Is your system calibrated? MRI gradient system calibration for pre-clinical, high-resolution imaging

Deep learning-based automated kidney and cyst segmentation of autosomal dominant polycystic kidney disease using single vs. multi-institutional data

PURPOSE

This study aimed to investigate if a deep learning model trained with a single institution's data has comparable accuracy to that trained with multi-institutional data for segmenting kidney and cyst regions in magnetic resonance (MR) images of patients affected by autosomal dominant polycystic kidney disease (ADPKD).

METHODS

We used TensorFlow with a Keras custom UNet on 2D slices of 756 MRI images of kidneys with ADPKD obtained from four institutions in the Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP) study. The ground truth was determined via a manual plus global thresholding method. Five models were trained with 80 % of all institutional data (n = 604) and each institutional data (n = 232, 172, 148, or 52), respectively, and validated with 10 % and tested on an unseen 10 % of the data. The model's performance was evaluated using the Dice Similarity Coefficient (DSC).

RESULTS

The DSCs by the model trained with all institutional data ranged from 0.92 to 0.95 for kidney image segmentation, only 1-2 % higher than those by the models trained with single institutional data (0.90-0.93).In cyst segmentation, however, the DSCs by the model trained with all institutional data ranged from 0.83 to 0.89, which were 2-20 % higher than those by the models trained with single institutional data (0.66-0.86).

CONCLUSION

The UNet performance, when trained with a single institutional dataset, exhibited similar accuracy to the model trained on a multi-institutional dataset. Segmentation accuracy increases with models trained on larger sample sizes, especially in more complex cyst segmentation.

A Practical Quality Assurance Procedure for Data Acquisitions in Preclinical Simultaneous PET/MR Systems

The availability of preclinical simultaneous PET/MR imaging systems has been increasing in recent years. Therefore, this technique is progressively moving from the hands of pure physicists towards those of scientists more involved in pharmacology and biology. Unfortunately, these combined scanners can be prone to artefacts and deviation of their characteristics under the influence of external factors or mutual interference between subsystems. This may compromise the image quality as well as the quantitative aspects of PET and MR data. Hence, quality assurance is crucial to avoid loss of animals and experiments. A possible risk to the acceptance of quality control by preclinical teams is that the complexity and duration of this quality control are increased by the addition of MR and PET tests. To avoid this issue, we have selected over the past 5 years, simple tests that can be easily and quickly performed each day before starting an animal PET/MR acquisition. These tests can be performed by the person in charge of the experiment even if this person has a limited expertise in instrumentation and performance evaluation. In addition to these daily tests, other tests are suggested for an advanced system follow-up at a lower frequency. In the present paper, the proposed tests are sorted by periodicity from daily to annual. Besides, we have selected test materials that are available at moderate cost either commercially or through 3D printing.

Standardization of Small Animal Imaging-Current Status and Future Prospects

The benefit of small animal imaging is directly linked to the validity and reliability of the collected data. If the data (regardless of the modality used) are not reproducible and/or reliable, then the outcome of the data is rather questionable. Therefore, standardization of the use of small animal imaging equipment, as well as of animal handling in general, is of paramount importance. In a recent paper, guidance for efficient small animal imaging quality control was offered and discussed, among others, the use of phantoms in setting up a quality control program (Osborne et al. 2016). The same phantoms can be used to standardize image quality parameters for multi-center studies or multi-scanners within center studies. In animal experiments, the additional complexity due to animal handling needs to be addressed to ensure standardized imaging procedures. In this review, we will address the current status of standardization in preclinical imaging, as well as potential benefits from increased levels of standardization.

Study the Longitudinal in vivo and Cross-Sectional ex vivo Brain Volume Difference for Disease Progression and Treatment Effect on Mouse Model of Tauopathy Using Automated MRI Structural Parcellation

Brain volume measurements extracted from structural MRI data sets are a widely accepted neuroimaging biomarker to study mouse models of neurodegeneration. Whether to acquire and analyze data in vivo or ex vivo is a crucial decision during the phase of experimental designs, as well as data analysis. In this work, we extracted the brain structures for both longitudinal in vivo and single-time-point ex vivo MRI acquired from the same animals using accurate automatic multi-atlas structural parcellation, and compared the corresponding statistical and classification analysis. We found that most gray matter structures volumes decrease from in vivo to ex vivo, while most white matter structures volume increase. The level of structural volume change also varies between different genetic strains and treatment. In addition, we showed superior statistical and classification power of ex vivo data compared to the in vivo data, even after resampled to the same level of resolution. We further demonstrated that the classification power of the in vivo data can be improved by incorporating longitudinal information, which is not possible for ex vivo data. In conclusion, this paper demonstrates the tissue-specific changes, as well as the difference in statistical and classification power, between the volumetric analysis based on the in vivo and ex vivo structural MRI data. Our results emphasize the importance of longitudinal analysis for in vivo data analysis.

Optic nerve thinning and neurosensory retinal degeneration in the rTg4510 mouse model of frontotemporal dementia

Visual impairments, such as difficulties in reading and finding objects, perceiving depth and structure from motion, and impaired stereopsis, have been reported in tauopathy disorders, such as frontotemporal dementia (FTD). These impairments however have been previously attributed to cortical pathologies rather than changes in the neurosensory retina or the optic nerve. Here, we examined tau pathology in the neurosensory retina of the rTg(tauP301L)4510 mouse model of FTD. Optic nerve pathology in mice was also assessed using MRI, and corresponding measurements taken in a cohort of five FTD sufferers and five healthy controls. rTg(tauP301L)4510 mice were imaged (T2-weighted MRI) prior to being terminally anesthetized and eyes and brains removed for immunohistochemical and histological analysis. Central and peripheral retinal labelling of tau and phosphorylated tau (pTau) was quantified and retinal layer thicknesses and cell numbers assessed. MR volumetric changes of specific brain regions and the optic nerve were compared to tau accumulation and cell loss in the visual pathway. In addition, the optic nerves of a cohort of healthy controls and behavioural variant FTD patients, were segmented from T1- and T2-weighted images for volumetric study. Accumulation of tau and pTau were observed in both the central and peripheral retinal ganglion cell (RGC), inner plexiform and inner nuclear layers of the neurosensory retina of rTg(tauP301L)4510 mice. This pathology was associated with reduced nuclear density (− 24.9 ± 3.4%) of the central RGC layer, and a reduced volume (− 19.3 ± 4.6%) and elevated T2 signal (+ 27.1 ± 1.8%) in the optic nerve of the transgenic mice. Significant atrophy of the cortex (containing the visual cortex) was observed but not in other area associated with visual processing, e.g. the lateral geniculate nucleus or superior colliculus. Atrophic changes in optic nerve volume were similarly observed in FTD patients (− 36.6 ± 2.6%). The association between tau-induced changes in the neurosensory retina and reduced optic nerve volume in mice, combined with the observation of optic nerve atrophy in clinical FTD suggests that ophthalmic tau pathology may also exist in the eyes of FTD patients. If tau pathology and neurodegeneration in the retina were to reflect the degree of cortical tau burden, then cost-effective and non-invasive imaging of the neurosensory retina could provide valuable biomarkers in tauopathy. Further work should aim to validate whether these observations are fully translatable to a clinical scenario, which would recommend follow-up retinal and optic nerve examination in FTD.

Characterizing geometrical accuracy in clinically optimised 7T and 3T magnetic resonance images for high-precision radiation treatment of brain tumours

Background and purpose

In neuro-oncology, high spatial accuracy is needed for clinically acceptable high-precision radiation treatment planning (RTP). In this study, the clinical applicability of anatomically optimised 7-Tesla (7T) MR images for reliable RTP is assessed with respect to standard clinical imaging modalities.

Materials and methods

System- and phantom-related geometrical distortion (GD) were quantified on clinically-relevant MR sequences at 7T and 3T, and on CT images using a dedicated anthropomorphic head phantom incorporating a 3D grid-structure, creating 436 points-of-interest. Global GD was assessed by mean absolute deviation (MAD_Global). Local GD relative to the magnetic isocentre was assessed by MAD_Local. Using 3D displacement vectors of individual points-of-interest, GD maps were created. For clinically acceptable radiotherapy, 7T images need to meet the criteria for accurate dose delivery (GD < 1 mm) and present comparable GD as tolerated in clinically standard 3T MR/CT-based RTP.

Results

MAD_Global in 7T and 3T images ranged from 0.3 to 2.2 mm and 0.2-0.8 mm, respectively. MAD_Local increased with increasing distance from the isocentre, showed an anisotropic distribution, and was significantly larger in 7T MR sequences (MAD_Local = 0.2-1.2 mm) than in 3T (MAD_Local = 0.1-0.7 mm) (p < 0.05). Significant differences in GD were detected between 7T images (p < 0.001). However, maximum MAD_Local remained ≤1 mm within 68.7 mm diameter spherical volume. No significant differences in GD were found between 7T and 3T protocols near the isocentre.

Conclusions

System- and phantom-related GD remained ≤1 mm in central brain regions, suggesting that 7T MR images could be implemented in radiotherapy with clinically acceptable spatial accuracy and equally tolerated GD as in 3T MR/CT-based RTP. For peripheral regions, GD should be incorporated in safety margins for treatment uncertainties. Moreover, the effects of sequence-related factors on GD needs further investigation to obtain RTP-specific MR protocols.

Non-invasive imaging of CSF-mediated brain clearance pathways via assessment of perivascular fluid movement with diffusion tensor MRI

The glymphatics system describes a CSF-mediated clearance pathway for the removal of potentially harmful molecules, such as amyloid beta, from the brain. As such, its components may represent new therapeutic targets to alleviate aberrant protein accumulation that defines the most prevalent neurodegenerative conditions. Currently, however, the absence of any non-invasive measurement technique prohibits detailed understanding of glymphatic function in the human brain and in turn, it’s role in pathology. Here, we present the first non-invasive technique for the assessment of glymphatic inflow by using an ultra-long echo time, low b-value, multi-direction diffusion weighted MRI sequence to assess perivascular fluid movement (which represents a critical component of the glymphatic pathway) in the rat brain. This novel, quantitative and non-invasive approach may represent a valuable biomarker of CSF-mediated brain clearance, working towards the clinical need for reliable and early diagnostic indicators of neurodegenerative conditions such as Alzheimer’s disease.

Our brain is bathed in cerebrospinal fluid, a clear liquid that ‘cushions’ the fragile organ. This liquid travels into the brain along special channels – the perivascular space – that surround certain blood vessels. As the fluid washes in and out of the brain, it takes with it potentially harmful molecules, such as the aggregates that build up to cause Alzheimer’s disease. If this brain-cleaning system becomes faulty, it could lead to neurodegenerative diseases. However, it is extremely difficult to measure the activity of this intricate and delicate system, and most studies so far have had to use invasive techniques that usually require brain surgery.

Now, Harrison et al. adapt a technique, called diffusion tensor magnetic resonance imaging (MRI), to visualise how the cerebrospinal fluid moves in the perivascular space in healthy rats. The non-invasive MRI method captures how the cerebrospinal fluid is driven into the brain when the blood vessels nearby expand and contract; as the vessels pulsate with each heartbeat, there is a 300% increase in the movement of the fluid in the perivascular space.

This approach could be applied to understand exactly how neurodegenerative diseases emerge when the cerebrospinal fluid stops to properly clean the brain. Ultimately, the method could be used to detect when the cleansing system starts to fail in people, which could help to treat patients before their brains accumulate too many harmful substances.

Diffusion tensor imaging using multiple coils for mouse brain connectomics

The correlation between brain connectivity and psychiatric or neurological diseases has intensified efforts to develop brain connectivity mapping techniques on mouse models of human disease. The neural architecture of mouse brain specimens can be shown non-destructively and three-dimensionally by diffusion tensor imaging, which enables tractography, the establishment of a connectivity matrix and connectomics. However, experiments on cohorts of animals can be prohibitively long. To improve throughput in a 7-T preclinical scanner, we present a novel two-coil system in which each coil is shielded, placed off-isocenter along the axis of the magnet and connected to a receiver circuit of the scanner. Preservation of the quality factor of each coil is essential to signal-to-noise ratio (SNR) performance and throughput, because mouse brain specimen imaging at 7 T takes place in the coil-dominated noise regime. In that regime, we show a shielding configuration causing no SNR degradation in the two-coil system. To acquire data from several coils simultaneously, the coils are placed in the magnet bore, around the isocenter, in which gradient field distortions can bias diffusion tensor imaging metrics, affect tractography and contaminate measurements of the connectivity matrix. We quantified the experimental alterations in fractional anisotropy and eigenvector direction occurring in each coil. We showed that, when the coils were placed 12 mm away from the isocenter, measurements of the brain connectivity matrix appeared to be minimally altered by gradient field distortions. Simultaneous measurements on two mouse brain specimens demonstrated a full doubling of the diffusion tensor imaging throughput in practice. Each coil produced images devoid of shading or artifact. To further improve the throughput of mouse brain connectomics, we suggested a future expansion of the system to four coils. To better understand acceptable trade-offs between imaging throughput and connectivity matrix integrity, studies may seek to clarify how measurement variability, post-processing techniques and biological variability impact mouse brain connectomics.

MR-CBCT image-guided system for radiotherapy of orthotopic rat prostate tumors

Multi-modality image-guided radiotherapy is the standard of care in contemporary cancer management; however, it is not common in preclinical settings due to both hardware and software limitations. Soft tissue lesions, such as orthotopic prostate tumors, are difficult to identify using cone beam computed tomography (CBCT) imaging alone. In this study, we characterized a research magnetic resonance (MR) scanner for preclinical studies and created a protocol for combined MR-CBCT image-guided small animal radiotherapy. Two in-house dual-modality, MR and CBCT compatible, phantoms were designed and manufactured using 3D printing technology. The phantoms were used for quality assurance tests and to facilitate end-to-end testing for combined preclinical MR and CBCT based treatment planning. MR and CBCT images of the phantoms were acquired utilizing a Varian 4.7 T scanner and XRad-225Cx irradiator, respectively. The geometry distortion was assessed by comparing MR images to phantom blueprints and CBCT. The corrected MR scans were co-registered with CBCT and subsequently used for treatment planning. The fidelity of 3D printed phantoms compared to the blueprint design yielded favorable agreement as verified with the CBCT measurements. The geometric distortion, which varied between -5% and 11% throughout the scanning volume, was substantially reduced to within 0.4% after correction. The distortion free MR images were co-registered with the corresponding CBCT images and imported into a commercial treatment planning software SmART Plan. The planning target volume (PTV) was on average 19% smaller when contoured on the corrected MR-CBCT images relative to raw images without distortion correction. An MR-CBCT based preclinical workflow was successfully designed and implemented for small animal radiotherapy. Combined MR-CBCT image-guided radiotherapy for preclinical research potentially delivers enhanced relevance to human radiotherapy for various disease sites. This novel protocol is wide-ranging and not limited to the orthotopic prostate tumor study presented in the study.

ESTRO ACROP: Technology for precision small animal radiotherapy research: Optimal use and challenges

Many radiotherapy research centers have recently installed novel research platforms enabling the investigation of the radiation response of tumors and normal tissues in small animal models, possibly in combination with other treatment modalities. Many more research institutes are expected to follow in the coming years. These novel platforms are capable of mimicking human radiotherapy more closely than older technology. To facilitate the optimal use of these novel integrated precision irradiators and various small animal imaging devices, and to maximize the impact of the associated research, the ESTRO committee on coordinating guidelines ACROP (Advisory Committee in Radiation Oncology Practice) has commissioned a report to review the state of the art of the technology used in this new field of research, and to issue recommendations. This report discusses the combination of precision irradiation systems, small animal imaging (CT, MRI, PET, SPECT, bioluminescence) systems, image registration, treatment planning, and data processing. It also provides guidelines for reporting on studies.

An open source, 3D printed preclinical MRI phantom for repeated measures of contrast agents and reference standards

In medical imaging, clinicians, researchers and technicians have begun to use 3D printing to create specialized phantoms to replace commercial ones due to their customizable and iterative nature. Presented here is the design of a 3D printed open source, reusable magnetic resonance imaging (MRI) phantom, capable of flood-filling, with removable samples for measurements of contrast agent solutions and reference standards, and for use in evaluating acquisition techniques and image reconstruction performance. The phantom was designed using SolidWorks, a computer-aided design software package. The phantom consists of custom and off-the-shelf parts and incorporates an air hole and Luer Lock system to aid in flood filling, a marker for orientation of samples in the filled mode and bolt and tube holes for assembly. The cost of construction for all materials is under $90. All design files are open-source and available for download. To demonstrate utility, B₀ field mapping was performed using a series of gadolinium concentrations in both the unfilled and flood-filled mode. An excellent linear agreement (R²>0.998) was observed between measured relaxation rates (R₁/R₂) and gadolinium concentration. The phantom provides a reliable setup to test data acquisition and reconstruction methods and verify physical alignment in alternative nuclei MRI techniques (e.g. carbon-13 and fluorine-19 MRI). A cost-effective, open-source MRI phantom design for repeated quantitative measurement of contrast agents and reference standards in preclinical research is presented. Specifically, the work is an example of how the emerging technology of 3D printing improves flexibility and access for custom phantom design.

Portable perfusion phantom for quantitative DCE-MRI of the abdomen

PURPOSE

The aim of this study was to develop a portable perfusion phantom and validate its utility in quantitative dynamic contrast-enhanced magnetic resonance imaging of the abdomen.

METHODS

A portable perfusion phantom yielding a reproducible contrast enhancement curve (CEC) was developed. A phantom package including perfusion and static phantoms were imaged simultaneously with each of three healthy human volunteers in two different 3T MR scanners. Look-up tables correlating reference (known) contrast concentrations with measured ones were created using either the static or perfusion phantom. Contrast maps of image slices showing four organs (liver, spleen, pancreas, and paravertebral muscle) were generated before and after data correction using the look-up tables. The contrast concentrations at 4.5 min after dosing in each of the four organs were averaged for each volunteer. The mean contrast concentrations (4 organs × 3 volunteers = 12) were compared for the two scanners, and the intra-class correlation coefficient (ICC) was calculated. Also, the ICC of the mean K^trans values between the two scanners was calculated before and after data correction.

RESULTS

The repeatability coefficient of CECs of perfusion phantom was higher than 0.997 in all measurements. The ICC of the tissue contrast concentrations between the two scanners was 0.693 before correction, but increased to 0.974 after correction using the look-up tables (LUTs) of perfusion phantom. However, the ICC was not increased after correction using static phantom (ICC: 0.617). Similarly, the ICC of the K^trans values was 0.899 before correction, but increased to 0.996 after correction using perfusion phantom LUTs. The ICC of the K^trans values, however, was not increased when static phantom LUTs were used (ICC: 0.866).

CONCLUSIONS

The perfusion phantom reduced variability in quantitating contrast concentration and K^trans values of human abdominal tissues across different MR units, but static phantom did not. The perfusion phantom has the potential to facilitate multi-institutional clinical trials employing quantitative DCE-MRI to evaluate various abdominal malignancies.

Comparison of In Vivo and Ex Vivo MRI for the Detection of Structural Abnormalities in a Mouse Model of Tauopathy

With increasingly large numbers of mouse models of human disease dedicated to MRI studies, compromises between in vivo and ex vivo MRI must be fully understood in order to inform the choice of imaging methodology. We investigate the application of high resolution in vivo and ex vivo MRI, in combination with tensor-based morphometry (TBM), to uncover morphological differences in the rTg4510 mouse model of tauopathy. The rTg4510 mouse also offers a novel paradigm by which the overexpression of mutant tau can be regulated by the administration of doxycycline, providing us with a platform on which to investigate more subtle alterations in morphology with morphometry. Both in vivo and ex vivo MRI allowed the detection of widespread bilateral patterns of atrophy in the rTg4510 mouse brain relative to wild-type controls. Regions of volume loss aligned with neuronal loss and pathological tau accumulation demonstrated by immunohistochemistry. When we sought to investigate more subtle structural alterations in the rTg4510 mice relative to a subset of doxycycline-treated rTg4510 mice, ex vivo imaging enabled the detection of more regions of morphological brain changes. The disadvantages of ex vivo MRI may however mitigate this increase in sensitivity: we observed a 10% global shrinkage in brain volume of the post-mortem tissues due to formalin fixation, which was most notable in the cerebellum and olfactory bulbs. However, many central brain regions were not adversely affected by the fixation protocol, perhaps due to our “in-skull” preparation. The disparity between our TBM findings from in vivo and ex vivo MRI underlines the importance of appropriate study design, given the trade-off between these two imaging approaches. We support the utility of in vivo MRI for morphological phenotyping of mouse models of disease; however, for subtler phenotypes, ex vivo offers enhanced sensitivity to discrete morphological changes.

Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome

We describe a fully automated pipeline for the morphometric phenotyping of mouse brains from μMRI data, and show its application to the Tc1 mouse model of Down syndrome, to identify new morphological phenotypes in the brain of this first transchromosomic animal carrying human chromosome 21. We incorporate an accessible approach for simultaneously scanning multiple ex vivo brains, requiring only a 3D-printed brain holder, and novel image processing steps for their separation and orientation. We employ clinically established multi-atlas techniques–superior to single-atlas methods–together with publicly-available atlas databases for automatic skull-stripping and tissue segmentation, providing high-quality, subject-specific tissue maps. We follow these steps with group-wise registration, structural parcellation and both Voxel- and Tensor-Based Morphometry–advantageous for their ability to highlight morphological differences without the laborious delineation of regions of interest. We show the application of freely available open-source software developed for clinical MRI analysis to mouse brain data: NiftySeg for segmentation and NiftyReg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. We used this pipeline to compare 29 Tc1 brains with 26 wild-type littermate controls, imaged ex vivo at 9.4T. We show an unexpected increase in Tc1 total intracranial volume and, controlling for this, local volume and grey matter density reductions in the Tc1 brain compared to the wild-types, most prominently in the cerebellum, in agreement with human DS and previous histological findings.

Multicenter Evaluation of Geometric Accuracy of MRI Protocols Used in Experimental Stroke

It has recently been suggested that multicenter preclinical stroke studies should be carried out to improve translation from bench to bedside, but the accuracy of magnetic resonance imaging (MRI) scanners routinely used in experimental stroke has not yet been evaluated. We aimed to assess and compare geometric accuracy of preclinical scanners and examine the longitudinal stability of one scanner using a simple quality assurance (QA) protocol. Six 7 Tesla animal scanners across six different preclinical imaging centers throughout Europe were used to scan a small structural phantom and estimate linear scaling errors in all orthogonal directions and volumetric errors. Between-scanner imaging consisted of a standard sequence and each center's preferred sequence for the assessment of infarct size in rat models of stroke. The standard sequence was also used to evaluate the drift in accuracy of the worst performing scanner over a period of six months following basic gradient calibration. Scaling and volumetric errors using the standard sequence were less variable than corresponding errors using different stroke sequences. The errors for one scanner, estimated using the standard sequence, were very high (above 4% scaling errors for each orthogonal direction, 18.73% volumetric error). Calibration of the gradient coils in this system reduced scaling errors to within ±1.0%; these remained stable during the subsequent 6-month assessment. In conclusion, despite decades of use in experimental studies, preclinical MRI still suffers from poor and variable geometric accuracy, influenced by the use of miscalibrated systems and various types of sequences for the same purpose. For effective pooling of data in multicenter studies, centers should adopt standardized procedures for system QA and in vivo imaging.

The effect of using components from different manufacturers on the rate of wear and corrosion of the head–stem taper junction of metal-on-metal hip arthroplasties

Aims

Surgeons have commonly used modular femoral heads and stems from different manufacturers, although this is not recommended by orthopaedic companies due to the different manufacturing processes. We compared the rate of corrosion and rate of wear at the trunnion/head taper junction in two groups of retrieved hips; those with mixed manufacturers (MM) and those from the same manufacturer (SM).

Materials and Methods

We identified 151 retrieved hips with large-diameter cobalt-chromium heads; 51 of two designs that had been paired with stems from different manufacturers (MM) and 100 of seven designs paired with stems from the same manufacturer (SM). We determined the severity of corrosion with the Goldberg corrosion score and the volume of material loss at the head/stem junction. We used multivariable statistical analysis to determine if there was a significant difference between the two groups.

Results

We found no significant difference in the corrosion scores of the two groups. The median rate of material loss at the head/stem junction for the MM and SM groups were 0.39 mm3/year (0.00 to 4.73) and 0.46 mm3/year (0.00 to 6.71) respectively; this difference was not significant after controlling for confounding factors (p = 0.06).

Conclusion

The use of stems with heads of another manufacturer does not appear to affect the amount of metal lost from the surfaces between these two components at total hip arthroplasty. Other surgical, implant and patient factors should be considered when determining the mechanisms of failure of large diameter metal-on-metal hip arthroplasties. Cite this article: Bone Joint J 2016;98-B:917–24.

Imaging the accumulation and suppression of tau pathology using multiparametric MRI

Mouse models of Alzheimer's disease have served as valuable tools for investigating pathogenic mechanisms relating to neurodegeneration, including tau-mediated and neurofibrillary tangle pathology-a major hallmark of the disease. In this work, we have used multiparametric magnetic resonance imaging (MRI) in a longitudinal study of neurodegeneration in the rTg4510 mouse model of tauopathy, a subset of which were treated with doxycycline at different time points to suppress the tau transgene. Using this paradigm, we investigated the sensitivity of multiparametric MRI to both the accumulation and suppression of pathologic tau. Tau-related atrophy was discernible from 5.5 months within the cortex and hippocampus. We observed markedly less atrophy in the treated rTg4510 mice, which was enhanced after doxycycline intervention from 3.5 months. We also observed differences in amide proton transfer, cerebral blood flow, and diffusion tensor imaging parameters in the rTg4510 mice, which were significantly less altered after doxycycline treatment. We propose that these non-invasive MRI techniques offer insight into pathologic mechanisms underpinning Alzheimer's disease that may be important when evaluating emerging therapeutics targeting one of more of these processes.

Efficient gradient calibration based on diffusion MRI

Purpose

To propose a method for calibrating gradient systems and correcting gradient nonlinearities based on diffusion MRI measurements.

Methods

The gradient scaling in x, y, and z were first offset by up to 5% from precalibrated values to simulate a poorly calibrated system. Diffusion MRI data were acquired in a phantom filled with cyclooctane, and corrections for gradient scaling errors and nonlinearity were determined. The calibration was assessed with diffusion tensor imaging and independently validated with high resolution anatomical MRI of a second structured phantom.

Results

The errors in apparent diffusion coefficients along orthogonal axes ranged from −9.2% ± 0.4% to + 8.8% ± 0.7% before calibration and −0.5% ± 0.4% to + 0.8% ± 0.3% after calibration. Concurrently, fractional anisotropy decreased from 0.14 ± 0.03 to 0.03 ± 0.01. Errors in geometric measurements in x, y and z ranged from −5.5% to + 4.5% precalibration and were likewise reduced to −0.97% to + 0.23% postcalibration. Image distortions from gradient nonlinearity were markedly reduced.

Conclusion

Periodic gradient calibration is an integral part of quality assurance in MRI. The proposed approach is both accurate and efficient, can be setup with readily available materials, and improves accuracy in both anatomical and diffusion MRI to within ±1%. Magn Reson Med 77:170–179, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Correction of MRI-induced geometric distortions in whole-body small animal PET-MRI

PURPOSE

The fusion of positron emission tomography (PET) and magnetic resonance imaging (MRI) data can be a challenging task in whole-body PET-MRI. The quality of the registration between these two modalities in large field-of-views (FOV) is often degraded by geometric distortions of the MRI data. The distortions at the edges of large FOVs mainly originate from MRI gradient nonlinearities. This work describes a method to measure and correct for these kind of geometric distortions in small animal MRI scanners to improve the registration accuracy of PET and MRI data.

METHODS

The authors have developed a geometric phantom which allows the measurement of geometric distortions in all spatial axes via control points. These control points are detected semiautomatically in both PET and MRI data with a subpixel accuracy. The spatial transformation between PET and MRI data is determined with these control points via 3D thin-plate splines (3D TPS). The transformation derived from the 3D TPS is finally applied to real MRI mouse data, which were acquired with the same scan parameters used in the phantom data acquisitions. Additionally, the influence of the phantom material on the homogeneity of the magnetic field is determined via field mapping.

RESULTS

The spatial shift according to the magnetic field homogeneity caused by the phantom material was determined to a mean of 0.1 mm. The results of the correction show that distortion with a maximum error of 4 mm could be reduced to less than 1 mm with the proposed correction method. Furthermore, the control point-based registration of PET and MRI data showed improved congruence after correction.

CONCLUSIONS

The developed phantom has been shown to have no considerable negative effect on the homogeneity of the magnetic field. The proposed method yields an appropriate correction of the measured MRI distortion and is able to improve the PET and MRI registration. Furthermore, the method is applicable to whole-body small animal imaging routines including different standard MRI sequences.

On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images

X-ray microcomputed tomography (μCT) allows nondestructive visualisation of plant root systems within their soil environment and thus offers an alternative to the commonly used destructive methodologies for the examination of plant roots and their interaction with the surrounding soil. Various methods for the recovery of root system information from X-ray computed tomography (CT) image data have been presented in the literature. Detailed, ideally quantitative, evaluation is essential, in order to determine the accuracy and limitations of the proposed methods, and to allow potential users to make informed choices among them. This, however, is a complicated task. Three-dimensional ground truth data are expensive to produce and the complexity of X-ray CT data means that manually generated ground truth may not be definitive. Similarly, artificially generated data are not entirely representative of real samples. The aims of this work are to raise awareness of the evaluation problem and to propose experimental approaches that allow the performance of root extraction methods to be assessed, ultimately improving the techniques available. To illustrate the issues, tests are conducted using both artificially generated images and real data samples.

3D-printed Shepp-Logan phantom as a real-world benchmark for MRI

PURPOSE

As prescribed and reliable geometrical entities, phantoms have served as indispensable validation tools in a variety of MR-related topics. Though a number of phantoms have been conceived, certain applications may warrant highly customized geometries. The purpose of this study was to demonstrate the expediency of rapid prototyping for generating a flexible class of MR-compatible phantom designs.

METHODS

An incarnation of the three-dimensional Shepp-Logan numerical phantom, amended for use in magnetic resonance spectroscopic imaging, was actualized using rapid prototyping. Each of the comprising compartments was filled with a solution containing prepared concentrations of common (1)H brain metabolites. Analytical Fourier expressions for the phantom class were established in order to generate a set of simulated measurements, which were then contrasted with acquired data.

RESULTS

Experimental results for both structural and spectroscopic imaging substantiate the suitability of rapid prototyping for MR phantom applications. The analytically simulated measurements show excellent agreement with the measured data, but also highlight the various consequences effectuated when certain aspects of the acquisition model are disregarded or misrepresented.

CONCLUSION

Rapid prototyping offers a novel and versatile framework for MR phantom-based validation studies. Furthermore, the growing accessibility and open-source compatibility may provide an important link between the often disparate numerical and haptic testing.