Xin Shen’s research while affiliated with University of California, San Francisco and other places
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In this work, we evaluate the sodium magnetic resonance imaging (MRI) capabilities of a three-dimensional (3D) dual-echo ultrashort echo time (UTE) sequence with a novel rosette petal trajectory (PETALUTE), in comparison to the 3D density-adapted (DA) radial spokes UTE sequence in human articular cartilage in the knee.
We scanned five healthy subjects using a 3D dual-echo PETALUTE acquisition and two comparable implementations of 3D DA-radial spokes acquisitions, one matching the number of k-space projections (Radial – Matched Spokes) and the other matching the total number of samples (Radial – Matched Samples) acquired in k-space.
The PETALUTE acquisition enabled equivalent sodium quantification in articular cartilage volumes of interest (168.8 ± 29.9 mM, mean ± standard deviation) to those derived from the 3D radial acquisitions (171.62 ± 28.7 mM and 149.8 ± 22.2 mM, respectively). We achieved a 41% shorter scan time of 2:06 for 3D PETALUTE, compared to 3:36 for 3D radial acquisitions. We also evaluated the feasibility of further acceleration of the PETALUTE sequence through retrospective compressed sensing with 2 × and 4 × acceleration of the first echo and showed structural similarity of 0.89 ± 0.03 and 0.87 ± 0.03 when compared to non-retrospectively accelerated reconstruction.
We demonstrate improved scan time with equivalent performance using a 3D dual-echo PETALUTE sequence compared to the 3D DA-radial sequence for sodium MRI of articular cartilage.
In this work, we demonstrate the sodium magnetic resonance imaging (MRI) capabilities of a three-dimensional (3D) dual-echo ultrashort echo time (UTE) sequence with a novel rosette petal trajectory (PETALUTE), in comparison to the 3D density-adapted (DA) radial spokes UTE sequence. We scanned five healthy subjects using a 3D dual-echo PETALUTE acquisition and two comparable implementations of 3D DA-radial spokes acquisitions, one matching the number of k-space projections (Radial-Matched Trajectories) and the other matching the total number of samples (Radial-Matched Samples) acquired in k-space. The PETALUTE acquisition enabled equivalent sodium quantification in articular cartilage volumes of interest (168.8 ± 29.9 mM) to those derived from the 3D radial acquisitions (171.62 ± 28.7 mM and 149.8 ± 22.2 mM, respectively). We achieved a shorter scan time of 2:06 for 3D PETALUTE, compared to 3:36 for 3D radial acquisitions. We also evaluated the feasibility of further acceleration of the PETALUTE sequence through retrospective compressed sensing with 2× and 4× acceleration of the first echo and showed structural similarity of 0.89 ± 0.03 and 0.87 ± 0.03 when compared to non-retrospectively accelerated reconstruction. Together, these results demonstrate improved scan time with equivalent performance of the PETALUTE sequence compared to the 3D DA-radial sequence for sodium MRI of articular cartilage.
Motivation: Well established techniques for fast 3D T1 mapping with cartesian/radial trajectories are prone to respiratory artifacts.Previously established non-cartesian sequences have mitigated the influence of motion artifacts, though still suffer from long measurement times. Goal(s): Implementation of a novel 3D dual-echo rosette k-space trajectory for preclinical UTE MRI(PETALUTE) for abdominal imaging of both anatomical and quantitative T1 measurements and retrospective 4-fold acceleration. Approach: PETALUTE(resolution 0.24x0.24x0.24mm3,accelerated scan-time 2:15min) acquisition for T1 mapping via variable flip angle method and evaluation of T1 values and acceleration effects. Results: High-resolution non-gated abdominal imaging with the ability to clearly distinguish anatomy and T1 values,that did not deprecate when accelerated. Impact: Well established methods for T1 mapping using cartesian/radial trajectories suffer from motion artifacts due to long acquisition duration.PETALUTE,a novel 3D dual-echo rosette k-space trajectory for preclinical UTE-MRI,is able to generate high-resolution non-gated abdominal anatomical images and T1 mapping in ~2min.
Introduction Shen et al. 2021, 2022, and 2023 demonstrated the addition of novel rosette trajectory measurements in MRI and MRSI at ultra-high and high-field scanners (1-3). The dual-echo 3D rosette trajectories offer greater efficiency, allowing a center-out (1st echo) and center-in (2nd echo) sampling pattern that provides more outer and center k-space per petal samples than radial spokes. In addition, the rosette k-space trajectory samples center k-space in a more incoherent pattern. There, it offers the potential for further acceleration using higher under-sampling factors and the compressed sensing technique for reconstruction. This study demonstrated PETAL MR(S)I sequences for preclinical ultra-high field (7T, 9.4T) scanners. Methods Mice were scanned in a 7T and 9.4T horizontal-bore small animal MRI system (BioSpec 70/30 and BioSpec 94/20; Bruker Instruments) with a volume transmit and receive 1H 40-mm RF coil (7T) and a 2 × 2 phased array surface coil (9.4T). A custom dual-tune transceive coil for 31 P/ 1 H at 7T was used for 31P MRSI. Three experiments were conducted to implement the dual-echo novel rosette k-space trajectory for preclinical applications of 3D VFA PETALUTE, 3D PETALUTE MRSI, and MEGA-SLASER PETAL MRSI. § Abdominal Variable Flip Angle (VFA) T1 Mapping with accelerated PETALUTE (7T): VFA-PETALUTE T1 Mapping, FA: 4°,20°, DUAL-TEs = 16 µs and 2 ms, TR = 7 ms, # petals =18,192, Resolution 240 µm 3 , Acceleration Factor = 4 § Abdominal 31 P 3D PETALUTE MRSI (7T): PETALUTE 1 H, FA: 4°, Dual TEs = 0.016, 2 ms, TR = 7 ms, # petals =18,192, Resolution 175 µm 3 , Acceleration Factor = 1 Total acquisition duration =2.15 minutes. 3D PETALUTE 31 P MRSI, TE=16 µs TR = 500 ms, # petals =1444, Spectral bandwidth =6.5kHz, Resolution 1 mm 3 , Acceleration Factor = 1, Number of averages = 4, Total Acquisition duration= 48 minutes. § Neurotransmitter imaging with MEGA-SLASER PETAL MRSI (9.4T): GABA Editing, TE=68 m, TR =1000ms, #petals=256, in-plane Resolution 1 mm 2 , SLASER Localization The regular regridding applying a density-compensated adjoint nonuniform fast Fourier transform was performed using the Berkeley Advanced Reconstruction Toolbox (BART) toolbox. Results Figure 1 Abdominal Variable Flip Angle (VFA) T1 Mapping with accelerated PETALUTE: VFA measurement with an isotropic 240µm 3 resolution in ~ 2 minutes Figure 2 Abdominal 31P 3D PETALUTE MRSI Outcome: Metabolite maps with an isotropic 1mm 3 resolution in 48 minutes Figure 3 Neurotransmitter imaging with MEGA-SLASER PETAL MRSI Outcome: Neurotransmitter maps with 1mm 2 resolution in 8.5 minutes Discussion High-quality images, higher SNR, and higher resolution data were obtained with accelerated PETALUTE sequence on a preclinical scanner, resulting in (1) increased sampling density in the outer/inner k-space, (2) improved PSF and SNR compared, (3) a smooth transition (zero-delay) between the two echoes of dual-echo acquisition and (4) further acceleration using higher under-sampling factors. The novel Rosette space dual-echo Acquisition/ PETALUTE strategy could further enhance integrated and translational research studies to understand better human and non-human complex structures and physiologies.
References
1. Shen, X., Chiew, M., & Emir, U. (2021, June). Development of 3D Rosette K-Space Trajectory in Ultra-Short Echo Time MRI Applications. In MEDICAL PHYSICS (Vol. 48, No. 6). 111
2. Shen, Xin (2022). Development and Applications of 3D Ultra-short Echo Time MRI with Rosette k-Space Pattern. Purdue University Graduate School. Thesis. https://doi.org/10.25394/PGS.20323671.v1
3. Ultra-short T2 components imaging of the whole brain using 3D dual-echo UTE MRI with rosette k-space pattern. Magn Reson Med 89, 508–521 (2023).
Phosphorus-31 magnetic resonance spectroscopic imaging ( ³¹ P-MRSI) provides valuable non-invasive in vivo information on tissue metabolism but is burdened by poor sensitivity and prolonged scan duration. Ultra-short echo time (UTE) acquisitions minimize signal loss when probing signals with relatively short spin-spin relaxation time (T 2 ), while also preventing first-order dephasing. Here, a three-dimensional (3D) UTE sequence with a rosette k-space trajectory is applied to ³¹ P-MRSI at 3T. Conventional chemical shift imaging (CSI) employs highly regular Cartesian k-space sampling, susceptible to substantial artifacts when accelerated via undersampling. In contrast, this novel sequence’s “petal-like” pattern offers incoherent sampling more suitable for compressed sensing (CS). These results showcase the competitive performance of UTE rosette ³¹ P-MRSI against conventional weighted CSI with simulation, phantom, and in vivo leg muscle comparisons.
Purpose
This study aimed to develop a new high‐resolution MRI sequence for the imaging of the ultra‐short transverse relaxation time (uT2) components in the brain, while simultaneously providing proton density (PD) contrast for reference and quantification.
Theory
The sequence combines low flip angle balanced SSFP (bSSFP) and UTE techniques, together with a 3D dual‐echo rosette k‐space trajectory for readout.
Methods
The expected image contrast was evaluated by simulations. A study cohort of six healthy volunteers and eight multiple sclerosis (MS) patients was recruited to test the proposed sequence. Subtraction between two TEs was performed to extract uT2 signals. In addition, conventional longitudinal relaxation time (T1) weighted, T2‐weighted, and PD‐weighted MRI sequences were also acquired for comparison.
Results
Typical PD‐contrast was found in the second TE images, while uT2 signals were selectively captured in the first TE images. The subtraction images presented signals primarily originating from uT2 components, but only if the first TE is short enough. Lesions in the MS subjects showed hyperintense signals in the second TE images but were hypointense signals in the subtraction images. The lesions had significantly lower signal intensity in subtraction images than normal white matter (WM), which indicated a reduction of uT2 components likely associated with myelin.
Conclusion
3D isotropic sub‐millimeter (0.94 mm) spatial resolution images were acquired with the novel bSSFP UTE sequence within 3 min. It provided easy extraction of uT2 signals and PD‐contrast for reference within a single acquisition.
Purpose: This study aims 1) to implement an operator-independent acquisition, reconstruction, and processing pipeline using a novel rosette k-space pattern for UTE 31P 3D MRSI and 2) to evaluate the clinical applicability and replicability at different experimental setups.
Methods: A multicenter repeatability study was conducted for the novel UTE 31P 3D Rosette MRSI at three institutions with different experimental setups. Non-localized 31P MRSI data of 5 healthy subjects at each site were acquired with an acquisition delay of 65 microseconds and a final resolution of 10 x 10 x 10 mm3 in 9 minutes. Spectra were quantified using the LCModel package. The potential acceleration was achieved using compressed sensing on retrospectively undersampled data. Reproducibility at each site was evaluated using the inter-subject coefficient of variance.
Results: This novel acquisition and advanced processing techniques yielded high-quality spectra and enabled the detection of the critical brain metabolites at three different sites with different hardware specifications. In vivo feasibility with an acceleration factor of 4 in 6.75 min resulted in a mean Cramer-Rao lower bounds below 20% for PCr, ATPs, and PME, and the mean CoV of ATP/PCr resulted in below 20%.
Conclusion We demonstrated that UTE 31P 3D Rosette MRSI acquisition, combined with compressed sensing and LCModel analysis, allows patient-friendly, operator-independent, high-resolution 31P MRSI to be acquired at clinical setups.
Purpose
Recent work has shown MRI is able to measure and quantify signals of phospholipid membrane‐bound protons associated with myelin in the human brain. This work seeks to develop an improved technique for characterizing this brain ultrashort‐T2∗ component in vivo accounting for T1 weighting.
Methods
Data from ultrashort echo time scans from 16 healthy volunteers with variable flip angles (VFA) were collected and fitted into an advanced regression model to quantify signal fraction, relaxation time, and frequency shift of the ultrashort‐T2∗ component.
Results
The fitted components show intra‐subject differences of different white matter structures and significantly elevated ultrashort‐T2∗ signal fraction in the corticospinal tracts measured at 0.09 versus 0.06 in other white matter structures and significantly elevated ultrashort‐T2∗ frequency shift in the body of the corpus callosum at −1.5 versus −2.0 ppm in other white matter structures.
Conclusion
The significantly different measured components and measured T1 relaxation time of the ultrashort‐T2∗ component suggest that this method is picking up novel signals from phospholipid membrane‐bound protons.
Background: The iron concentration increases during normal brain development and is identified as a risk factor for many neurodegenerative diseases, it is vital to monitor iron content in the brain non-invasively.
Purpose: This study aimed to quantify in vivo brain iron concentration with a 3D rosette-based ultra-short echo time (UTE) magnetic resonance imaging (MRI) sequence.
Methods: A cylindrical phantom containing nine vials of different iron concentrations (iron (II) chloride) from 0.5 millimoles to 50 millimoles and six healthy subjects were scanned using 3D high-resolution (0.94x0.94x0.94 mm3) rosette UTE sequence at an echo time (TE) of 20 s.
Results: Iron-related hyperintense signals (i.e., positive contrast) were detected based on the phantom scan, and were used to establish an association between iron concentration and signal intensity. The signal intensities from in vivo scans were then converted to iron concentrations based on the association. The deep brain structures, such as the substantia nigra, putamen, and globus pallidus, were highlighted after the conversion, which indicated potential iron accumulations.
Conclusion: This study suggested that T1-weighted signal intensity could be used for brain iron mapping.
... Across all subjects, the Radial -Matched Samples acquisition displayed a pronounced ringing artifact that was not evident in either Radial -Matched Spokes or PETALUTE (Fig. 1), an effect likely attributable to undersampling. On the other hand, the rosette trajectory of PETALUTE provides improved k-space coverage which enables undersampling without losing image quality [15,26]. Because of this improved efficiency, PETALUTE enabled an appreciably shorter total scan time of 2:06 (min:sec) compared to 3:36 while not significantly affecting sodium concentration measurements (Fig. 1). ...
... This limitation can be addressed by speeding up data acquisition using accelerated k-space trajectories, advanced reconstruction approaches, and compressed sensing methods. 39,40 Conclusion In vivo MRS including 1 H sLASER with long-TE and 3D 31 P CSI may be used at clinical field strengths for monitoring diet-induced changes in brain tumor tissue. The integration of multiparametric brain tumor segmentation with MRSI could facilitate the understanding of altered tumor metabolism under intervention despite intratumoral heterogeneity. ...
... The T 1 and T 2 values were chosen based on previous review papers. 23,[28][29][30] The signal decay from macromolecules followed GRE steady-state equations, while the water component signals were calculated in the bSSFP steady-state. Because of some T 2 refocusing at the center of TR in bSSFP setup, the signal decay between TE 1 and TE 2 is a mix of T 2 and T 2 * weighted, which is the main reason T 2 instead of T 2 * was chosen in this simulation process. ...
... To overcome this compressed sensing (CS) techniques have been implemented together with a 3D modified rosette trajectory, benefitting from its incoherent sampling pattern. [26][27][28] Compared to density-weighted-CRT 19,20 the rosette trajectory has a reduced SNR efficiency because of unfavorable k-space weighting. Kasper et al. 29 showed that SNR can be maximized if no k-space density compensation needs to be performed because the k-space weighting function of a trajectory already matches the desired target weighting (density-weighting). ...
... To address these points, we propose a three-dimensional (3D), ultra-short echo time (UTE) sequence with a novel rosette k-space trajectory (previously validated in ultra-short-T 2 imaging 25,26 and brain iron mapping 27,28 ) for 31 P magnetic resonance spectroscopic imaging (MRSI). 29 Compared to conventional CSI Cartesian k-space trajectories, rosette's "petal-like" pattern ( Fig. 1) maps 3D k-space far more e ciently. Additionally, rosette's relatively inchorent data sampling allows the possibility of signi cant acceleration through higher undersampling factors and compressed sensing (CS) reconstruction; offering better k-space coverage when compared to radial and spiral trajectories, generalized rosette's curvature affords superior SNR performance under aggressive acceleration. ...
... The Rosette trajectory, a non-Cartesian trajectory which traces a petal-like path through k-space, provides particularly effective k-space coverage [26]. The efficient sampling pattern of the Rosette trajectory can yield a higher signal-to-noise ratio (SNR) compared to spiral or radial trajectories for MRI acquisition under high acceleration factors [27]. ...
... These techniques also improve the detection of calcifications and demyelination, aiding in the diagnosis and monitoring of multiple sclerosis and other neurological conditions. Karnik et al. [141] developed a method to generate high-resolution QSM using UTE MRI with a novel 3D rosette k-space trajectory. This method produced high-resolution mag-netic susceptibility maps in an iron chloride phantom and the human brain, signifying that UTE-QSM could yield susceptibility values comparable to those obtained using traditional methods, thus demonstrating its potential for detailed susceptibility mapping in neural imaging. ...
... The possibility of accelerating modified rosette trajectories using CS reconstruction approaches proved useful to a variety of application in recent publications. [48][49][50][51][52][53][54] Modified rosette trajectories will likely require a combination with complimentary acceleration methods such as parallel imaging or compressed sensing to reach clinically attractive scan times. ...
... The possibility of accelerating modified rosette trajectories using CS reconstruction approaches proved useful to a variety of application in recent publications. [48][49][50][51][52][53][54] Modified rosette trajectories will likely require a combination with complimentary acceleration methods such as parallel imaging or compressed sensing to reach clinically attractive scan times. ...
... The measurement of T2* spectrum from FID signals of entire brain and the application of a global set of T2* values (T2*fr, T2*bs, T2*bl) were tested feasible to humans. In case of not plausible for a global set of T2* values (i.e., T2* spatially varying substantially [40][41][42][43][44][45][46][47] ), multiregional sets, or a linear combination of them, may be used. ...