Repeatability of Open-MOLLI: An open-source inversion recovery myocardial T1 mapping sequence for fast prototyping.

PURPOSE: To develop an open-source prototype of myocardial T1 mapping (Open-MOLLI) to improve accessibility to cardiac T1 mapping and evaluate its repeatability. With Open-MOLLI, we aim to enable faster implementation and testing of sequence modifications and to facilitate inter-scanner and cross-vendor reproducibility studies. METHODS: Open-MOLLI is an inversion-recovery sequence using a balanced SSFP (bSSFP) readout, with inversion and triggering schemes based on the 5(3)3 MOLLI sequence, developed in Pulseq. Open-MOLLI and MOLLI sequences were acquired in the ISMRM/NIST phantom and 21 healthy volunteers. In 18 of those subjects, Open-MOLLI and MOLLI were repeated in the same session (test-retest). RESULTS: Phantom T1 values were comparable between methods, specifically for the vial with reference T1 value most similar to healthy myocardium T1 (T1vial3 = 1027 ms): T1MOLLI = 1011 ± 24 ms versus T1Open-MOLLI = 1009 ± 20 ms. In vivo T1 estimates were similar between Open-MOLLI and MOLLI (T1MOLLI = 1004 ± 33 ms vs. T1Open-MOLLI = 998 ± 52 ms), with a mean difference of -17 ms (p = 0.20), despite noisier Open-MOLLI weighted images and maps. Repeatability measures were slightly higher for Open-MOLLI (RCMOLLI = 3.0% vs. RCOpen-MOLLI = 4.4%). CONCLUSION: The open-source sequence Open-MOLLI can be used for T1 mapping in vivo with similar mean T1 values to the MOLLI method. Open-MOLLI increases the accessibility to cardiac T1 mapping, providing also a base sequence to which further improvements can easily be added and tested.

Open-source myocardial T1 mapping with simultaneous multi-slice acceleration: Combining an auto-calibrated blipped-bSSFP readout with VERSE-MB pulses.

PURPOSE: Enabling fast and accessible myocardial T1 mapping is crucial for extending its clinical application. We introduce Open-MOLLI-SMS combining simultaneous multi-slice (SMS) with auto-calibration and variable-rate selective excitation (VERSE)-multiband pulses to obtain all slices in a fast single-shot T1 mapping sequence. METHODS: Open-MOLLI-SMS was developed by integrating SMS with the open-source method Open-MOLLI previously implemented in Pulseq. Three methods were integrated for Open-MOLLI-SMS: (1) auto-calibration blip patterns to ensure consistency between the data and coil information; (2) a blipped-balanced SSFP (bSSFP) readout to induce controlled aliasing in parallel imaging shifts without disturbing the bSSFP frequency response; and (3) a VERSE-multiband pulse for minimizing the achievable TR and the specific absortion rate (SAR) impact of SMS. Two (SMS2) or three (SMS3) slices were excited simultaneously and encoded with an in-plane acceleration factor of 2. Experiments were performed in the International Society for Magnetic Resonance in Medicine/National Institute of Standards and Technology phantom and five healthy volunteers. RESULTS: Phantom results show accurate T1 estimates for reference values between 400 to 2200 ms. Artifacts were visible for Open-MOLLI-SMS3 but not replicated in vivo. In vivo Open-MOLLI-SMS (T1 SMS2 = 993 ± 10 ms; T1 SMS3 = 1031 ± 17 ms) provided similar values to mean T1 single-band Open-MOLLI estimates (T1 Open-MOLLI = 1005 ± 47 ms). Open-MOLLI-SMS2 provided the closest estimates to the reference. CONCLUSION: This proof-of-principle implementation study demonstrates the feasibility of speeding up T1 -mapping acquisitions and increasing coverage by combining auto-calibration strategies with a blipped-bSFFP readout and VERSE multiband RF excitation pulses. The proposed methodology was built on the Open-MOLLI mapping sequence, which provides a fast means for prototyping and enables open-source sharing of the method.

Myocardial T1 mapping with magnetic resonance imaging - a useful tool to understand the diseased heart.

Cardiac magnetic resonance imaging (MRI) is increasingly used in clinical practice due to its versatility. T1 mapping of the myocardium, a recently introduced MRI technique that is becoming available enables quantitative tissue characterization, overcoming some of the limitations of late enhancement. This promising technique has the ability to identify diffuse myocardial fibrosis and is beginning to be used in the diagnostic and prognostic assessment of several heart diseases. In this review, we start by explaining the physical principles of myocardial T1 mapping and possible confounding factors in its measurement. We then analyze the evidence supporting its potential usefulness as a complement to the existing cardiac MRI methods. Finally, we discuss the current limitations of T1 mapping and possible areas of future research.

Open-source magnetic resonance imaging acquisition: Data and documentation for two validated pulse sequences.

Raw data, simulated and acquired phantom images, and quantitative longitudinal and transverse relaxation times (T1/T2) maps from two open-source Magnetic Resonance Imaging (MRI) pulse sequences are presented in this dataset along with corresponding ".seq" files, sequence implementation scripts, and reconstruction/analysis scripts [1]. Real MRI data were collected from a 3T Siemens Prisma Fit and a 1.5T Siemens Aera via the Pulseq open-source MR sequence platform, and corresponding in silico data were generated using the simulation module of Virtual Scanner [2]. This dataset and its associated code can be used to validate the pipeline for using the same pulse sequences at other research sites using Pulseq, to provide guidelines for documenting and sharing open-source pulse sequences in general, and to demonstrate practical, customizable acquisition scripts using the PyPulseq library.

A framework for validating open-source pulse sequences.

Open-source pulse sequence programs offer an accessible and transparent approach to sequence development and deployment. However, a common framework for testing, documenting, and sharing open-source sequences is still needed to ensure sequence usability and repeatability. We propose and demonstrate such a framework by implementing two sequences, Inversion Recovery Spin Echo (IRSE) and Turbo Spin Echo (TSE), with PyPulseq, and testing them on a commercial 3 T scanner. We used the ACR and ISMRM/NIST phantoms for qualitative imaging and T1/T2 mapping, respectively. The qualitative sequences show good agreement with vendor-provided counterparts (mean Structural Similarity Index Measure (SSIM) = 0.810 for IRSE and 0.826 for TSE). Both sequences passed five out of the seven standard ACR tests, performing at similar levels to vendor counterparts. Compared to reference values, the coefficient of determination R2 was 0.9946 for IRSE T1 mapping and 0.9331 for TSE T2 mapping. All sequences passed the scanner safety check for a 70 kg, 175 cm subject. The framework was demonstrated by packaging the sequences and sharing them on GitHub with data and documentation on the file generation, acquisition, reconstruction, and post-processing steps. The same sequences were tested at a second site using a 1.5 T scanner with the information shared. PDF templates for both sequence developers and users were created and filled.

Improving B1+ parametric estimation in the brain from multispin-echo sequences using a fusion bootstrap moves solver.

PURPOSE: To simultaneously estimate the B1+ field (along with the T2 ) in the brain with multispin-echo (MSE) sequences and dictionary matching. METHODS: T2 mapping provides clinically relevant information such as in the assessment of brain degenerative diseases. It is commonly obtained with MSE sequences, and accuracy can be further improved by matching the MSE signal to a precomputed dictionary of echo-modulation curves. For additional T1 quantification, transmit B1+ field knowledge is also required. Preliminary work has shown that although simultaneous brain B1+ estimation along with T2 is possible, it presents a bimodal distribution with the main peak coinciding with the true value. By taking advantage of this, the B1+ maps are expected to be spatially smooth by applying an iterative method that takes into account each pixel neighborhood known as the fusion bootstrap moves solver (FBMS). The effect of the FBMS on B1+ accuracy and piecewise smoothness is investigated and different spatial regularization levels are compared. Total variation regularization was used for both B1+ and T2 simultaneous estimation because of its simplicity as an initial proof-of-concept; future work could explore non edge-preserving regularization independently for B1+ . RESULTS: Improvements in B1+ accuracy (up to 45.37% and 16.81% B1+ error decrease) and recovery of spatially homogeneous maps are shown in simulations and in vivo 3.0T brain data, respectively. CONCLUSION: Accurate B1+ estimated values can be obtained from widely available MSE sequences while jointly estimating T2 maps with the use of echo-modulation curve matching and FBMS at no further cost.

Optimizing maternal fat suppression with constrained image-based shimming in fetal MR.

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.

Accelerated magnetic resonance fingerprinting using soft-weighted key-hole (MRF-SOHO).

OBJECT: To develop a novel approach for highly accelerated Magnetic Resonance Fingerprinting (MRF) acquisition. MATERIALS AND METHODS: The proposed method combines parallel imaging, soft-gating and key-hole approaches to highly accelerate MRF acquisition. Slowly varying flip angles (FA), commonly used during MRF acquisition, lead to a smooth change in the signal contrast of consecutive time-point images. This assumption enables sharing of high frequency data between different time-points, similar to what is done in some dynamic MR imaging methods such as key-hole. The proposed approach exploits this information using a SOft-weighted key-HOle (MRF-SOHO) reconstruction to achieve high acceleration factors and/or increased resolution without compromising image quality or increasing scan time. MRF-SOHO was validated on a standard T1/T2 phantom and in in-vivo brain acquisitions reconstructing T1, T2 and proton density parametric maps. RESULTS: Accelerated MRF-SOHO using less data per time-point and less time-point images enabled a considerable reduction in scan time (up to 4.6x), while obtaining similar T1 and T2 accuracy and precision when compared to zero-filled MRF reconstruction. For the same number of spokes and time-points, the proposed method yielded an enhanced performance in quantifying parameters than the zero-filled MRF reconstruction, which was verified with 2, 1 and 0.7 (sub-millimetre) resolutions. CONCLUSION: The proposed MRF-SOHO enabled a 4.6x scan time reduction for an in-plane spatial resolution of 2x2 mm2 when compared to zero-filled MRF and enabled sub-millimetric (0.7x0.7 mm2) resolution MRF.

Inner-volume echo volumar imaging (IVEVI) for robust fetal brain imaging.

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 T2* 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 B0 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 T2* 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.

An exploration of task based fMRI in neonates using echo-shifting to allow acquisition at longer TE without loss of temporal efficiency.

Optimal contrast to noise ratio of the BOLD signal in neonatal and foetal fMRI has been hard to achieve because of the much longer T2(⁎) values in developing brain tissue in comparison to those in the mature adult brain. The conventional approach of optimizing fMRI sequences would suggest matching the echo time (TE) and the T2(⁎) of the neonatal and foetal brain. However, the use of a long echo time would typically increase the minimum repetition time (TR) resulting in inefficient sampling. Here we apply the concept of echo shifting to task based neonatal fMRI in order to achieve an improved contrast to noise ratio and efficient data sampling at the same time. Echo shifted EPI (es-EPI) is a modification of a standard 2D-EPI sequence which enables echo times longer than the time between consecutive excitations (TE>TS=TRNS, where NS is the number of acquired slices and TS the inter-slice repetition time). The proposed method was tested on neonatal subjects using a passive sensori-motor task paradigm. Dual echo EPI datasets with an identical readout structure to es-EPI were also acquired and used as control data to assess BOLD activation. From the results of the latter analysis, an average increase of 78±41% in contrast to noise ratio was observable when comparing late to short echoes. Furthermore, es-EPI allowed the acquisition of data with an identical contrast to the late echo, but more efficiently since a higher number of slices could be acquired in the same amount of time.