arXiv subjects

Oliver Bieri

Publications and source records attributed to Oliver Bieri.

6 recordsLinked to original sources

arXiv2026

Free-breathing Pulmonary Relaxometry at 0.55T

Purpose: To evaluate the feasibility of an integrated, free-breathing workflow for automated 2D pulmonary relaxometry (T1, T2) at 0.55T. Methods: A 2D inversion recovery ultra-fast balanced steady-state free precession (IR-uf-bSSFP) sequence was adapted to achieve high-temporal sampling of the transient phase at 0.55T. The technique was validated in a phantom and tested in eight healthy volunteers as well as one patient. A fully automated pipeline was developed, featuring multi-contrast registration for motion correction and deep learning based lung segmentation to enable voxel-wise nonlinear fitting for T1 and T2 map generation. Results: Phantom results were in close agreement with reference scans. In-vivo, the proposed free-breathing framework effectively mitigated respiratory motion, yielding quantitative maps in close agreement with breath-hold references. Healthy lung parenchyma relaxation times were T1 = (930+-40)ms and T2 = (90+-8)ms. In a patient case, the method successfully distinguished a solid lung mass from healthy parenchyma, with the lesion showing elevated T1 (960ms vs 810ms in the surrounding parenchyma). Conclusions: Simultaneous free-breathing T1 and T2 mapping of the lung is feasible at 0.55T using a fully automated pipeline. By eliminating breath-holds and external gating, this approach improves patient compliance and potentially facilitates the use of quantitative lung MRI in routine clinical practice.

physics.med-ph↗

arXiv2026

VQ-Wave: A physics-driven spatio-temporal deep learning approach for non-contrast-enhanced lung ventilation and perfusion MRI

Purpose: To develop a robust deep learning framework for non-contrast-enhanced functional lung MRI, overcoming the limitations of spectral decomposition in the presence of physiological non-stationarity. Methods: We introduce VQ-Wave (Ventilation/Q-perfusion Waveform-based Assessment of Variable Evolutions), a physics-driven spatio-temporal inception neural network trained on synthetic signal models to estimate ventilation and perfusion parameters. By processing local spatial context alongside temporal evolution, the network learns to decouple physiological signals from noise. The training generator simulated non-stationary dynamics, including amplitude modulations, frequency drifts, and noise. Performance was validated against matrix pencil (MP) decomposition using numerical phantoms and in-vivo lung MRI acquired in four healthy volunteers and two children with cystic fibrosis (CF) at 1.5T. Results: In numerical benchmarks, VQ-Wave demonstrated superior robustness to non-stationarity, maintaining low global and regional error rates where MP exhibited stochastic instability due to spectral leakage. In-vivo, VQ-Wave accurately captured functional defects in patients with CF yielding ventilation and perfusion maps with high quantitative stability (mean variation < 12%) even when scan time was reduced from 45s to 15s. Conversely, under irregular physiology and short scan lengths, MP decomposition severely degraded, exhibiting systematic amplitude instability, overestimation bias, and regional signal dropouts. Conclusion: VQ-Wave offers a robust, physics-driven neural network-based alternative to spectral decomposition. By effectively handling physiological irregularity and noise, it enables reliable functional lung imaging with substantially shortened acquisition protocols.

physics.med-ph↗

arXiv2024

An automated pipeline for computation and analysis of functional ventilation and perfusion lung MRI with matrix pencil decomposition: TrueLung

Purpose: To introduce and evaluate TrueLung, an automated pipeline for computation and analysis of free-breathing and contrast-agent free pulmonary functional MRI. Material and Methods: time-resolved ultra-fast bSSFP acquisitions are transferred to TrueLung, which includes image quality checks, image registration, and computation of perfusion and ventilation maps with matrix pencil decomposition. Neural network whole-lung and lobar segmentations allow quantification of impaired relative perfusion (RQ) and fractional ventilation (RFV). TrueLung delivers functional maps and quantitative outcomes, reported for clinicians in concise documents. We evaluated the pipeline in 75 cystic fibrosis children. Whole-lung and lobar segmentations were manually refined when necessary, and the impact on RQ and RFV was quantified. Results: Functional imaging was performed at 7.9 $\pm$ 1.8 (mean $\pm$ SD) coronal slice positions per patient, totaling on average 6min 20s scan time per patient. The whole pipeline required 20min calculation time per subject. TrueLung delivered the functional maps of all the subjects for radiological assessment. Quality controlling maps and segmentations lasted 1min 12s per patient. The automated segmentations and quantification of whole-lung defects were satisfying in 88% of patients (97% of slices) and the lobar quantification in 73% (93% of slices). The segmentations refinements required 16s per patient for the whole-lung, and 2min 10s for the lobe masks. The relative differences in RFV and RQ between fully-automated and manually refined data were marginal. Conclusions: TrueLung quickly delivers functional maps and quantitative outcomes in an objective and standardized way, suitable for radiological and pneumological assessment with minimal manual input. TrueLung can be used for clinical research in cystic fibrosis and might be applied across various lung diseases.

physics.med-ph↗

arXiv2021

MRI lung lobe segmentation in pediatric cystic fibrosis patients using a recurrent neural network trained with publicly accessible CT datasets

Purpose: To introduce a widely applicable workflow for pulmonary lobe segmentation of MR images using a recurrent neural network (RNN) trained with chest computed tomography (CT) datasets. The feasibility is demonstrated for 2D coronal ultra-fast balanced steady-state free precession (ufSSFP) MRI. Methods: Lung lobes of 250 publicly accessible CT datasets of adults were segmented with an open-source CT-specific algorithm. To match 2D ufSSFP MRI data of pediatric patients, both CT data and segmentations were translated into pseudo-MR images, masked to suppress anatomy outside the lung. Network-1 was trained with pseudo-MR images and lobe segmentations, and applied to 1000 masked ufSSFP images to predict lobe segmentations. These outputs were directly used as targets to train Network-2 and Network-3 with non-masked ufSSFP data as inputs, and an additional whole-lung mask as input for Network-2. Network predictions were compared to reference manual lobe segmentations of ufSSFP data in twenty pediatric cystic fibrosis patients. Manual lobe segmentations were performed by splitting available whole-lung segmentations into lobes. Results: Network-1 was able to segment the lobes of ufSSFP images, and Network-2 and Network-3 further increased segmentation accuracy and robustness. The average all-lobe Dice similarity coefficients were 95.0$\pm$2.8 (mean$\pm$pooled SD [%]), 96.4$\pm$2.0, 93.0$\pm$2.0, and the average median Hausdorff distances were 6.1$\pm$0.9 (mean$\pm$SD [mm]), 5.3$\pm$1.1, 7.1$\pm$1.3, for Network-1, Network-2, and Network-3, respectively. Conclusions: RNN lung lobe segmentation of 2D ufSSFP imaging is feasible, in good agreement with manual segmentations. The proposed workflow might provide access to automated lobe segmentations for various lung MRI examinations and quantitative analyses.

physics.med-ph↗

arXiv2020

Dynamic MR imaging of the skeletal muscle in young and senior volunteers during minimal synchronized neuromuscular electrical stimulation

$\textbf{Object}$ Neuromuscular electrical stimulation (NMES)-induced isometric contraction is feasible during MRI and can be combined with acquisition of volumetric dynamic MR data, in a synchronous and controlled way. Since NMES is a potent resource for rehabilitation, MRI synchronized with NMES presents a valuable validation tool. Our aim was to show how minimal NMES-induced muscle contraction characterization, as evaluated through phase contrast MRI, differs between senior and young volunteers. $\textbf{Materials and Methods}$ Simultaneous NMES of the quadriceps muscle and phase contrast imaging were applied at 3T to 11 senior (75 $\pm$ 3 years) and 6 young volunteers (29 $\pm$ 7 years). A current sufficient to induce muscle twitch without knee extension was applied to both groups. $\textbf{Results}$ Strain vectors were extracted from the velocity fields and strain datasets were compared with non-parametric tests and descriptive statistics. Strain values were noticeably different between both groups at both current intensities and significant differences were observed in the regions of interest between the two electrodes. $\textbf{Discussion}$ In conclusion, NMES-synchronized MRI could be successfully applied in senior volunteers with strain results clearly different from the younger volunteers. Also, differences within the senior group were detected both in the magnitude of strain and in the position of maximum strain pixels.

physics.med-ph↗

arXiv2019

Accelerated Motion-Aware MR Imaging via Motion Prediction from K-Space Center

Motion has been a challenge for magnetic resonance (MR) imaging ever since the MR has been invented. Especially in volumetric imaging of thoracic and abdominal organs, motion-awareness is essential for reducing motion artifacts in the final image. A recently proposed MR imaging approach copes with motion by observing the motion patterns during the acquisition. Repetitive scanning of the k-space center region enables the extraction of the patient motion while acquiring the remaining part of the k-space. Due to highly redundant measurements of the center, the required scanning time of over 11 min and the reconstruction time of 2 h exceed clinical applicability though. We propose an accelerated motion-aware MR imaging method where the motion is inferred from small-sized k-space center patches and an initial training phase during which the characteristic movements are modeled. Thereby, acquisition times are reduced by a factor of almost 2 and reconstruction times by two orders of magnitude. Moreover, we improve the existing motion-aware approach with a systematic temporal shift correction to achieve a sharper image reconstruction. We tested our method on 12 volunteers and scanned their lungs and abdomen under free breathing. We achieved equivalent to higher reconstruction quality using the motion-prediction compared to the slower existing approach.

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