giulio, Hughes, Emer J., Hutter, Jana, Malik, Shaihan J., McCabe, Laura, Baruteau, Kelly P., Rutherford, Mary A., Hajnal, Joseph V., and Price, Anthony N.
- Abstract
Purpose: Echo planar imaging (EPI) is the primary sequence for functional and diffusion MRI. In fetal applications, the large field of view needed to encode the maternal abdomen leads to prolonged EPI readouts, which may be further extended due to safety considerations that limit gradient performance. The resulting images become very sensitive to water‐fat shift and susceptibility artefacts. The purpose of this study was to reduce artefacts and increase stability of EPI in fetal brain imaging, balancing local field homogeneity across the fetal brain with longer range variations to ensure compatibility with fat suppression of the maternal abdomen. Methods: Spectral Pre‐saturation with Inversion‐Recovery (SPIR) fat suppression was optimized by investigating SPIR pulse frequency offsets. Subsequently, fetal brain EPI data were acquired using image‐based (IB) shimming on 6 pregnant women by (1) minimizing B0 field variations within the fetal brain (localized IB shimming) and (2) with added constraint to limit B0 variation in maternal fat (fat constrained IB shimming). Results: The optimal offset for the SPIR pulse at 3 Tesla was 550 Hz. Both shimming approaches had similar performances in terms of B0 homogeneity within the brain, but constrained IB shimming enabled higher fat suppression efficiency. Conclusion: Optimized SPIR in combination with constrained IB shimming can improve maternal fat suppression while minimizing EPI distortions in the fetal brain. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
213. Beschleunigte kontrastmittelfreie morphologische und funktionelle Magnetresonanzangiograpie
- Author
-
Hutter, Jana
- Subjects
Bildrekonstruktion ,Technische Fakultät ,Magnetresonanzangiographie ,Bildverarbeitung ,ddc:600 - Abstract
Cardiovascular diseases such as stroke, stenosis, peripheral or renal artery disease require accurate angiographic visualization techniques both for diagnosis and treatment planning. Beside the morphological imaging, the in-vivo acquisition of blood flow information gained increasing clinical importance in recent years. Non-contrast-enhanced Magnetic Resonance Angiography (nceMRA) provides techniques for both fields. For morphological imaging, Time of Flight (TOF) and magnetization-prepared balanced Steady State Free Precession (mp-bSSFP) offer non-invasive, ionizing-radiation free and user independent alternatives to clinically established methods such as Digital Subtraction Angiography, Computed Tomography or Ultrasound. In the field of functional imaging, unique novel possibilities are given with three-directional velocity fields, acquired simultaneously to the morphological information using Phase Contrast Imaging (PCI). But the wider clinical use of nceMRA is still hampered by long acquisition times. Thus, accelerating nceMRA is a problem of high relevance and with great potential clinical impact. In this thesis, acceleration strategies based on k-sampling below the Nyquist limit and adapted reconstruction techniques, combining parallel MRI (pMRI) methods with Compressed Sensing (CS), are developed for both types of nceMRA methods. This includes contributions to all relevant parts of the reconstruction algorithms, the sampling strategy, the regularization technique and the optimization method. For morphological imaging, a novel analytical pattern combining aspects of pMRI and CS, called the MICCS pattern, is proposed in combination with an adapted Split Bregman algorithm. This allows for a reduction in the acquisition time for peripheral TOF imaging of the entire lower vasculature from over 30 minutes to less than 8 minutes. Further acceleration is achieved for 3-D free-breathing renal angiography using mp-bSSFP, where the entire volume can be acquired in less than 1 minute instead of over 8 minutes. In addition, organ based evaluations including the vessel sharpness at important positions show the diagnostic usability and the increased accuracy over clinically established acceleration methods. For PCI, advances are achieved with a dedicated novel sampling strategy, called I-VT sampling, including interleaved variations for all dimensions. Furthermore, two novel regularization techniques for PCI are developed in this thesis. First, a novel temporally masked and weighted strategy focusing on enhanced temporal fidelity, referred to as TMW is developed. This fully automatic approach uses dynamic and static vessel masks to guide the influence specifically to the static areas. Second, the low rank and sparse decomposition model, is extended to PCI, combined with adapted sparsity assumptions and the unconstrained Split Bregman algorithm. These methods are successfully applied to the carotid bifurcation, a region with a huge demand of significant acceleration as well high spatial and temporal accuracy of the flow values. But all algorithmic contributions exploit inherent properties of the acquisition technique, and thus can be applied for further applications. In summary, the main contribution of this thesis is significant acceleration of nceMRA achieved with novel sampling, regularization and optimization elements. Kardiovaskuläre Erkrankungen wie Schlaganfall, Gefäßverengungen und Gefäßerkrankungen erfordern sowohl für die Diagnose als auch die Planung operativer Eingriffe akkurate angiographische Bildgebung. Neben den morphologischen Techniken gewinnen Techniken, die die Aufnahme von Flussinformationen ermöglichen, zunehmend an klinischer Bedeutung. Kontrastmittelfreie Magnetresonanzangiographie bietet für beide Bereiche Techniken. Für morphologische Bildgebung stehen mit Time of Flight und magnetization-prepared balanced Steady State Free Precession nicht invasive strahlungsfreie Alternativen zu klinisch etablierten Verfahren wie Digitale Subtraktionsangiographie, Computer Tomographie und Ultraschall zur Verfügung. Im Bereich der funktionellen bildgebenden Verfahren ermöglicht Phasenkontrastbildgebung die gleichzeitige Aufnahme dreidimensionaler Geschwindigkeitsfelder und morphologischer Information. Ein Nachteil kontrastmittelfreier Verfahren sind lange Aufnahmezeiten, die noch immer ihre weitere klinische Nutzung verhindern. Deswegen ist die Beschleunigung dieser Methoden ein Problem mit hoher Bedeutung und großem klinischen Nutzen. In dieser Arbeit werden für beide Arten kontrastmittelfreier Angiographie Strategien zur Beschleunigung entwickelt, die auf einer Unterabtastung des k-Raums und geeigneten Rekonstruktionsverfahren (parallele MR Bildgebungstechniken und Compressed Sensing) basieren. Für die morphologische Bildgebung wird ein neuartiges analytisches Abtastmuster (MICCS), das Aspekte der parallelen MR Bildgebung mit den Anforderungen von Compressed Sensing vereint, in Verbindung mit einem angepassten Split Bregman Algorithmus vorgestellt. Diese Methode erlaubt die Reduktion der Aufnahmezeit für eine TOF basierte Darstellung der Beingefäße von 30 zu weniger als acht Minuten. Weiterhin wurde bei 3D Nierenbildgebung unter freier Atmung für das gesamte Volumen eine Aufnahmezeit von unter einer statt über acht Minuten erzielt. Darüber hinaus zeigen organbasierte Auswertemethoden wie die Schärfe der Gefäßränder eine erhöhte Genauigkeit im Vergleich zu klinische etablierten Methoden. Im Bereich der Phasenkontrastbildgebung wurden Fortschritte erzielt mit einer neuartigen Abtaststrategie, die Variation in alle vorhandenen Dimensionen erlaubt. Weitergehend wurden zwei neuartige Regularisierungsstrategien entwickelt. Erstens wurde eine neue zeitlich maskierte und gewichtete Strategie, mit dem Fokus die zeitliche Datentreue zu erhalten, entwickelt. Dieser komplett automatisierte Ansatz verwendet dynamische und statische Adermasken um den Einfluss der Regularisierung auf die statischen Bereiche zu beschränken. Die zweite Methode erweitert das sogenannte low rank-sparse model auf Phasenkontrastdaten und verwendet den Split Bregman Algorithmus zur Lösung. Diese Methoden wurden erfolgreich auf Aufnahmen der Halsschlagadern angewandt. Dieser Bereich erfordert hohe Beschleunigung sowie räumliche und zeitliche Genauigkeit der Flussgeschwindigkeiten. Alle algorithmischen Beiträge beruhen auf intrinsischen Eigenschaften von Phasenkontrast und können somit auf weitere Körperregionen angewandt werden. Zusammenfassend ist der Hauptbeitrag dieser Arbeit die signifikante Beschleunigung kontrastmittelfreier Magnetresonanzangiographie mittels neuartigen Abtast-, Regularisierungs- und Optimierungselementen.
- Published
- 2014
214. Sensitivity Encoding for Aligned Multishot Magnetic Resonance Reconstruction
- Author
-
Cordero-Grande, Lucilio, primary, Teixeira, Rui Pedro A. G., additional, Hughes, Emer J., additional, Hutter, Jana, additional, Price, Anthony N., additional, and Hajnal, Joseph V., additional
- Published
- 2016
- Full Text
- View/download PDF
215. Märchen - Es war einmal, gilt heute noch!
- Author
-
Liberatore, Mariangela, Hutter, Jana, Liberatore, Mariangela, and Hutter, Jana
- Abstract
Diese produktorientierte Arbeit beschäftigt sich mit dem Thema Märchen. Sie gliedert sich in zwei Teile, diese enthalten einerseits die selbstgeschriebene märchenhafte Geschichte und andererseits den Theorieteil. Durch das Volksmärchen und dessen Charakter inspiriert, haben wir uns dann mit der Begriffsklärung, den Merkmalen, der Kritik sowie den pädagogischen Funktionen des Märchens befasst. Die Theorie steht jeweils im Zusammenhang mit dem erstellten „Märchen“. So beziehen sich auch die Analyse, die Symbolik und teils auch die Merkmale auf dieses. Die Fragestellung, an welcher sich diese Bachelorarbeit orientiert, lautet: Was steckt in Märchen und macht sie aus, damit ihre positive, die kindliche Entwicklung fördernde Wirkung zum Tragen kommt und welche konkreten (pädagogischen) Potentiale verbergen sich in den Märchen?
- Published
- 2015
216. An efficient sequence for fetal brain imaging at 3T with enhanced T1 contrast and motion robustness.
- Author
-
Ferrazzi, Giulio, Price, Anthony N., Teixeira, Rui Pedro A. G., Cordero‐Grande, Lucilio, Hutter, Jana, Gomes, Ana, Padormo, Francesco, Hughes, Emer, Schneider, Torben, Rutherford, Mary, Kuklisova Murgasova, Maria, and Hajnal, Joseph V.
- Abstract
Purpose: Ultrafast single‐shot T
2 ‐weighted images are common practice in fetal MR exams. However, there is limited experience with fetal T1 ‐weighted acquisitions. This study aims at establishing a robust framework that allows fetal T1 ‐weighted scans to be routinely acquired in utero at 3T. Methods: A 2D gradient echo sequence with an adiabatic inversion was optimized to be robust to fetal motion and maternal breathing optimizing grey/white matter contrast at the same time. This was combined with slice to volume registration and super resolution methods to produce volumetric reconstructions. The sequence was tested on 22 fetuses. Results: Optimized grey/white matter contrast and robustness to fetal motion and maternal breathing were achieved. Signal from cerebrospinal fluid (CSF) and amniotic fluid was nulled and 0.75 mm isotropic anatomical reconstructions of the fetal brain were obtained using slice‐to‐volume registration and super resolution techniques. Total acquisition time for a single stack was 56 s, all acquired during free breathing. Enhanced sensitivity to normal anatomy and pathology with respect to established methods is demonstrated. A direct comparison with a 3D spoiled gradient echo sequence and a controlled motion experiment run on an adult volunteer are also shown. Conclusion: This paper describes a robust framework to perform T1 ‐weighted acquisitions and reconstructions of the fetal brain in utero. Magn Reson Med 80:137–146, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
217. Inner‐volume echo volumar imaging (IVEVI) for robust fetal brain imaging.
- Author
-
Nunes, Rita G., Ferrazzi, Giulio, Price, Anthony N., Hutter, Jana, Gaspar, Andreia S., Rutherford, Mary A., and Hajnal, Joseph V.
- Abstract
Purpose: Fetal functional MRI studies using conventional 2‐dimensional single‐shot echo‐planar imaging sequences may require discarding a large data fraction as a result of fetal and maternal motion. Increasing the temporal resolution using echo volumar imaging (EVI) could provide an effective alternative strategy. Echo volumar imaging was combined with inner volume (IV) imaging (IVEVI) to locally excite the fetal brain and acquire full 3‐dimensional images, fast enough to freeze most fetal head motion. Methods: IVEVI was implemented by modifying a standard multi‐echo echo‐planar imaging sequence. A spin echo with orthogonal excitation and refocusing ensured localized excitation. To introduce T 2 * weighting and to save time, the k‐space center was shifted relative to the spin echo. Both single and multi‐shot variants were tested. Acoustic noise was controlled by adjusting the amplitude and switching frequency of the readout gradient. Image‐based shimming was used to minimize B
0 inhomogeneities within the fetal brain. Results: The sequence was first validated in an adult. Eight fetuses were scanned using single‐shot IVEVI at a 3.5 × 3.5 × 5.0 mm3 resolution with a readout duration of 383 ms. Multishot IVEVI showed reduced geometric distortions along the second phase‐encode direction. Conclusions: Fetal EVI remains challenging. Although effective echo times comparable to the T 2 * values of fetal cortical gray matter at 3 T could be achieved, controlling acoustic noise required longer readouts, leading to substantial distortions in single‐shot images. Although multishot variants enabled us to reduce susceptibility‐induced geometric distortions, sensitivity to motion was increased. Future studies should therefore focus on improvements to multishot variants. Magn Reson Med 80:279–285, 2018. © 2017 International Society for Magnetic Resonance in Medicine. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
218. Multi-Dimensional Flow-Preserving Compressed Sensing (MuFloCoS) for Time-Resolved Velocity-Encoded Phase Contrast MRI
- Author
-
Hutter, Jana, primary, Schmitt, Peter, additional, Saake, Marc, additional, Stubinger, Axel, additional, Grimm, Robert, additional, Forman, Christoph, additional, Greiser, Andreas, additional, Hornegger, Joachim, additional, and Maier, Andreas, additional
- Published
- 2015
- Full Text
- View/download PDF
219. Reduction of respiratory motion artifacts for free-breathing whole-heart coronary MRA by weighted iterative reconstruction
- Author
-
Forman, Christoph, primary, Piccini, Davide, additional, Grimm, Robert, additional, Hutter, Jana, additional, Hornegger, Joachim, additional, and Zenge, Michael O., additional
- Published
- 2014
- Full Text
- View/download PDF
220. Multi-dimensional flow-adapted compressed sensing (MDFCS) for time-resolved velocity-encoded Phase Contrast MRA
- Author
-
Hutter, Jana, primary, Grimm, Robert, additional, Forman, Christoph, additional, Greiser, Andreas, additional, Hornegger, Joachim, additional, and Schmitt, Peter, additional
- Published
- 2013
- Full Text
- View/download PDF
221. Passive time-multiplexing super-resolved technique for axially moving targets
- Author
-
Zalevsky, Zeev, primary, Gaffling, Simone, additional, Hutter, Jana, additional, Chen, Lizhuo, additional, Iff, Wolfgang, additional, Tobisch, Alexander, additional, Garcia, Javier, additional, and Mico, Vicente, additional
- Published
- 2013
- Full Text
- View/download PDF
222. Virtual angiography using CFD simulations based on patient-specific parameter optimization
- Author
-
Endres, Juergen, primary, Redel, Thomas, additional, Kowarschik, Markus, additional, Hutter, Jana, additional, Hornegger, Joachim, additional, and Doerfler, Arnd, additional
- Published
- 2012
- Full Text
- View/download PDF
223. Low-Rank and Sparse Matrix Decomposition for Compressed Sensing Reconstruction of Magnetic Resonance 4D Phase Contrast Blood Flow Imaging (LoSDeCoS 4D-PCI).
- Author
-
Hutter, Jana, Schmitt, Peter, Aandal, Gunhild, Greiser, Andreas, Forman, Christoph, Grimm, Robert, Hornegger, Joachim, and Maier, Andreas
- Published
- 2013
- Full Text
- View/download PDF
224. Self-gated Radial MRI for Respiratory Motion Compensation on Hybrid PET/MR Systems.
- Author
-
Grimm, Robert, Fürst, Sebastian, Dregely, Isabel, Forman, Christoph, Hutter, Jana Maria, Ziegler, Sibylle I., Nekolla, Stephan, Kiefer, Berthold, Schwaiger, Markus, Hornegger, Joachim, and Block, Tobias
- Published
- 2013
- Full Text
- View/download PDF
225. Free-Breathing Whole-Heart Coronary MRA: Motion Compensation Integrated into 3D Cartesian Compressed Sensing Reconstruction.
- Author
-
Forman, Christoph, Grimm, Robert, Hutter, Jana Maria, Maier, Andreas, Hornegger, Joachim, and Zenge, Michael O.
- Published
- 2013
- Full Text
- View/download PDF
226. Prior-Based Automatic Segmentation of the Carotid Artery Lumen in TOF MRA (PASCAL).
- Author
-
Hutter, Jana, Hofmann, Hannes G., Grimm, Robert, Greiser, Andreas, Saake, Marc, Hornegger, Joachim, Dörfler, Arnd, and Schmitt, Peter
- Published
- 2012
- Full Text
- View/download PDF
227. The developing brain structural and functional connectome fingerprint.
- Author
-
Ciarrusta, Judit, Christiaens, Daan, Fitzgibbon, Sean P., Dimitrova, Ralica, Hutter, Jana, Hughes, Emer, Duff, Eugene, Price, Anthony N., Cordero-Grande, Lucilio, Tournier, J.-Donald, Rueckert, Daniel, Hajnal, Joseph V., Arichi, Tomoki, McAlonan, Grainne, Edwards, A. David, and Batalle, Dafnis
- Abstract
In the mature brain, structural and functional 'fingerprints' of brain connectivity can be used to identify the uniqueness of an individual. However, whether the characteristics that make a given brain distinguishable from others already exist at birth remains unknown. Here, we used neuroimaging data from the developing Human Connectome Project (dHCP) of preterm born neonates who were scanned twice during the perinatal period to assess the developing brain fingerprint. We found that 62% of the participants could be identified based on the congruence of the later structural connectome to the initial connectivity matrix derived from the earlier timepoint. In contrast, similarity between functional connectomes of the same subject at different time points was low. Only 10% of the participants showed greater self-similarity in comparison to self-to-other-similarity for the functional connectome. These results suggest that structural connectivity is more stable in early life and can represent a potential connectome fingerprint of the individual: a relatively stable structural connectome appears to support a changing functional connectome at a time when neonates must rapidly acquire new skills to adapt to their new environment. [Display omitted] • The brain structural connectome can be used to identify an individual at birth • Functional connectivity is less stable and cannot be used as a fingerprint • Age at first scan and days between scans impacts on similarity • Structural and functional similarity appear closest in central sulcus • Age at first scan significantly impacts on parietal functional similarity [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
228. High-resolution 3D whole-heart coronary MRA: a study on the combination of data acquisition in multiple breath-holds and 1D residual respiratory motion compensation.
- Author
-
Forman, Christoph, Piccini, Davide, Grimm, Robert, Hutter, Jana, Hornegger, Joachim, and Zenge, Michael
- Subjects
MAGNETIC resonance angiography ,CORONARY angiography ,DATA acquisition systems ,IMAGE quality in imaging systems ,COMPRESSED sensing ,THREE-dimensional imaging in biology - Abstract
Object: To study a scan protocol for coronary magnetic resonance angiography based on multiple breath-holds featuring 1D motion compensation and to compare the resulting image quality to a navigator-gated free-breathing acquisition. Image reconstruction was performed using L1 regularized iterative SENSE. Materials and methods: The effects of respiratory motion on the Cartesian sampling scheme were minimized by performing data acquisition in multiple breath-holds. During the scan, repetitive readouts through a k-space center were used to detect and correct the respiratory displacement of the heart by exploiting the self-navigation principle in image reconstruction. In vivo experiments were performed in nine healthy volunteers and the resulting image quality was compared to a navigator-gated reference in terms of vessel length and sharpness. Results: Acquisition in breath-hold is an effective method to reduce the scan time by more than 30 % compared to the navigator-gated reference. Although an equivalent mean image quality with respect to the reference was achieved with the proposed method, the 1D motion compensation did not work equally well in all cases. Conclusion: In general, the image quality scaled with the robustness of the motion compensation. Nevertheless, the featured setup provides a positive basis for future extension with more advanced motion compensation methods. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
229. Neonatal multi-modal cortical profiles predict 18-month developmental outcomes.
- Author
-
Fenchel, Daphna, Dimitrova, Ralica, Robinson, Emma C., Batalle, Dafnis, Chew, Andrew, Falconer, Shona, Kyriakopoulou, Vanessa, Nosarti, Chiara, Hutter, Jana, Christiaens, Daan, Pietsch, Maximilian, Brandon, Jakki, Hughes, Emer J., Allsop, Joanna, O'Keeffe, Camilla, Price, Anthony N., Cordero-Grande, Lucilio, Schuh, Andreas, Makropoulos, Antonios, and Passerat-Palmbach, Jonathan
- Abstract
Developmental delays in infanthood often persist, turning into life-long difficulties, and coming at great cost for the individual and community. By examining the developing brain and its relation to developmental outcomes we can start to elucidate how the emergence of brain circuits is manifested in variability of infant motor, cognitive and behavioural capacities. In this study, we examined if cortical structural covariance at birth, indexing coordinated development, is related to later infant behaviour. We included 193 healthy term-born infants from the Developing Human Connectome Project (dHCP). An individual cortical connectivity matrix derived from morphological and microstructural features was computed for each subject (morphometric similarity networks, MSNs) and was used as input for the prediction of behavioural scores at 18 months using Connectome-Based Predictive Modeling (CPM). Neonatal MSNs successfully predicted social-emotional performance. Predictive edges were distributed between and within known functional cortical divisions with a specific important role for primary and posterior cortical regions. These results reveal that multi-modal neonatal cortical profiles showing coordinated maturation are related to developmental outcomes and that network organization at birth provides an early infrastructure for future functional skills. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
230. Corrigendum to "Visual assessment of the placenta in antenatal magnetic resonance imaging across gestation in normal and compromised pregnancies: Observations from a large cohort study" [117 January 2022 29-38].
- Author
-
Ho, Alison, Chappell, Lucy C., Story, Lisa, Al-Adnani, Mudher, Egloff, Alexia, Routledge, Emma, Rutherford, Mary, and Hutter, Jana
- Published
- 2022
- Full Text
- View/download PDF
231. A flexible generative algorithm for growing in silico placentas.
- Author
-
de Oliveira, Diana C., Cheikh Sleiman, Hani, Payette, Kelly, Hutter, Jana, Story, Lisa, Hajnal, Joseph V., Alexander, Daniel C., Shipley, Rebecca J., and Slator, Paddy J.
- Abstract
The placenta is crucial for a successful pregnancy, facilitating oxygen exchange and nutrient transport between mother and fetus. Complications like fetal growth restriction and pre-eclampsia are linked to placental vascular structure abnormalities, highlighting the need for early detection of placental health issues. Computational modelling offers insights into how vascular architecture correlates with flow and oxygenation in both healthy and dysfunctional placentas. These models use synthetic networks to represent the multiscale feto-placental vasculature, but current methods lack direct control over key morphological parameters like branching angles, essential for predicting placental dysfunction. We introduce a novel generative algorithm for creating in silico placentas, allowing user-controlled customisation of feto-placental vasculatures, both as individual components (placental shape, chorionic vessels, placentone) and as a complete structure. The algorithm is physiologically underpinned, following branching laws (i.e. Murray's Law), and is defined by four key morphometric statistics: vessel diameter, vessel length, branching angle and asymmetry. Our algorithm produces structures consistent with in vivo measurements and ex vivo observations. Our sensitivity analysis highlights how vessel length variations and branching angles play a pivotal role in defining the architecture of the placental vascular network. Moreover, our approach is stochastic in nature, yielding vascular structures with different topological metrics when imposing the same input settings. Unlike previous volume-filling algorithms, our approach allows direct control over key morphological parameters, generating vascular structures that closely resemble real vascular densities and allowing for the investigation of the impact of morphological parameters on placental function in upcoming studies. Author summary: The placenta is important in ensuring a healthy pregnancy by facilitating the exchange of oxygen and nutrients between the mother and the fetus. Disturbances of placental function are often associated with abnormalities in the placental vascular structure, and detecting these issues early on is crucial. To understand the connection between placental vascular architecture, blood flow, and oxygenation, computational models have been used. These use synthetic networks which lack precise control over crucial morphological parameters, such as branching angles, essential for predicting placental dysfunction. Our contribution is a new approach that allows for the creation of virtual placentas that closely resemble real vascular characteristics. It enables users to customize the feto-placental vascular architecture at various levels, including individual components like placental shape, chorionic vessels, and placentone, as well as the complete structure. The flexibility of this pipeline opens the door for investigating the direct impact of morphological parameters on placental function. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
232. The Fetal Spleen in Low-Risk Pregnancies and prior to Preterm Birth: Observational Study of the Role of Anatomical and Functional Magnetic Resonance Imaging.
- Author
-
Hall, Megan, Uus, Alena, Preston, Megan, Suff, Natalie, Gibbons, Deena, Rutherford, Mary, Shennan, Andrew, Hutter, Jana, and Story, Lisa
- Subjects
- *
FUNCTIONAL magnetic resonance imaging , *MAGNETIC resonance imaging , *PREMATURE labor , *FETAL imaging , *SPLEEN - Abstract
Introduction: Spontaneous preterm birth complicates ∼7% of pregnancies and causes morbidity and mortality. Although infection is a common etiology, our understanding of the fetal immune system in vivo is limited. This study aimed to utilize T2-weighted imaging and T2* relaxometry (which is a proxy of tissue oxygenation) of the fetal spleen in uncomplicated pregnancies and in fetuses that were subsequently delivered spontaneously prior to 32 weeks. Methods: Women underwent imaging including T2-weighted fetal body images and multi-eco gradient echo single-shot echo planar sequences on a Phillips Achieva 3T system. Previously described postprocessing techniques were applied to obtain T2- and T2*-weighted imaging of the fetal spleen and T2-weighted fetal body volumes. Results: Among 55 women with uncomplicated pregnancies, an increase in fetal splenic volume, splenic:body volume, and a decrease in splenic T2* signal intensity was demonstrated across gestation. Compared to controls, fetuses who were subsequently delivered prior to 32 weeks' gestation (n = 19) had a larger spleen when controlled for the overall size of the fetus (p = 0.027), but T2* was consistent (p = 0.76). Conclusion: These findings provide evidence of a replicable method of studying the fetal immune system and give novel results on the impact of impending preterm birth on the spleen. While T2* decreases prior to preterm birth in other organs, preservation demonstrated here suggests preferential sparing of the spleen. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
233. CRAFT (Cerclage after full dilatation caesarean section): protocol of a mixed methods study investigating the role of previous in-labour caesarean section in preterm birth risk.
- Author
-
Carlisle, Naomi, Glazewska-Hallin, Agnieszka, Story, Lisa, Carter, Jenny, Seed, Paul T., Suff, Natalie, Giblin, Lucie, Hutter, Jana, Napolitano, Raffaele, Rutherford, Mary, Alexander, Daniel C., Simpson, Nigel, Banerjee, Amrita, David, Anna L., and Shennan, Andrew H.
- Subjects
PREMATURE labor ,PREGNANCY ,MATERNAL health ,CHILDBIRTH ,MISCARRIAGE - Abstract
Background: Full dilatation caesarean sections are associated with recurrent early spontaneous preterm birth and late miscarriage. The risk following first stage caesarean sections, are less well defined, but appears to be increased in late-first stage of labour. The mechanism for this increased risk of late miscarriage and early spontaneous preterm birth in these women is unknown and there are uncertainties with regards to clinical management. Current predictive models of preterm birth (based on transvaginal ultrasound and quantitative fetal fibronectin) have not been validated in these women and it is unknown whether the threshold to define a short cervix (≤25 mm) is reliable in predicting the risk of preterm birth. In addition the efficacy of standard treatments or whether benefit may be derived from prophylactic interventions such as a cervical cerclage is unknown.Methods: There are three distinct components to the CRAFT project (CRAFT-OBS, CRAFT-RCT and CRAFT-IMG).Craft-obs: Observational Study; To evaluate subsequent pregnancy risk of preterm birth in women with a prior caesarean section in established labour. This prospective study of cervical length and quantitative fetal fibronectin data will establish a predictive model of preterm birth.Craft-rct: Randomised controlled trial arm; To assess treatment for short cervix in women at high risk of preterm birth following a fully dilated caesarean section.Craft-img: Imaging sub-study; To evaluate the use of MRI and transvaginal ultrasound imaging of micro and macrostructural cervical features which may predispose to preterm birth in women with a previous fully dilated caesarean section, such as scar position and niche.Discussion: The CRAFT project will quantify the risk of preterm birth or late miscarriage in women with previous in-labour caesarean section, define the best management and shed light on pathological mechanisms so as to improve the care we offer to women and their babies.Trial Registration: CRAFT was prospectively registered on 25th November 2019 with the ISRCTN registry ( https://doi.org/10.1186/ISRCTN15068651 ). [ABSTRACT FROM AUTHOR]- Published
- 2020
- Full Text
- View/download PDF
234. Investigating altered brain development in infants with congenital heart disease using tensor-based morphometry.
- Author
-
Ng, Isabel H. X., Bonthrone, Alexandra F., Kelly, Christopher J., Cordero-Grande, Lucilio, Hughes, Emer J., Price, Anthony N., Hutter, Jana, Victor, Suresh, Schuh, Andreas, Rueckert, Daniel, Hajnal, Joseph V., Simpson, John, Edwards, A. David, Rutherford, Mary A., Batalle, Dafnis, and Counsell, Serena J.
- Subjects
NEURAL development ,MAGNETIC resonance imaging of the brain ,INFANT diseases ,CONGENITAL heart disease in children ,BRAIN imaging ,MORPHOMETRICS - Abstract
Magnetic resonance (MR) imaging studies have demonstrated reduced global and regional brain volumes in infants with congenital heart disease (CHD). This study aimed to provide a more detailed evaluation of altered structural brain development in newborn infants with CHD compared to healthy controls using tensor-based morphometry (TBM). We compared brain development in 64 infants with CHD to 192 age- and sex-matched healthy controls. T2-weighted MR images obtained prior to surgery were analysed to compare voxel-wise differences in structure across the whole brain between groups. Cerebral oxygen delivery (CDO
2 ) was measured in infants with CHD (n = 49) using phase contrast MR imaging and the relationship between CDO2 and voxel-wise brain structure was assessed using TBM. After correcting for global scaling differences, clusters of significant volume reduction in infants with CHD were demonstrated bilaterally within the basal ganglia, thalami, corpus callosum, occipital, temporal, parietal and frontal lobes, and right hippocampus (p < 0.025 after family-wise error correction). Clusters of significant volume expansion in infants with CHD were identified in cerebrospinal fluid spaces (p < 0.025). After correcting for global brain size, there was no significant association between voxel-wise brain structure and CDO2 . This study localizes abnormal brain development in infants with CHD, identifying areas of particular vulnerability. [ABSTRACT FROM AUTHOR]- Published
- 2020
- Full Text
- View/download PDF
235. Placental multimodal MRI prior to spontaneous preterm birth <32 weeks' gestation: An observational study.
- Author
-
Hall, Megan, Suff, Natalie, Slator, Paddy, Rutherford, Mary, Shennan, Andrew, Hutter, Jana, and Story, Lisa
- Subjects
- *
PREMATURE labor , *PREMATURE rupture of fetal membranes , *PREGNANCY , *CHORIOAMNIONITIS , *PLACENTA , *PREGNANT women , *MAGNETIC resonance imaging - Abstract
Objective Design Setting Population Methods Main Outcome Measures Results Conclusions To utilise combined diffusion‐relaxation MRI techniques to interrogate antenatal changes in the placenta prior to extreme preterm birth among both women with PPROM and membranes intact, and compare this to a control group who subsequently delivered at term.Observational study.Tertiary Obstetric Unit, London, UK.Cases: pregnant women who subsequently spontaneously delivered a singleton pregnancy prior to 32 weeks' gestation without any other obstetric complications. Controls: pregnant women who delivered an uncomplicated pregnancy at term.All women consented to an MRI examination. A combined diffusion‐relaxation MRI of the placenta was undertaken and analysed using fractional anisotropy, a combined T2*‐apparent diffusion coefficient model and a combined T2*‐intravoxel incoherent motion model, in order to provide a detailed placental phenotype associated with preterm birth. Subgroup analyses based on whether women in the case group had PPROM or intact membranes at time of scan, and on latency to delivery were performed.Fractional anisotropy, apparent diffusion coefficients and T2* placental values, from two models including a combined T2*‐IVIM model separating fast‐ and slow‐flowing (perfusing and diffusing) compartments.This study included 23 women who delivered preterm and 52 women who delivered at term. Placental T2* was lower in the T2*‐apparent diffusion coefficient model (p < 0.001) and in the fast‐ and slow‐flowing compartments (p = 0.001 and p < 0.001) of the T2*‐IVIM model. This reached a higher level of significance in the preterm prelabour rupture of the membranes group than in the membranes intact group. There was a reduced perfusion fraction among the cases with impending delivery.Placental diffusion‐relaxation reveals significant changes in the placenta prior to preterm birth with greater effect noted in cases of preterm prelabour rupture of the membranes. Application of this technique may allow clinically valuable interrogation of histopathological changes before preterm birth. In turn, this could facilitate more accurate antenatal prediction of preterm chorioamnionitis and so aid decisions around the safest time of delivery. Furthermore, this technique provides a research tool to improve understanding of the pathological mechanisms associated with preterm birth in vivo. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
236. Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project
- Author
-
Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, Sotiropoulos, Stamatios N., Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, and Sotiropoulos, Stamatios N.
- Abstract
The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38-44 weeks post-menstrual age.
- Full Text
- View/download PDF
237. Time-efficient and flexible design of optimized multishell HARDI diffusion
- Author
-
Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, Hajnal, Joseph V., Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, and Hajnal, Joseph V.
- Abstract
Purpose: Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time-efficient and flexible diffusion acquisition capability with built-in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible. Methods: Complete flexibility in the sampling of diffusion space combined with free choice of phase-encode-direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split-diffusion-gradient preparation, multiband acceleration, and a restart capacity were added. Results: The framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high-angular resolution, maximally time-efficient (20 min) multishell protocol with 300 diffusion-weighted volumes was acquired in >400 neonates. An optimal design of a high-resolution (1.2 × 1.2 mm2) two-shell acquisition with 54 diffusion weighted volumes was obtained using a split-gradient design. Conclusion: The presented framework provides flexibility to generate time-efficient and motion-robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub-optimal choices. Magn Reson Med, 2017. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work
- Full Text
- View/download PDF
238. A framework for calculating time-efficient diffusion MRI protocols for anisotropic IVIM and an application in the placenta
- Author
-
Bonet-Carne, Elisenda, Grussu, Francesco, Ning, Lipeng, Sepehrband, Farshid, Tax, Chantal M.W., Slator, Paddy J., Hutter, Jana, Ianus, Andrada, Panagiotaki, Eleftheria, Rutherford, Mary A., Hajnal, Joseph V., Alexander, Daniel C., Bonet-Carne, Elisenda, Grussu, Francesco, Ning, Lipeng, Sepehrband, Farshid, Tax, Chantal M.W., Slator, Paddy J., Hutter, Jana, Ianus, Andrada, Panagiotaki, Eleftheria, Rutherford, Mary A., Hajnal, Joseph V., and Alexander, Daniel C.
- Abstract
We develop a framework for calculating clinically-viable diffusion MRI (dMRI) protocols for anisotropic IVIM modelling. The proposed multi-stage framework combines previous approaches to dMRI protocol optimisation: first optimising b-values by minimizing Cramer-Rao lower bounds on parameter variances, and subsequently optimising gradient directions jointly to provide maximum angular coverage across all shells. This removes unnecessary measurements of closely spaced b-values with the same gradient directions, which encode very similar information, and hence reduces the total number of dMRI measurements. We applied the framework to establish an organ-specific, data-driven, set of optimised b-values and gradient directions for dMRI of the placenta. The optimised protocol leads to higher contrast-to-noise ratios in parameter maps compared to a naive protocol of comparable scan time. Applying this framework in other organs has the potential to reduce scanning times required for anisotropic IVIM modelling.
239. Dynamic field mapping and motion correction using interleaved double spin-echo diffusion MRI
- Author
-
Hutter, Jana, Christiaens, Daan, Deprez, Maria, Cordero-Grande, Lucilio, Slator, Paddy, Price, Anthony, Rutherford, Mary, Hajnal, Joseph V., Hutter, Jana, Christiaens, Daan, Deprez, Maria, Cordero-Grande, Lucilio, Slator, Paddy, Price, Anthony, Rutherford, Mary, and Hajnal, Joseph V.
- Abstract
Diffusion MRI (dMRI) analysis requires combining data from many images and this generally requires corrections for image distortion and for subject motion during what may be a prolonged acquisition. Particularly in non-brain applications, changes in pose such as respiration can cause image distortion to be time varying, impeding static field map-based correction. In addition, motion and distortion correction is challenging at high b-values due to the low signal-to-noise ratio (SNR). In this work we develop a new approach that breaks the traditional “one-volume, one-weighting” paradigm by interleaving low-b and high-b slices, and combine this with a reverse phase-encoded double-spin echo sequence. Interspersing low and high b-value slices ensures that the low-b, high-SNR data is in close spatial and temporal proximity to support dynamic field map estimation from the double spin-echo acquisition and image-based motion correction. This information is propagated to high-b slices with interpolation across space and time. The method is tested in the challenging environment of fetal dMRI and it is demonstrated using data from 8 pregnant volunteers that combining dynamic distortion correction with slice-by-slice motion correction increases data consistency to facilitate advanced analyses where conventional methods fail.
240. InSpect: INtegrated SPECTral component estimation and mapping for multi-contrast microstructural MRI
- Author
-
Chung, Albert C. S., Gee, James C., Yushkevich, Paul A., Bao, Siqi, Slator, Paddy, Hutter, Jana, Marinescu, Ravzan V., Palombo, Marco, Young, Alexandra L., Jackson, Laurence H., Ho, Alison, Chappell, Lucy C., Rutherford, Mary, Hajnal, Joseph V., Alexander, Daniel C., Chung, Albert C. S., Gee, James C., Yushkevich, Paul A., Bao, Siqi, Slator, Paddy, Hutter, Jana, Marinescu, Ravzan V., Palombo, Marco, Young, Alexandra L., Jackson, Laurence H., Ho, Alison, Chappell, Lucy C., Rutherford, Mary, Hajnal, Joseph V., and Alexander, Daniel C.
- Abstract
We introduce a novel algorithm for deriving meaningful maps from multi-contrast MRI experiments. Such experiments enable the estimation of multidimensional correlation spectra, in domains such as T1-diffusivity, T2-diffusivity, or T1-T2. These spectra combine information from complementary MR properties, and therefore have the potential for improved quantification of distinct tissue types compared to single-contrast analyses. However, spectral estimation is an ill-conditioned problem which is highly sensitive to noise and requires significant regularisation. We propose an Expectation-Maximisation based method - which we term InSpect - for unified analysis of multi-contrast MR images. The algorithm simultaneously estimates canonical spectra associated with distinct tissue types within an image, and produces maps quantifying the spatial distribution of these spectra. We test the algorithm’s capabilities on simulated data, then apply to placental diffusion-relaxometry data. On placental data we identified significant within-organ and across-subject variation in T2*-ADC spectra - showing the potential of InSpect for detailed separation and quantification of distinct microstructural environments.
241. Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project
- Author
-
Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, Sotiropoulos, Stamatios N., Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, and Sotiropoulos, Stamatios N.
- Abstract
The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38-44 weeks post-menstrual age.
- Full Text
- View/download PDF
242. Time-efficient and flexible design of optimized multishell HARDI diffusion
- Author
-
Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, Hajnal, Joseph V., Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, and Hajnal, Joseph V.
- Abstract
Purpose: Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time-efficient and flexible diffusion acquisition capability with built-in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible. Methods: Complete flexibility in the sampling of diffusion space combined with free choice of phase-encode-direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split-diffusion-gradient preparation, multiband acceleration, and a restart capacity were added. Results: The framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high-angular resolution, maximally time-efficient (20 min) multishell protocol with 300 diffusion-weighted volumes was acquired in >400 neonates. An optimal design of a high-resolution (1.2 × 1.2 mm2) two-shell acquisition with 54 diffusion weighted volumes was obtained using a split-gradient design. Conclusion: The presented framework provides flexibility to generate time-efficient and motion-robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub-optimal choices. Magn Reson Med, 2017. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work
- Full Text
- View/download PDF
243. Data-driven multi-contrast spectral microstructure imaging with InSpect
- Author
-
Martel, A.L., Abolmaesumi, P., Stoyanov, D., Mateus, D., Zuluaga, M.A., Zhou, S.K., Racoceanu, D., Joskowicz, L., Slator, Paddy J., Hutter, Jana, Marinescu, Razvan V., Palombo, Marco, Jackson, Laurence H., Ho, Alison, Chappell, Lucy C., Rutherford, Mary, Hajnal, Joseph V., Alexander, Daniel C., Martel, A.L., Abolmaesumi, P., Stoyanov, D., Mateus, D., Zuluaga, M.A., Zhou, S.K., Racoceanu, D., Joskowicz, L., Slator, Paddy J., Hutter, Jana, Marinescu, Razvan V., Palombo, Marco, Jackson, Laurence H., Ho, Alison, Chappell, Lucy C., Rutherford, Mary, Hajnal, Joseph V., and Alexander, Daniel C.
- Abstract
We introduce and demonstrate an unsupervised machine learning method for spectroscopic analysis of quantitative MRI (qMRI) experiments. qMRI data can support estimation of multidimensional correlation (or single-dimensional) spectra, which allow model-free investigation of tissue properties, but this requires an ill-posed calculation. Moreover, in the vast majority of applications ground truth knowledge is unobtainable, preventing the application of supervised machine learning. Here we present a new method that addresses these limitations in a data-driven way. The algorithm simultaneously estimates a canonical basis of spectral components and voxelwise maps of their weightings, thereby pooling information across whole images to regularise the ill-posed problem. We show that our algorithm substantially outperforms current voxelwise spectral approaches. We demonstrate the method on combined diffusion-relaxometry placental MRI scans, revealing anatomically-relevant substructures, and identifying dysfunctional placentas. Our algorithm vastly reduces the data required to reliably estimate multidimensional correlation (or single-dimensional) spectra, opening up the possibility of spectroscopic imaging in a wide range of new applications.
244. Q-Space quantitative diffusion MRI measures using a stretched-exponential representation
- Author
-
Gyori, Noemi, Hutter, Jana, Nath, Vishwesh, Palombo, Marco, Pieciak, Tomasz, Afzali, Maryam, Bogusz, Fabian, Aja-Fernández, Santiago, Jones, Derek K., Gyori, Noemi, Hutter, Jana, Nath, Vishwesh, Palombo, Marco, Pieciak, Tomasz, Afzali, Maryam, Bogusz, Fabian, Aja-Fernández, Santiago, and Jones, Derek K.
- Abstract
Diffusion magnetic resonance imaging (dMRI) is a relatively modern technique used to study tissue microstructure in a non-invasive way. Non-Gaussian diffusion representation is related to the restricted diffusion and can provide information about the underlying tissue properties. In this paper, we analytically derive nth order statistics of the signal considering a stretched-exponential representation of the diffusion. Then, we retrieve the Q-space quantitative measures such as the Return-To-the-Origin Probability (RTOP), Q-space mean square displacement (QMSD), Q-space mean fourth-order displacement (QMFD). The stretched-exponential representation enables the handling of the diffusion contributions from a higher b-value regime under a non-Gaussian assumption, which can be useful in diagnosing or prognosis of neurodegenerative diseases in the early stages. Numerical implementation of the method is freely available at https://github.com/TPieciak/Stretched.
245. Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project
- Author
-
Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, Sotiropoulos, Stamatios N., Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, and Sotiropoulos, Stamatios N.
- Abstract
The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38-44 weeks post-menstrual age.
- Full Text
- View/download PDF
246. Time-efficient and flexible design of optimized multishell HARDI diffusion
- Author
-
Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, Hajnal, Joseph V., Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, and Hajnal, Joseph V.
- Abstract
Purpose: Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time-efficient and flexible diffusion acquisition capability with built-in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible. Methods: Complete flexibility in the sampling of diffusion space combined with free choice of phase-encode-direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split-diffusion-gradient preparation, multiband acceleration, and a restart capacity were added. Results: The framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high-angular resolution, maximally time-efficient (20 min) multishell protocol with 300 diffusion-weighted volumes was acquired in >400 neonates. An optimal design of a high-resolution (1.2 × 1.2 mm2) two-shell acquisition with 54 diffusion weighted volumes was obtained using a split-gradient design. Conclusion: The presented framework provides flexibility to generate time-efficient and motion-robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub-optimal choices. Magn Reson Med, 2017. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work
- Full Text
- View/download PDF
247. Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project
- Author
-
Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, Sotiropoulos, Stamatios N., Bastiani, Matteo, Andersson, Jesper L.R., Cordero-Grande, Lucilio, Murgasova, Maria, Hutter, Jana, Price, Anthony N., Makropoulos, Antonios, Fitzgibbon, Sean P., Hughes, Emer J., Rueckert, Daniel, Suresh, Victor, Rutherford, Mary, Edwards, A. David, Smith, Steve, Tournier, J. Donald, Hajnal, Joseph V., Jbabdi, Saad, and Sotiropoulos, Stamatios N.
- Abstract
The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38-44 weeks post-menstrual age.
- Full Text
- View/download PDF
248. Time-efficient and flexible design of optimized multishell HARDI diffusion
- Author
-
Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, Hajnal, Joseph V., Hutter, Jana, Tournier, J. Donald, Price, Anthony N., Cordero-Grande, Lucilio, Hughes, Emer J., Malik, Shaihan, Steinweg, Johannes, Bastiani, Matteo, Sotiropoulos, Stamatios N., Jbabdi, Saad, Andersson, Jesper, Edwards, A. David, and Hajnal, Joseph V.
- Abstract
Purpose: Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time-efficient and flexible diffusion acquisition capability with built-in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible. Methods: Complete flexibility in the sampling of diffusion space combined with free choice of phase-encode-direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split-diffusion-gradient preparation, multiband acceleration, and a restart capacity were added. Results: The framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high-angular resolution, maximally time-efficient (20 min) multishell protocol with 300 diffusion-weighted volumes was acquired in >400 neonates. An optimal design of a high-resolution (1.2 × 1.2 mm2) two-shell acquisition with 54 diffusion weighted volumes was obtained using a split-gradient design. Conclusion: The presented framework provides flexibility to generate time-efficient and motion-robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub-optimal choices. Magn Reson Med, 2017. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work
- Full Text
- View/download PDF
249. Acquiring and predicting multidimensional diffusion (MUDI) data: an open challenge
- Author
-
Bonet-Carne, Elisenda, Hutter, Jana, Palombo, Marco, Pizzolato, Marco, Sepehrband, Farshid, Zhang, Fan, Tax, Chantal M. W., Grussu, Francesco, Ianus, Andrada, Bogusz, Fabian, Pieciak, Tomasz, Ning, Lipeng, Larochelle, Hugo, Descoteaux, Maxime, Chamberland, Maxime, Blumberg, Stefano B., Mertzanidou, Thomy, Alexander, Daniel C., Afzali, Maryam, Aja-Fernández, Santiago, Jones, Derek K., Westin, Carl-Fredrik, Rathi, Yogesh, Baete, Steven H., Cordero-Grande, Lucilio, Ladner, Thilo, Slator, Paddy J., Hajnal, Joseph V, Thiran, Jean-Philippe, Price, Anthony N., Bonet-Carne, Elisenda, Hutter, Jana, Palombo, Marco, Pizzolato, Marco, Sepehrband, Farshid, Zhang, Fan, Tax, Chantal M. W., Grussu, Francesco, Ianus, Andrada, Bogusz, Fabian, Pieciak, Tomasz, Ning, Lipeng, Larochelle, Hugo, Descoteaux, Maxime, Chamberland, Maxime, Blumberg, Stefano B., Mertzanidou, Thomy, Alexander, Daniel C., Afzali, Maryam, Aja-Fernández, Santiago, Jones, Derek K., Westin, Carl-Fredrik, Rathi, Yogesh, Baete, Steven H., Cordero-Grande, Lucilio, Ladner, Thilo, Slator, Paddy J., Hajnal, Joseph V, Thiran, Jean-Philippe, and Price, Anthony N.
- Abstract
In magnetic resonance imaging (MRI), the image contrast is the result of the subtle interaction between the physicochemical properties of the imaged living tissue and the parameters used for image acquisition. By varying parameters such as the echo time (TE) and the inversion time (TI), it is possible to collect images that capture different expressions of this sophisticated interaction. Sensitization to diffusion-summarized by the b-value-constitutes yet another explorable “dimension” to modify the image contrast, which reflects the degree of dispersion of water in various directions within the tissue microstructure. The full exploration of this multidimensional acquisition parameter space offers the promise of a more comprehensive description of the living tissue but at the expense of lengthy MRI acquisitions, often unfeasible in clinical practice. The harnessing of multidimensional information passes through the use of intelligent sampling strategies for reducing the amount of images to acquire, and the design of methods for exploiting the redundancy in such information. This chapter reports the results of the MUDI challenge, comparing different strategies for predicting the acquired densely sampled multidimensional data from sub-sampled versions of it.
250. DWI simulation-assisted machine learning models for microstructure estimation
- Author
-
Bonet-Carne, Elisenda, Hutter, Jana, Palombo, Marco, Pizzolato, Marco, Sepehrband, Farshid, Zhang, Fan, Rafael-Patino, Jonathan, Yu, Thomas, Delvigne, Victor, Barakovic, Muhamed, Girard, Gabriel, Jones, Derek K., Canales-Rodríguez, Erick J., Thiran, Jean-Philippe, Bonet-Carne, Elisenda, Hutter, Jana, Palombo, Marco, Pizzolato, Marco, Sepehrband, Farshid, Zhang, Fan, Rafael-Patino, Jonathan, Yu, Thomas, Delvigne, Victor, Barakovic, Muhamed, Girard, Gabriel, Jones, Derek K., Canales-Rodríguez, Erick J., and Thiran, Jean-Philippe
- Abstract
Diffusion MRI (DW-MRI) allows for the detailed exploration of the brain white matter microstructure, with applications in both research and the clinic. However, state-of-the-art methods for microstructure estimation suffer from known limitations, such as the overestimation of the mean axon diameter, and the infeasibility of fitting diameter distributions. In this study, we propose to eschew current modeling-based approaches in favor of a novel, simulation-assisted machine learning approach. In particular, we train machine learning (ML) algorithms on a large dataset of simulated diffusion MRI signals from white matter regions with different axon diameter distributions and packing densities. We show, on synthetic data, that the trained models provide an accurate and efficient estimation of microstructural parameters in-silico and from DW-MRI data with moderately high b-values (4000 s/mm 2 ). Further, we show, on in-vivo data, that the estimators trained from simulations can provide parameter estimates which are close to the values expected from histology.
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.