Browsing by Author "Castillo Passi, Carlos"
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- Item3D Whole‐Heart Joint T1/T1ρ Mapping and Water‐Fat Imaging on a Clinical 0.55‐T Low‐Field Scanner(2026) Crabb, Michael G.; Kunze, Karl P.; Castillo Passi, Carlos; Si, Dongyue; Littlewood, Simon J.; Prieto Vásquez, Claudia; Botnar, Rene MichaelMyocardial maps are conventionally acquired in 2D breath-hold single-parameter scans that are slow and have limited heart coverage. To overcome limitations associated with 2D breath-hold mapping sequences, we develop a novel free-breathing 3D joint T₁ / T₁ρ mapping sequence with Dixon encoding to provide co-registered 3D T₁ and T₁ρ maps and water-fat volumes with isotropic spatial resolution in a single scan for comprehensive contrast-agent free myocardial tissue characterization and visualization of the whole-heart anatomy on a clinical 0.55-T MR scanner. The proposed sequence acquires four interleaved 3D volumes with preparation modules to provide T₁ and T₁ρ encoding, with data acquired with a two-echo Dixon readout and 2D image navigators to enable 100% respiratory scan efficiency. Images were reconstructed with nonrigid respiratory motion-corrected iterative SENSE with multi-dimensional low-rank patch-based denoising, and maps generated by matching with simulated dictionaries. The proposed sequence was tested in phantoms, 11 healthy subjects and 1 patient, and compared with conventional techniques. For phantoms, the proposed 3D T₁ and T₁ρ measurements showed good correlation with 2D spin-echo reference measurements. For healthy subjects, septal myocardial tissue mapping values were T₁ = 743 ± 19 ms and T₁ρ = 46.9 ± 2.7 ms for the proposed sequence, against T₁ = 681 ± 23 ms and T₁ρ = 57.9 ± 3.6 ms for 2D modified Look-Locker inversion recovery and 2D T₁ρ, respectively. Promising results were obtained when the proposed mapping was compared to 2D late-gadolinium enhancement imaging in a patient. The proposed approach enables simultaneous 3D whole-heart joint T₁ / T₁ρ mapping and water-fat imaging at 0.55 T in a single scan of ≈ 11 min, demonstrating good agreement with conventional techniques in phantoms and healthy subjects, and promising results in a patient.
- ItemA Spatial Off-Resonance Correction in Spirals for Magnetic Resonance Fingerprinting(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2021) Coronado, Ronal; Cruz, Gastao; Castillo Passi, Carlos; Tejos, Cristian; Uribe, Sergio; Prieto, Claudia; Irarrazaval, PabloIn MR Fingerprinting (MRF), balanced Steady-State Free Precession (bSSFP) has advantages over unbalanced SSFP because it retains the spin history achieving a higher signal-to-noise ratio (SNR) and scan efficiency. However, bSSFP-MRF is not frequently used because it is sensitive to off-resonance, producing artifacts and blurring, and affecting the parametric map quality. Here we propose a novel Spatial Off-resonance Correction (SOC) approach for reducing these artifacts in bSSFP-MRF with spiral trajectories. SOC-MRF uses each pixel's Point Spread Function to create system matrices that encode both off-resonance and gridding effects. We iteratively compute the inverse of these matrices to reduce the artifacts. We evaluated the proposed method using brain simulations and actual MRF acquisitions of a standardized T1/T2 phantom and five healthy subjects. The results show that the off-resonance distortions in T1/T2 maps were considerably reduced using SOC-MRF. For T2, the Normalized Root Mean Square Error (NRMSE) was reduced from 17.3 to 8.3% (simulations) and from 35.1 to 14.9% (phantom). For T1, the NRMS was reduced from 14.7 to 7.7% (simulations) and from 17.7 to 6.7% (phantom). For in-vivo, the mean and standard deviation in different ROI in white and gray matter were significantly improved. For example, SOC-MRF estimated an average T2 for white matter of 77ms (the ground truth was 74ms) versus 50 ms of MRF. For the same example the standard deviation was reduced from 18 ms to 6ms. The corrections achieved with the proposed SOC-MRF may expand the potential applications of bSSFP-MRF, taking advantage of its better SNR property.
- ItemAutomated Segmentation of Thoracic Aortic Lumen and Vessel Wall on 3D Bright- and Black-Blood MRI using nnU-Net(2025) Cesario, Matteo; Littlewood, Simon J.; Nadel, James; Fletcher, Thomas J.; Fotaki, Anastasia; Castillo Passi, Carlos; Hajhosseiny, Reza; Pouliopoulos, Jim; Jabbour, Andrew; Olivero, Ruperto; Rodríguez Palomares, José; Kooi, M. Eline; Prieto Vásquez, Claudia; Botnar, René MichaelBACKGROUND: Magnetic resonance angiography (MRA) is an important tool for aortic assessment in several cardiovascular diseases. Assessment of MRA images relies on manual segmentation; a time-intensive process that is subject to operator variability. We aimed to optimize and validate two deep-learning models for automatic segmentation of the aortic lumen and vessel wall in high-resolution ECG-triggered free-breathing respiratory motion-corrected 3D bright- and black-blood MRA images. METHODS: Manual segmentation, serving as the ground truth, was performed on 25 bright-blood and 15 black-blood 3D MRA image sets acquired with the iT2PrepIR-BOOST sequence (1.5T) in thoracic aortopathy patients. The training was performed with nnU-Net for bright-blood (lumen) and black-blood image sets (lumen and vessel wall). Training consisted of a 70:20:10% training: validation: testing split. Inference was run on datasets (single vendor) from different centres (UK, Spain, and Australia), sequences (iT2PrepIR-BOOST, T2 prepared CMRA, and TWIST MRA), acquired resolutions (from 0.9 mm 3 to 3 mm 3), and field strengths (0.55T, 1.5T, and 3T). Predictive measurements comprised Dice Similarity Coefficient (DSC), and Intersection over Union (IoU). Postprocessing (3D slicer) included centreline extraction, diameter measurement, and curved planar reformatting (CPR). RESULTS: The optimal configuration was the 3D U-Net. Bright blood segmentation at 1.5T on iT2PrepIR-BOOST datasets (1.3 and 1.8 mm 3) and 3D CMRA datasets (0.9 mm 3) resulted in DSC ≥ 0.96 and IoU ≥ 0.92. For bright-blood segmentation on 3D CMRA at 0.55T, the nnUNet achieved DSC and IoU scores of 0.93 and 0.88 at 1.5 mm³, and 0.68 and 0.52 at 3.0 mm³, respectively. DSC and IoU scores of 0.89 and 0.82 were obtained for CMRA image sets (1 mm 3) at 1.5T (Barcelona dataset). DSC and IoU score of the BRnnUNet model were 0.90 and 0.82 respectively for the contrast-enhanced dataset (TWIST MRA). Lumen segmentation on black blood 1.5T iT2PrepIR-BOOST image sets achieved DSC ≥ 0.95 and IoU ≥ 0.90, and vessel wall segmentation resulted in DSC ≥ 0.80 and IoU ≥ 0.67. Automated centreline tracking, diameter measurement and CPR were successfully implemented in all subjects. CONCLUSION: Automated aortic lumen and wall segmentation on 3D bright- and black-blood image sets demonstrated excellent agreement with ground truth. This technique demonstrates a fast and comprehensive assessment of aortic morphology with great potential for future clinical application in various cardiovascular diseases.
- ItemDesign of Pulse Sequences for Low-Field Cardiac MRI Using Bloch Simulations(2024) Castillo Passi, Carlos; Irarrázaval Mena, Pablo; Botnar, René Michael; Pontificia Universidad Católica de Chile. Instituto de Ingeniería Biológica y MédicaThe recent development of high-end scanners offers the potential to make cardiac Magnetic Resonance Imaging (MRI) more accessible and affordable. However, adapting cardiac imaging sequences from higher fields such as to presents significant challenges.To address these challenges, we employed MRI simulations, which have proven effective for optimizing imaging parameters at novel field strengths. Nevertheless, current MRI simulators have performance, ease of use, and extensibility problems. Consequently, a new open-source MRI simulator with GPU acceleration, written in Julia, was developed. Its speed, accuracy, extensibility, and ease of use were demonstrated to be superior to currently available alternatives.This simulator was used to adapt two sequences, previously implemented at traditional field strengths, to . These sequences are for free-breathing 3D whole-heart cardiac MRI: (1) CMRA for cardiac angiography and (2) iprep-BOOST for simultaneous angiography and vessel wall imaging. Image navigators (iNAVs) were employed for non-rigid respiratory motion correction to enable 100% respiratory scan efficiency, while patch-based denoising techniques were used to mitigate the reduced signal-to-noise ratio at and accelerate the scans. As explained, for both sequences, the parameters were adjusted using MRI simulations and in-vivo experiments, focusing on improving SNR, contrast, and fat suppression. Both sequences were assessed using quantitative and qualitative scores, achieving excellent image quality and vessel sharpness comparable to previous studies.Finally, a comparison between the optimized sequences and their counterparts was conducted by acquiring images from the same cohort of healthy subjects. Image quality was comparable, with improvements observed in regions of high susceptibility, such as the lung vessels.In conclusion, this work successfully developed cardiac MRI sequences at using MRI simulations, demonstrating image quality comparable to their counterparts. Further evaluation of these sequences in patients with cardiovascular diseases will be necessary to determine the diagnostic quality provided.
- ItemHigh-resolution 3D whole-heart bright- and black-blood imaging with co-registered T2 mapping at 0.55 T(Cambridge University Press, 2025) Kokhanovskyi, Ivan; Castillo Passi, Carlos; Crabb, Michael G.; Ganter, Carl; Littlewood, Simon J.; Kunze, Karl P.; Karampinos, Dimitrios C.; Makowski, Marcus R.; Rueckert, Daniel; Prieto Vásquez, Claudia; Botnar, René MichaelConventional CMR exams for assessment of cardiac anatomy and tissue characterization require multiple sequential 2D acquisitions under breath-hold in different orientations, in addition to being limited to 1.5 T and 3 T. Methods: In this study, we sought to develop a novel 3D motion-compensated free-breathing sequence for comprehensive high-resolution whole-heart assessment of cardiovascular anatomy via simultaneous bright- and black-blood imaging and co-registered (Formula presented.) myocardial tissue quantification in a one-click scan at 0.55 T. Results: Good agreement with a spin-echo reference sequence was found in the phantom for (Formula presented.) mapping. In-vivo, the proposed research sequence was evaluated in 10 healthy subjects, providing great delineation of cardiac and vascular structures, good visibility of coronary arteries and accurate (Formula presented.) parametric mapping in a clinically feasible time of less than 9 min.
- ItemKomaMRI.jl: An open‐source framework for general MRI simulations with GPU acceleration(2023) Castillo Passi, Carlos; Coronado, Ronal Manuel; Varela Mattatall, Gabriel; Alberola López, Carlos; Botnar, René Michael; Irarrázaval Mena, PabloPurpose: To develop an open-source, high-performance, easy-to-use, extensible, cross-platform, and general MRI simulation framework (Koma). Methods: Koma was developed using the Julia programming language. Like other MRI simulators, it solves the Bloch equations with CPU and GPU parallelization. The inputs are the scanner parameters, the phantom, and the pulse sequence that is Pulseq-compatible. The raw data is stored in the ISMRMRD format. For the reconstruction, MRIReco.jl is used. A graphical user interface utilizing web technologies was also designed. Two types of experiments were performed: one to compare the quality of the results and the execution speed, and the second to compare its usability. Finally, the use of Koma in quantitative imaging was demonstrated by simulating Magnetic Resonance Fingerprinting (MRF) acquisitions. Results: Koma was compared to two well-known open-source MRI simulators, JEMRIS and MRiLab. Highly accurate results (with mean absolute differences below 0.1% compared to JEMRIS) and better GPU performance than MRiLab were demonstrated. In an experiment with students, Koma was proved to be easy to use, eight times faster on personal computers than JEMRIS, and 65% of test subjects recommended it. The potential for designing acquisition and reconstruction techniques was also shown through the simulation of MRF acquisitions, with conclusions that agree with the literature. Conclusions: Koma's speed and flexibility have the potential to make simulations more accessible for education and research. Koma is expected to be used for designing and testing novel pulse sequences before implementing them in the scanner with Pulseq files, and for creating synthetic data to train machine learning models.
- ItemNovel techniques and signal models with applications in MRI(2018) Castillo Passi, Carlos; Irarrázaval Mena, Pablo; Pontificia Universidad Católica de Chile. Escuela de IngenieríaLas adquisiciones submuestreadas son comúnmente usadas para reducir el tiempo de escaneo en Imágenes por Resonancia Magnética (IRM). Compressed Sensing permite la reconstrucción de la imagen subyacente a partir de estos datos resolviendo un problema de optimización convexo. Este método explota la raleza de la imagen usando la norma-l1 como una medida de raleza. Esta medida es esencial en el desempeño del algoritmo. En este trabajo, proponemos un método que utiliza el ´Índice de Gini (IG), un concepto originado en economía, como una medida de raleza para la reconstrucción de IRM, debido a que satisface todas las propiedades deseables para una medida de raleza. Debido a que el IG es una función cuasi-convexa, el problema de optimización es resuelto a través de resolver problemas l1 iterativamente pesados. Este algoritmo fue testeado en un fantoma numérico y con datos de IRM in vivo. Para el fantoma, una reconstrucción perfecta fue alcanzada usando el IG con Factores de Sub Muestreo (FSM) más altos que la norma-l1. Mejoras fueron también observadas para los datos in vivo, reduciendo el error al usar el IG lo que hizo posible disminuir el FSM en 0.5 al comparar el error con la norma-l1. La novedad del método propuesto es la aplicación del IG con datos complejos, submuestreo y condiciones débiles de raleza, haciéndolo apropiado para muchas aplicaciones en resonancia magnética, sin un excesivo aumento de la carga computacional.
- ItemSimultaneous 3D aortic lumen and vessel wall imaging at 0.55 T at either systole or diastole(John Wiley & Sons, 2025) Paredes Gálvez, Matías Ignacio; Castillo Passi, Carlos; Kunze, Karl P.; Fotaki, Anastasia; Littlewood, Simon; Botnar, René Michael; Prieto Vásquez, ClaudiaPurpose: To evaluate the feasibility of a novel, non-contrast enhanced, 3D, simultaneous bright-blood, and black-blood sequence (iT2prep-BOOST) for aortic imaging at 0.55 T at either systole or diastole. Methods: Simultaneous contrast-free 3D aortic lumen and vessel wall imaging at 0.55 T is achieved using the recently introduced iT2prep-BOOST framework that interleaves the acquisition of two bright blood images (with inversion recovery T-2 preparation [T2prep-IR] and no preparation). To enable either systolic or diastolic aortic imaging, three T-2 preparation pulses were investigated-an adiabatic RF pulse and two Malcolm-Levitt (MLEV) pulses (MLEV4 and MLEV8)-to improve image quality in regions with high flow and susceptibility. The proposed approach was evaluated in phantom, 10 healthy subjects and 3 patients with suspected cardiovascular disease. Bright- and black-blood images resulting from the three different T-2 preparation pulses were compared both qualitatively and quantitatively, using a 4-point Likert scale for vessel sharpness and presence of blood artifacts. Additionally, the contrast ratio between the lumen and myocardium was computed. Aortic measurements, including the aortic annulus area at systole and diastole, cusp-commissure measurement at the aortic root level during diastole, and aortic diameter at the ascending aortic level during diastole were also performed. Results: Excellent or good image quality scores were obtained for both bright- and black-blood images with iT2prep-BOOST at 0.55 T with all three preparation pulses. The use of MLEV8 T-2 preparation scheme improves systolic image quality, reducing the presence of artifacts with a significant difference (p < 0.05) at the mid descending aorta level. This scheme also increases the contrast ratio between aortic lumen and myocardium, compared to the previously used adiabatic RF T-2 preparation. The aortic root diameter and area were consistent with values reported in the literature for healthy subjects at 1.5 T. Conclusion: The feasibility of a novel, non-contrast-enhanced, 3D aortic imaging framework for simultaneous bright-blood and black-blood imaging was demonstrated at 0.55 T for either systole or diastole, with a scan time of 7 min. Good image quality scores and aortic measurements in agreement with literature values at 1.5 T were achieved with the MLEV8 T-2 preparation. Studies in a larger cohort of healthy subjects and patients with aortopathies are warranted.
- ItemSimultaneous liver T1, T2, and ADC MR fingerprinting using optimized motion-compensated diffusion preparations: An initial validation on volunteers(Cambridge University Press, 2025) Velasco, Carlos; Castillo Passi, Carlos; Chaher, N.; Karampinos, D.C.; Irarrázaval Mena, Pablo; Phinikaridou A.; Botnar, René Michael; Prieto Vásquez, ClaudiaMagnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.Purpose: To develop a novel MR fingerprinting sequence using optimized motion-compensated diffusion preparations for simultaneous T1, T2, and ADC quantification of liver tissue in a single breath-held scan. Methods: A radial spoiled gradient echo acquisition with magnetization preparation modules for T1, T2, and ADC encoding is proposed. To compensate for the signal voids generated by the diffusion preparation, the combination of (1) a breath-held scan, (2) peripheral pulse signal triggering, and (3) an optimized motion-compensated diffusion-preparation module is employed. Phantom experiments were performed to test the accuracy of the technique. The sequence was evaluated in 11 healthy subjects in comparison to conventional mapping techniques. Additional in vivo repeatability assessment experiments were performed. Results: T1, T2, and ADC quantification showed good correlation (r2 > 0.9 for all cases) with reference maps in phantoms and good agreement in vivo against clinical scans (bias not significantly different from zero). A peripheral pulse trigger delay of 200 ms was used to reduce cardiovascular motion artifacts. The repeatability tests prove a low interscan coefficient of variation and a high intraclass correlation coefficient of greater than 0.9 for all cases. Conclusions: Simultaneous quantification of T1, T2, and ADC in liver tissue in a single MR fingerprinting scan of ˜16 s has been proposed, enabling a comprehensive evaluation of hepatic disease through co-registered multiparametric imaging. Further studies are warranted to test this approach in patients with suspected diffuse liver disease to evaluate its potential for liver tissue characterization and tumor staging.