Mitosis domain generalization in histopathology images -- The MIDOG challenge

The density of mitotic figures within tumor tissue is known to be highly correlated with tumor proliferation and thus is an important marker in tumor grading. Recognition of mitotic figures by pathologists is known to be subject to a strong inter-rater bias, which limits the prognostic value. State-of-the-art deep learning methods can support the expert in this assessment but are known to strongly deteriorate when applied in a different clinical environment than was used for training. One decisive component in the underlying domain shift has been identified as the variability caused by using different whole slide scanners. The goal of the MICCAI MIDOG 2021 challenge has been to propose and evaluate methods that counter this domain shift and derive scanner-agnostic mitosis detection algorithms. The challenge used a training set of 200 cases, split across four scanning systems. As a test set, an additional 100 cases split across four scanning systems, including two previously unseen scanners, were given. The best approaches performed on an expert level, with the winning algorithm yielding an F_1 score of 0.748 (CI95: 0.704-0.781). In this paper, we evaluate and compare the approaches that were submitted to the challenge and identify methodological factors contributing to better performance.Comment: 19 pages, 9 figures, summary paper of the 2021 MICCAI MIDOG challeng

A comprehensive approach for correcting voxel‐wise b‐value errors in diffusion MRI

PURPOSE: In diffusion MRI, the actual b-value played out on the scanner may deviate from the nominal value due to magnetic field imperfections. A simple image-based correction method for this problem is presented. METHODS: The apparent diffusion constant (ADC) of a water phantom was measured voxel-wise along 64 diffusion directions at b = 1000 s/mm2 . The true diffusion constant of water was estimated, considering the phantom temperature. A voxel-wise correction factor, providing an effective b-value including any magnetic field deviations, was determined for each diffusion direction by relating the measured ADC to the true diffusion constant. To test the method, the measured b-value map was used to calculate the corrected voxel-wise ADC for additionally acquired diffusion data sets on the same water phantom and data sets acquired on a small water phantom at three different positions. Diffusion tensor was estimated by applying the measured b-value map to phantom and in vivo data sets. RESULTS: The b-value-corrected ADC maps of the phantom showed the expected spatial uniformity as well as a marked improvement in consistency across diffusion directions. The b-value correction for the brain data resulted in a 5.8% and 5.5% decrease in mean diffusivity and angular differences of the primary diffusion direction of 2.71° and 0.73° inside gray and white matter, respectively. CONCLUSION: The actual b-value deviates significantly from its nominal setting, leading to a spatially variable error in the common diffusion outcome measures. The suggested method measures and corrects these artifacts

Enhanced quantitative susceptibility mapping (QSM) using real-time field control

PURPOSE: To assess the potential of a real-time field-control (FC) system for mitigating effects of spatiotemporal field fluctuations in quantitative susceptibility mapping (QSM) at 7 T. METHODS: Magnitude, phase, and QSM images of phantoms and healthy volunteers were acquired under standard conditions and under induced field perturbation (FP) (phantoms: periodic water-bottle displacement; volunteers: deep breathing and forearm movement) with and without FC, which continuously detects and minimizes magnetic-field variations. RESULTS: Field control successfully eliminated FP-induced impairment of phantom image quality and deviations from a linear susceptibility increase for increasing gadolinium concentration in a Gd dilution series (y = 320x - 0.60, R(2)  = 0.93 for the scan with FP and FC versus y = 259x - 0.54, R(2)  = 0.78 for the scan with FP and no FC (slope literature value: 326 ppm L/mol)). Similarly, in volunteers, FC allowed a recovery of a FP-induced loss of identifiable brain structures and reduced the relative change of mean susceptibilities and standard deviations (93 ± 53% to 34 ± 46%) in all regions of interests with respect to the reference scan. CONCLUSIONS: Real-time FC improved the delineation of brain structures and the match of susceptibility values with reference values obtained without FP. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine

Minimizing the echo time in diffusion imaging using spiral readouts and a head gradient system

Purpose: Diffusion weighted imaging (DWI) is commonly limited by low signal-to-noise ratio (SNR) as well as motion artifacts. To address this limitation, a method that allows to maximize the achievable signal yield and increase the resolution in motion robust single-shot DWI is presented. Methods: DWI was performed on a 3T scanner equipped with a recently developed gradient insert (gradient strength: 200 mT/m, slew rate: 600 T/m/s). To further shorten the echo time, Stejskal-Tanner diffusion encoding with a single-shot spiral readout was implemented. To allow non-Cartesian image reconstruction using such strong and fast gradients, the characterization of eddy current and concomitant field effects was performed based on field-camera measurements. Results: An echo time of only 19 ms was achieved for a b-factor of 1000 s/mm2 . An in-plane resolution of 0.68 mm was encoded by a single-shot spiral readout of 40.5 ms using 3-fold undersampling. The resulting images did not suffer from off-resonance artifacts and T∗2 blurring that are common to single-shot images acquired with regular gradient systems. Conclusion: Spiral diffusion imaging using a head gradient system, together with an accurate characterization of the encoding process allows for a substantial reduction of the echo time, and improves the achievable resolution in motion-insensitive single-shot DWI

Advances in spiral fMRI: A high-resolution study with single-shot acquisition

Spiral fMRI has been put forward as a viable alternative to rectilinear echo-planar imaging, in particular due to its enhanced average k-space speed and thus high acquisition efficiency. This renders spirals attractive for contemporary fMRI applications that require high spatiotemporal resolution, such as laminar or columnar fMRI. However, in practice, spiral fMRI is typically hampered by its reduced robustness and ensuing blurring artifacts, which arise from imperfections in both static and dynamic magnetic fields. Recently, these limitations have been overcome by the concerted application of an expanded signal model that accounts for such field imperfections, and its inversion by iterative image reconstruction. In the challenging ultra-high field environment of 7 Tesla, where field inhomogeneity effects are aggravated, both multi-shot and single-shot 2D spiral imaging at sub-millimeter resolution was demonstrated with high depiction quality and anatomical congruency. In this work, we further these advances towards a time series application of spiral readouts, namely, single-shot spiral BOLD fMRI at 0.8 mm in-plane resolution. We demonstrate that high-resolution spiral fMRI at 7 T is not only feasible, but delivers both excellent image quality, BOLD sensitivity, and spatial specificity of the activation maps, with little artifactual blurring. Furthermore, we show the versatility of the approach with a combined in/out spiral readout at a more typical resolution (1.5 mm), where the high acquisition efficiency allows to acquire two images per shot for improved sensitivity by echo combination.ISSN:1053-8119ISSN:1095-957

Advances in spiral fMRI: A high-resolution dataset

We present data collected for the research article “Advances in Spiral fMRI: A High-resolution Study with Single-shot Acquisition” (Kasper et al. 2022). All data was acquired on a 7T ultra-high field MR system (Philips Achieva), equipped with a concurrent magnetic field monitoring setup based on 16 NMR probes. For task-based fMRI, a visual quarterfield stimulation paradigm was employed, alongside physiological monitoring via peripheral recordings. This data collection contains different datasets pertaining to different purposes: (1) Measured magnetic field dynamics (k0, spiral k-space trajectories, 2nd order spherical harmonics, concomitant fields) during ultra-high field fMRI sessions from six subjects, as well as concurrent temperature curves of the gradient coil, to explore MR system and subject-induced variability of field fluctuations and assess the impact of potential correction methods. (2) MR Raw Data, i.e., coil and concurrent encoding magnetic field (trajectory) data, of a single subject, as well as nominal spiral gradient waveforms, precomputed B0 and coil sensitivity maps, to enable testing of alternative image reconstruction approaches for spiral fMRI data. (3) Reconstructed image time series of the same subject alongside behavioral and physiological logfiles, to reproduce the fMRI preprocessing and analysis, as well as figures presented in the research article related to this article, using the published analysis code repository. All data is provided in standardized formats for the respective research area. In particular, ISMRMRD (HDF5) is used to store raw coil data and spiral trajectories, as well as measured field dynamics. Likewise, the NIfTI format is used for all imaging data (anatomical MRI and spiral fMRI, B0 and coil sensitivity maps).ISSN:2352-340

A high-performance gradient insert for rapid and short-T2 imaging at full duty cycle

Purpose The goal of this study was to devise a gradient system for MRI in humans that reconciles cutting‐edge gradient strength with rapid switching and brings up the duty cycle to 100% at full continuous amplitude. Aiming to advance neuroimaging and short‐T2 techniques, the hardware design focused on the head and the extremities as target anatomies. Methods A boundary element method with minimization of power dissipation and stored magnetic energy was used to design anatomy‐targeted gradient coils with maximally relaxed geometry constraints. The design relies on hollow conductors for high‐performance cooling and split coils to enable dual‐mode gradient amplifier operation. With this approach, strength and slew rate specifications of either 100 mT/m with 1200 mT/m/ms or 200 mT/m with 600 mT/m/ms were reached at 100% duty cycle, assuming a standard gradient amplifier and cooling unit. Results After manufacturing, the specified values for maximum gradient strength, maximum switching rate, and field geometry were verified experimentally. In temperature measurements, maximum local values of 63°C were observed, confirming that the device can be operated continuously at full amplitude. Testing for peripheral nerve stimulation showed nearly unrestricted applicability in humans at full gradient performance. In measurements of acoustic noise, a maximum average sound pressure level of 132 dB(A) was determined. In vivo capability was demonstrated by head and knee imaging. Full gradient performance was employed with echo planar and zero echo time readouts. Conclusion Combining extreme gradient strength and switching speed without duty cycle limitations, the described system offers unprecedented options for rapid and short‐T2 imaging. Magn Reson Med 79:3256–3266, 2018. © 2017 International Society for Magnetic Resonance in Medicine