All Publications

  • Extended hybrid-space SENSE for EPI: Off-resonance and eddy current corrected joint interleaved blip-up/down reconstruction. NeuroImage Zahneisen, B., Aksoy, M., Maclaren, J., Wuerslin, C., Bammer, R. 2017; 153: 97-108


    Geometric distortions along the phase encode direction caused by off-resonant spins are still a major issue in EPI based functional and diffusion imaging. If the off-resonance map is known it is possible to correct for distortions. Most correction methods operate as a post-processing step on the reconstructed magnitude images.Here, we present an algebraic reconstruction method (hybrid-space SENSE) that incorporates a physics based model of off-resonances, phase inconsistencies between k-space segments, and T2*-decay during the acquisition. The method can be used to perform a joint reconstruction of interleaved acquisitions with normal (blip-up) and inverted (blip-down) phase encode direction which results in reduced g-factor penalty.A joint blip-up/down simultaneous multi slice (SMS) reconstruction for SMS-factor 4 in combination with twofold in-plane acceleration leads to a factor of two decrease in maximum g-factor penalty while providing off-resonance and eddy-current corrected images.We provide an algebraic framework for reconstructing diffusion weighted EPI data that in addition to the general applicability of hybrid-space SENSE to 2D-EPI, SMS-EPI and 3D-EPI with arbitrary k-space coverage along z, allows for a modeling of arbitrary spatio-temporal effects during the acquisition period like off-resonances, phase inconsistencies and T2*-decay. The most immediate benefit is a reduction in g-factor penalty if an interleaved blip-up/down acquisition strategy is chosen which facilitates eddy current estimation and ensures no loss in k-space encoding in regions with strong off-resonance gradients.

    View details for DOI 10.1016/j.neuroimage.2017.03.052

    View details for PubMedID 28359788

  • Prospective motion correction for 3D pseudo-continuous arterial spin labeling using an external optical tracking system. Magnetic resonance imaging Aksoy, M., Maclaren, J., Bammer, R. 2017; 39: 44-52


    Head motion is an unsolved problem in magnetic resonance imaging (MRI) studies of the brain. Real-time tracking using a camera has recently been proposed as a way to prevent head motion artifacts. As compared to navigator-based approaches that use MRI data to detect and correct motion, optical motion correction works independently of the MRI scanner, thus providing low-latency real-time motion updates without requiring any modifications to the pulse sequence. The purpose of this study was two-fold: 1) to demonstrate that prospective optical motion correction using an optical camera mitigates artifacts from head motion in three-dimensional pseudo-continuous arterial spin labeling (3D PCASL) acquisitions and 2) to assess the effect of latency differences between real-time optical motion tracking and navigator-style approaches (such as PROMO). An optical motion correction system comprising a single camera and a marker attached to the patient's forehead was used to track motion at a rate of 60fps. In the presence of motion, continuous tracking data from the optical system was used to update the scan plane in real-time during the 3D-PCASL acquisition. Navigator-style correction was simulated by using the tracking data from the optical system and performing updates only once per repetition time. Three normal volunteers and a patient were instructed to perform continuous and discrete head motion throughout the scan. Optical motion correction yielded superior image quality compared to uncorrected images or images using navigator-style correction. The standard deviations of pixel-wise CBF differences between reference and non-corrected, navigator-style-corrected and optical-corrected data were 14.28, 14.35 and 11.09mL/100g/min for continuous motion, and 12.42, 12.04 and 9.60mL/100g/min for discrete motion. Data obtained from the patient revealed that motion can obscure pathology and that application of optical prospective correction can successfully reveal the underlying pathology in the presence of head motion.

    View details for DOI 10.1016/j.mri.2017.01.018

    View details for PubMedID 28137627

  • Trade-off between angular and spatial resolutions in in vivo fiber tractography. NeuroImage Vos, S. B., Aksoy, M., Han, Z., Holdsworth, S. J., Maclaren, J., Viergever, M. A., Leemans, A., Bammer, R. 2016; 129: 117-132


    Tractography is becoming an increasingly popular method to reconstruct white matter connections in vivo. The diffusion MRI data that tractography is based on requires a high angular resolution to resolve crossing fibers whereas high spatial resolution is required to distinguish kissing from crossing fibers. However, scan time increases with increasing spatial and angular resolutions, which can become infeasible in clinical settings. Here we investigated the trade-off between spatial and angular resolutions to determine which of these factors is most worth investing scan time in. We created a unique diffusion MRI dataset with 1.0mm isotropic resolution and a high angular resolution (100 directions) using an advanced 3D diffusion-weighted multi-slab EPI acquisition. This dataset was reconstructed to create subsets of lower angular (75, 50, and 25 directions) and lower spatial (1.5, 2.0, and 2.5mm) resolution. Using all subsets, we investigated the effects of angular and spatial resolutions in three fiber bundles-the corticospinal tract, arcuate fasciculus and corpus callosum-by analyzing the volumetric bundle overlap and anatomical correspondence between tracts. Our results indicate that the subsets of 25 and 50 directions provided inferior tract reconstructions compared with the datasets with 75 and 100 directions. Datasets with spatial resolutions of 1.0, 1.5, and 2.0mm were comparable, while the lowest resolution (2.5mm) datasets had discernible inferior quality. In conclusion, we found that angular resolution appeared to be more influential than spatial resolution in improving tractography results. Spatial resolutions higher than 2.0mm only appear to benefit multi-fiber tractography methods if this is not at the cost of decreased angular resolution.

    View details for DOI 10.1016/j.neuroimage.2016.01.011

    View details for PubMedID 26774615

  • Motion artifacts in MRI: A complex problem with many partial solutions. Journal of magnetic resonance imaging Zaitsev, M., Maclaren, J., Herbst, M. 2015; 42 (4): 887-901


    Subject motion during magnetic resonance imaging (MRI) has been problematic since its introduction as a clinical imaging modality. While sensitivity to particle motion or blood flow can be used to provide useful image contrast, bulk motion presents a considerable problem in the majority of clinical applications. It is one of the most frequent sources of artifacts. Over 30 years of research have produced numerous methods to mitigate or correct for motion artifacts, but no single method can be applied in all imaging situations. Instead, a "toolbox" of methods exists, where each tool is suitable for some tasks, but not for others. This article reviews the origins of motion artifacts and presents current mitigation and correction methods. In some imaging situations, the currently available motion correction tools are highly effective; in other cases, appropriate tools still need to be developed. It seems likely that this multifaceted approach will be what eventually solves the motion sensitivity problem in MRI, rather than a single solution that is effective in all situations. This review places a strong emphasis on explaining the physics behind the occurrence of such artifacts, with the aim of aiding artifact detection and mitigation in particular clinical situations. J. Magn. Reson. Imaging 2015;42:887-901.

    View details for DOI 10.1002/jmri.24850

    View details for PubMedID 25630632

  • Comparison of optical and MR-based tracking MAGNETIC RESONANCE IN MEDICINE Gumus, K., Keating, B., White, N., Andrews-Shigaki, B., Armstrong, B., Maclaren, J., Zaitsev, M., Dale, A., Ernst, T. 2015; 74 (3): 894-902

    View details for DOI 10.1002/mrm.25472

    View details for Web of Science ID 000360222900029

  • Comparison of optical and MR-based tracking. Magnetic resonance in medicine Gumus, K., Keating, B., White, N., Andrews-Shigaki, B., Armstrong, B., Maclaren, J., Zaitsev, M., Dale, A., Ernst, T. 2015; 74 (3): 894-902


    The goal of this study was to compare the accuracy of two real-time motion tracking systems in the MR environment: MR-based prospective motion correction (PROMO) and optical moiré phase tracking (MPT).Five subjects performed eight predefined head rotations of 8°?±?3° while being simultaneously tracked with PROMO and MPT. Structural images acquired immediately before and after each tracking experiment were realigned with SPM8 to provide a reference measurement.Mean signed errors (MSEs) in MPT tracking relative to SPM8 were less than 0.3 mm and 0.2° in all 6 degrees of freedom, and MSEs in PROMO tracking ranged up to 0.2 mm and 0.3°. MPT and PROMO significantly differed from SPM8 in y-translation and y-rotation values (P?

    View details for DOI 10.1002/mrm.25472

    View details for PubMedID 25257096

  • Contact-free physiological monitoring using a markerless optical system MAGNETIC RESONANCE IN MEDICINE Maclaren, J., Aksoy, M., Bammer, R. 2015; 74 (2): 571-577


    Physiological noise remains a major problem in MRI, particularly at higher imaging resolutions and field strengths. The aim of this work was to investigate the feasibility of using an MR-compatible in-bore camera system to perform contactless monitoring of cardiac and respiratory information during MRI of human subjects.An MR-compatible camera was mounted on an eight-channel head coil. Video data of the skin was processed offline to derive cardiac and respiratory signals from the pixel signal intensity and from head motion in the patient head-feet direction. These signals were then compared with data acquired simultaneously from the pulse oximeter and the respiratory belt.The cardiac signal computed using the average image pixel intensity closely resembled the signal obtained using the pulse oximeter. Trigger intervals obtained from both systems matched to within 50 ms (one standard deviation). The respiratory signal computed from small in-plane movements closely matched the signal obtained from the respiratory belt. Simultaneous MR imaging did not appear to have an effect on the physiological signals acquired by means of the contact-free monitoring system.Contact-free monitoring of human subjects to obtain cardiac and respiratory information is feasible using a small camera and light emitting diode mounted on the head coil of an MRI scanner. Magn Reson Med 74:571-577, 2015. © 2015 Wiley Periodicals, Inc.

    View details for DOI 10.1002/mrm.25781

    View details for Web of Science ID 000358607700034

  • Prevention of Motion-Induced Signal Loss in Diffusion-Weighted Echo-Planar Imaging by Dynamic Restoration of Gradient Moments MAGNETIC RESONANCE IN MEDICINE Gumus, K., Keating, B., Poser, B. A., Armstrong, B., Chang, L., Maclaren, J., Prieto, T., Speck, O., Zaitsev, M., Ernst, T. 2014; 71 (6): 2006-2013


    Head motion is a significant problem in diffusion-weighted imaging as it may cause signal attenuation due to residual dephasing during strong diffusion encoding gradients even in single-shot acquisitions. Here, we present a new real-time method to prevent motion-induced signal loss in DWI of the brain.The method requires a fast motion tracking system (optical in the current implementation). Two alterations were made to a standard diffusion-weighted echo-planar imaging sequence: first, real-time motion correction ensures that slices are correctly aligned relative to the moving brain. Second, the tracking data are used to calculate the motion-induced gradient moment imbalance which occurs during the diffusion encoding periods, and a brief gradient blip is inserted immediately prior to the signal readout to restore the gradient moment balance.Phantom experiments show that the direction as well as magnitude of the gradient moment imbalance affects the characteristics of unwanted signal attenuation. In human subjects, the addition of a moment-restoring blip prevented signal loss and improved the reproducibility and reliability of diffusion tensor measures even in the presence of substantial head movements.The method presented can improve robustness for clinical routine scanning in populations that are prone to head movements, such as children and uncooperative adult patients.

    View details for DOI 10.1002/mrm.24857

    View details for Web of Science ID 000336260900008

    View details for PubMedID 23821373

  • Knee Cartilage MRI with In Situ Mechanical Loading Using Prospective Motion Correction MAGNETIC RESONANCE IN MEDICINE Lange, T., Maclaren, J., Herbst, M., Lovell-Smith, C., Izadpanah, K., Zaitsev, M. 2014; 71 (2): 516-523

    View details for DOI 10.1002/mrm.24679

    View details for Web of Science ID 000330769700007

  • Reproduction of Motion Artifacts for Performance Analysis of Prospective Motion Correction in MRI MAGNETIC RESONANCE IN MEDICINE Herbst, M., Maclaren, J., Lovell-Smith, C., Sostheim, R., Egger, K., Harloff, A., Korvink, J., Hennig, J., Zaitsev, M. 2014; 71 (1): 182-190


    Despite numerous publications describing the ability of prospective motion correction to improve image quality in magnetic resonance imaging of the brain, a reliable approach to assess this improvement is still missing. A method that accurately reproduces motion artifacts correctable with prospective motion correction is developed, and enables the quantification of the improvements achieved.A software interface was developed to simulate rigid body motion by changing the scanning coordinate system relative to the object. Thus, tracking data recorded during a patient scan can be used to reproduce the prevented motion artifacts on a volunteer or a phantom. The influence of physiological motion on image quality was investigated by filtering these data. Finally, the method was used to reproduce and quantify the motion artifacts prevented in a patient scan.The accuracy of the method was tested in phantom experiments and in vivo. The calculated quality factor, as well as a visual inspection of the reproduced artifacts shows a good correspondence to the original.Precise reproduction of motion artifacts assists qualification of prospective motion correction strategies. The presented method provides an important tool to investigate the effects of rigid body motion on a wide range of sequences, and to quantify the improvement in image quality through prospective motion correction.

    View details for DOI 10.1002/mrm.24645

    View details for Web of Science ID 000328580300020

    View details for PubMedID 23440737

  • Reliability of brain volume measurements: A test-retest dataset SCIENTIFIC DATA Maclaren, J., Han, Z., Vos, S. B., Fischbein, N., Bammer, R. 2014; 1
  • Reliability of brain volume measurements: a test-retest dataset. Scientific data Maclaren, J., Han, Z., Vos, S. B., Fischbein, N., Bammer, R. 2014; 1: 140037-?


    Evaluation of neurodegenerative disease progression may be assisted by quantification of the volume of structures in the human brain using magnetic resonance imaging (MRI). Automated segmentation software has improved the feasibility of this approach, but often the reliability of measurements is uncertain. We have established a unique dataset to assess the repeatability of brain segmentation and analysis methods. We acquired 120 T1-weighted volumes from 3 subjects (40 volumes/subject) in 20 sessions spanning 31 days, using the protocol recommended by the Alzheimer's Disease Neuroimaging Initiative (ADNI). Each subject was scanned twice within each session, with repositioning between the two scans, allowing determination of test-retest reliability both within a single session (intra-session) and from day to day (inter-session). To demonstrate the application of the dataset, all 3D volumes were processed using FreeSurfer v5.1. The coefficient of variation of volumetric measurements was between 1.6% (caudate) and 6.1% (thalamus). Inter-session variability exceeded intra-session variability for lateral ventricle volume (P<0.0001), indicating that ventricle volume in the subjects varied between days.

    View details for DOI 10.1038/sdata.2014.37

    View details for PubMedID 25977792

  • Prospective slice-by-slice motion correction reduces false positive activations in fMRI with task-correlated motion NEUROIMAGE Schulz, J., Siegert, T., Bazin, P., MacLaren, J., Herbst, M., Zaitsev, M., Turner, R. 2014; 84: 124-132


    We aimed to test the hypothesis that slice-by-slice prospective motion correction at 7T using an optical tracking system reduces the rate of false positive activations in an fMRI group study with a paradigm that involves task-correlated motion.Brain activation during right leg movement was measured using a block design on 15 volunteers, with and without prospective motion correction. Clearly erroneous activations were compared between both cases, at the individual level. Additionally, conventional group analysis was performed.The number of falsely activated voxels with T-values higher than 5 was reduced by 48% using prospective motion correction alone, without additional retrospective realignment. In the group analysis, the statistical power was increased - the peak T-value was 26% greater, and the number of voxels in the cluster representing the right leg was increased by a factor of 9.3.Slice-by-slice prospective motion correction in fMRI studies with task-correlated motion can substantially reduce false positive activations and increase statistical power.

    View details for DOI 10.1016/j.neuroimage.2013.08.006

    View details for Web of Science ID 000328868600012

    View details for PubMedID 23954484

  • Prospective motion correction using inductively coupled wireless RF coils MAGNETIC RESONANCE IN MEDICINE Ooi, M. B., Aksoy, M., Maclaren, J., Watkins, R. D., Bammer, R. 2013; 70 (3): 639-647

    View details for DOI 10.1002/mrm.24845

    View details for Web of Science ID 000323543600005

  • Ballistocardiographic artifact removal from simultaneous EEG-fMRI using an optical motion-tracking system NEUROIMAGE LeVan, P., Maclaren, J., Herbst, M., Sostheim, R., Zaitsev, M., Hennig, J. 2013; 75: 1-11


    The combination of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) allows the investigation of neuronal activity with high temporal and spatial resolution. While much progress has been made to overcome the multiple technical challenges associated with the recording of EEG inside the MR scanner, the ballistocardiographic (BCG) artifact, which is caused by cardiac-related motion inside the magnetic field, remains a major issue affecting EEG quality. The BCG is difficult to remove by standard average artifact subtraction (AAS) methods due to its variability across cardiac cycles. We thus investigate the possibility of directly recording the BCG motion using an optical motion-tracking system. In 5 subjects, the system is shown to accurately measure BCG motion. Regressing out linear and quadratic functions of the measured motion parameters resulted in a significant reduction (p<0.05) in root-mean-square (RMS) amplitudes across cardiac cycles compared to AAS. A further significant RMS reduction was obtained when applying the regression and AAS methods sequentially, resulting in RMS amplitudes that were not significantly different from those of EEG recorded outside the scanner, although with higher residual variability. The large contributions of pure translational parameters and of non-linear terms to the BCG waveforms indicate that non-rigid motion of the EEG wires (originating from rigid head motion) is likely an important cause of the artifact.

    View details for DOI 10.1016/j.neuroimage.2013.02.039

    View details for Web of Science ID 000318208000001

    View details for PubMedID 23466939

  • Prospective motion correction in brain imaging: A review MAGNETIC RESONANCE IN MEDICINE Maclaren, J., Herbst, M., Speck, O., Zaitsev, M. 2013; 69 (3): 621-636


    Motion correction in magnetic resonance imaging by real-time adjustment of the imaging pulse sequence was first proposed more than 20 years ago. Recent advances have resulted from combining real-time correction with new navigator and external tracking mechanisms capable of quantifying rigid-body motion in all 6 degrees of freedom. The technique is now often referred to as "prospective motion correction." This article describes the fundamentals of prospective motion correction and reviews the latest developments in its application to brain imaging and spectroscopy. Although emphasis is placed on the brain as the organ of interest, the same principles apply whenever the imaged object can be approximated as a rigid body. Prospective motion correction can be used with most MR sequences, so it has potential to make a large impact in clinical routine. To maximize the benefits obtained from the technique, there are, however, several challenges still to be met. These include practical implementation issues, such as obtaining tracking data with minimal delay, and more fundamental problems, such as the magnetic field distortions caused by a moving object. This review discusses these challenges and summarizes the state of the art. We hope that this work will motivate further developments in prospective motion correction and help the technique to reach its full potential.

    View details for DOI 10.1002/mrm.24314

    View details for Web of Science ID 000315331300003

    View details for PubMedID 22570274

  • An embedded optical tracking system for motion-corrected magnetic resonance imaging at 7T MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE Schulz, J., Siegert, T., Reimer, E., Labadie, C., Maclaren, J., Herbst, M., Zaitsev, M., Turner, R. 2012; 25 (6): 443-453


    Prospective motion correction using data from optical tracking systems has been previously shown to reduce motion artifacts in MR imaging of the head. We evaluate a novel optical embedded tracking system.The home-built optical embedded tracking system performs image processing within a 7 T scanner bore, enabling high speed tracking. Corrected and uncorrected in vivo MR volumes are acquired interleaved using a modified 3D FLASH sequence, and their image quality is assessed and compared.The latency between motion and correction of the slice position was measured to be (19 ± 5) ms, and the tracking noise has a standard deviation no greater than 10 ?m/0.005° during conventional MR scanning. Prospective motion correction improved the edge strength by 16 % on average, even though the volunteers were asked to remain motionless during the acquisitions.Using a novel method for validating the effectiveness of in vivo prospective motion correction, we have demonstrated that prospective motion correction using motion data from the embedded tracking system considerably improved image quality.

    View details for DOI 10.1007/s10334-012-0320-0

    View details for Web of Science ID 000311675100004

    View details for PubMedID 22695771

  • Measurement and Correction of Microscopic Head Motion during Magnetic Resonance Imaging of the Brain PLOS ONE Maclaren, J., Armstrong, B. S., Barrows, R. T., Danishad, K. A., Ernst, T., Foster, C. L., Gumus, K., Herbst, M., Kadashevich, I. Y., Kusik, T. P., Li, Q., Lovell-Smith, C., Prieto, T., Schulze, P., Speck, O., Stucht, D., Zaitsev, M. 2012; 7 (11)


    Magnetic resonance imaging (MRI) is a widely used method for non-invasive study of the structure and function of the human brain. Increasing magnetic field strengths enable higher resolution imaging; however, long scan times and high motion sensitivity mean that image quality is often limited by the involuntary motion of the subject. Prospective motion correction is a technique that addresses this problem by tracking head motion and continuously updating the imaging pulse sequence, locking the imaging volume position and orientation relative to the moving brain. The accuracy and precision of current MR-compatible tracking systems and navigator methods allows the quantification and correction of large-scale motion, but not the correction of very small involuntary movements in six degrees of freedom. In this work, we present an MR-compatible tracking system comprising a single camera and a single 15 mm marker that provides tracking precision in the order of 10 m and 0.01 degrees. We show preliminary results, which indicate that when used for prospective motion correction, the system enables improvement in image quality at both 3 T and 7 T, even in experienced and cooperative subjects trained to remain motionless during imaging. We also report direct observation and quantification of the mechanical ballistocardiogram (BCG) during simultaneous MR imaging. This is particularly apparent in the head-feet direction, with a peak-to-peak displacement of 140 m.

    View details for DOI 10.1371/journal.pone.0048088

    View details for Web of Science ID 000311935800034

    View details for PubMedID 23144848

  • Spectroscopic imaging with prospective motion correction and retrospective phase correction MAGNETIC RESONANCE IN MEDICINE Lange, T., Maclaren, J., Buechert, M., Zaitsev, M. 2012; 67 (6): 1506-1514


    Motion-induced artifacts are much harder to recognize in magnetic resonance spectroscopic imaging than in imaging experiments and can therefore lead to erroneous interpretation. A method for prospective motion correction based on an optical tracking system has recently been proposed and has already been successfully applied to single voxel spectroscopy. In this work, the utility of prospective motion correction in combination with retrospective phase correction is evaluated for spectroscopic imaging in the human brain. Retrospective phase correction, based on the interleaved reference scan method, is used to correct for motion-induced frequency shifts and ensure correct phasing of the spectra across the whole spectroscopic imaging slice. It is demonstrated that the presented correction methodology can reduce motion-induced degradation of spectroscopic imaging data.

    View details for DOI 10.1002/mrm.23136

    View details for Web of Science ID 000304086000002

    View details for PubMedID 22135041

  • Prospective motion correction with continuous gradient updates in diffusion weighted imaging MAGNETIC RESONANCE IN MEDICINE Herbst, M., Maclaren, J., Weigel, M., Korvink, J., Hennig, J., Zaitsev, M. 2012; 67 (2): 326-338


    Despite the existence of numerous motion correction methods, head motion during MRI continues to be a major source of artifacts and can greatly reduce image quality. This applies particularly to diffusion weighted imaging, where strong gradients are applied during long encoding periods. These are necessary to encode microscopic movements. However, they also make the technique highly sensitive to bulk motion. In this work, we present a prospective motion correction method where all applied gradients are adjusted continuously to compensate for changes of the object position and ensure the desired phase evolution in the image coordinate frame. Additionally, in phantom experiments this new technique is used to reproduce motion artifacts with high accuracy by changing the position of the imaging frame relative to the measured object. In vivo measurements demonstrate the validity of the new correction method.

    View details for DOI 10.1002/mrm.23230

    View details for Web of Science ID 000299376500007

    View details for PubMedID 22161984

  • Optical motion tracking to improve image quality in MRI of the brain Conference on Image Reconstruction from Incomplete Data VII Maclaren, J., Aksoy, M., Ooi, M., Bammer, R. SPIE-INT SOC OPTICAL ENGINEERING. 2012

    View details for DOI 10.1117/12.953612

    View details for Web of Science ID 000312165100002

  • An Adaptive MR-Compatible Lens and Objective CONCEPTS IN MAGNETIC RESONANCE PART B-MAGNETIC RESONANCE ENGINEERING Maclaren, J., Schneider, F., Herbst, M., Hennig, J., Bammer, R., Zaitsev, M., Wallrabe, U. 2011; 39B (3): 141-148
  • Combined Prospective and Retrospective Motion Correction to Relax Navigator Requirements MAGNETIC RESONANCE IN MEDICINE Maclaren, J., Lee, K. J., Luengviriya, C., Speck, O., Zaitsev, M. 2011; 65 (6): 1724-1732


    Prospective motion correction can prevent motion artifacts in magnetic resonance imaging of the brain. However, for high-resolution imaging, the technique relies on precise tracking of head motion. This precision is often limited by tracking noise, which leads to residual errors in the prospectively-corrected k-space data and artifacts in the image. This work shows that it is possible to estimate these tracking errors, and hence the true k-space sample locations, by applying a two-sided filter to the tracking data after imaging. A conjugate gradient reconstruction is compared to gridding as a means of using this information to retrospectively correct for the effects of the residual errors.

    View details for DOI 10.1002/mrm.22754

    View details for Web of Science ID 000291115500023

    View details for PubMedID 21590805

  • Microcoil-based MRI: feasibility study and cell culture applications using a conventional animal system MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE Weber, H., Baxan, N., Paul, D., Maclaren, J., Schmidig, D., Mohammadzadeh, M., Hennig, J., von Elverfeldt, D. 2011; 24 (3): 137-145


    The aim of this study was to demonstrate the feasibility of MR microimaging on a conventional 9.4 T horizontal animal MRI system using commercial available microcoils in combination with only minor modifications to the system, thereby opening this field to a larger community.Commercially available RF microcoils designed for high-resolution NMR spectrometers were used in combination with a custom-made probehead. For this purpose, changes within the transmit chain and modifications to the adjustment routines and image acquisition sequences were made, all without requiring expensive hardware. To investigate the extent to which routine operation and high-resolution imaging is possible, the quality of phantom images was analysed. Surface and solenoidal microcoils were characterized with regard to their sensitive volume and signal-to-noise ratio. In addition, the feasibility of using planar microcoils to achieve high-resolution images of living glioma cells labelled with MnCl(2) was investigated.The setup presented in this work allows routine acquisition of high-quality images with high SNR and isotropic resolutions up to 10 ?m within an acceptable measurement time.This study demonstrates that MR microscopy can be applied at low cost on animal MR imaging systems, which are in widespread use. The successful imaging of living glioma cells indicates that the technique promises to be a useful tool in biomedical research.

    View details for DOI 10.1007/s10334-011-0244-0

    View details for Web of Science ID 000291041900003

    View details for PubMedID 21331647

  • Combining prospective motion correction and distortion correction for EPI: towards a comprehensive correction of motion and susceptibility-induced artifacts MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE Boegle, R., Maclaren, J., Zaitsev, M. 2010; 23 (4): 263-273


    State-of-the-art MR techniques that rely on echo planar imaging (EPI), such as real-time fMRI, are limited in their applicability by both subject motion and B(0) field inhomogeneities. The goal of this work is to demonstrate that in principle it is possible to accurately predict the B(0) field inhomogeneities that occur during echo planar imaging in the presence of large scale head motion and apply this knowledge for distortion correction.In this work, prospective motion correction is combined with a field-prediction method and a method for correcting geometric distortions in EPI. To validate the methods, echo planar images were acquired of a custom-made phantom rotated to different angles relative to the B(0) field. For each orientation, field maps were acquired for comparison with the field predictions.The calculated field maps are very similar to the measured field maps for all orientations used in the experiments. The root mean squared error (RMSE) of the difference maps was between 15 to 20 Hz. The quality of distortion correction using calculated field maps is comparable to distortion correction done with measured field maps.The results suggest that distortion-free echo planar imaging of moving objects may be feasible if prospective motion correction is combined with a field inhomogeneity estimation approach.

    View details for DOI 10.1007/s10334-010-0225-8

    View details for Web of Science ID 000281250700007

    View details for PubMedID 20694501

  • Navigator Accuracy Requirements for Prospective Motion Correction MAGNETIC RESONANCE IN MEDICINE Maclaren, J., Speck, O., Stucht, D., Schulze, P., Hennig, J., Zaitsev, M. 2010; 63 (1): 162-170


    Prospective motion correction in MRI is becoming increasingly popular to prevent the image artifacts that result from subject motion. Navigator information is used to update the position of the imaging volume before every spin excitation so that lines of acquired k-space data are consistent. Errors in the navigator information, however, result in residual errors in each k-space line. This paper presents an analysis linking noise in the tracking system to the power of the resulting image artifacts. An expression is formulated for the required navigator accuracy based on the properties of the imaged object and the desired resolution. Analytical results are compared with computer simulations and experimental data.

    View details for DOI 10.1002/mrm.22191

    View details for Web of Science ID 000273578600017

    View details for PubMedID 19918892

  • Determination of Myosin Filament Orientations in Electron Micrographs of Muscle Cross Sections IEEE TRANSACTIONS ON IMAGE PROCESSING Yoon, C. H., Bodvarsson, B., Klim, S., Morkebjerg, M., Mortensen, S., Chen, J., Maclaren, J. R., Luther, P. K., Squire, J. M., Bones, P. J., Millane, R. P. 2009; 18 (4): 831-839


    An automated image analysis system for determining myosin filament azimuthal rotations, or orientations, in electron micrographs of muscle cross sections is described. The micrographs of thin sections intersect the myosin filaments which lie on a triangular lattice. The myosin filament profiles are variable and noisy, and the images exhibit a variable contrast and background. Filament positions are determined by filtering with a point spread function that incorporates the local symmetry of the lattice. Filament orientations are determined by correlation with a template that incorporates the salient filament characteristics, and the orientations are classified using a Gaussian mixture model. The precision of the technique is assessed by application to a variety of micrographs and comparison with manual classification of the orientations. The system provides a convenient, robust, and rapid means of analysing micrographs containing many filaments to study the distribution of filament orientations.

    View details for DOI 10.1109/TIP.2008.2011379

    View details for Web of Science ID 000264397100012

    View details for PubMedID 19278921

  • A morphological image processing method for locating myosin filaments in muscle electron micrographs IMAGE AND VISION COMPUTING Bodvarsson, B., Klim, S., Morkebjerg, M., Mortensen, S., Yoon, C. H., Chen, J., Maclaren, J. R., Luther, P. K., Squire, J. M., Bones, P. J., Millane, R. P. 2008; 26 (8): 1073-1080
  • MRI with TRELLIS: a novel approach to motion correction MAGNETIC RESONANCE IMAGING Maclaren, J. R., Bones, P. J., Millane, R. P., Watts, R. 2008; 26 (4): 474-483


    A motion-correcting pulse sequence and reconstruction algorithm, termed TRELLIS, is presented. k-Space is filled using orthogonal overlapping strips and the directions for phase- and frequency-encoding are alternated such that the frequency-encode direction always runs lengthwise along each strip. The overlap between strips is used both for signal averaging and to produce a system of equations that, when solved, quantifies the rotational and translational motion of the object. Results obtained from simulations with computer-generated phantoms, a purpose-built moving phantom, and in human subjects show the method is effective. TRELLIS offers some advantages over existing techniques in that k-space is sampled uniformly and all acquired data are used for both motion detection and image reconstruction.

    View details for DOI 10.1016/j.mri.2007.08.013

    View details for Web of Science ID 000255299100005

    View details for PubMedID 18068932

  • Ordered k-space acquisition in contrast enhanced magnetic resonance angiography (CE-MRA) Medical Imaging 2008 Conference Wu, B., Maclaren, J. R., Millane, R. P., Watts, R., Bones, P. J. SPIE-INT SOC OPTICAL ENGINEERING. 2008

    View details for DOI 10.1117/12.769429

    View details for Web of Science ID 000256660300139

  • Robust statistical extension to TRELLIS motion correction in MRI Conference on Image Reconstruction from Incomplete Data V Bones, P. J., Maclaren, J. R. SPIE-INT SOC OPTICAL ENGINEERING. 2008

    View details for DOI 10.1117/12.796814

    View details for Web of Science ID 000263955500016

  • A modified view ordering for artifact reduction in MRI 2007 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-16 Maclaren, J. R., Bones, P. J., Millane, R. P., Watts, R. 2007: 2053-2056


    Fast spin echo (FSE) is a means of rapidly acquiring k-space data in magnetic resonance imaging (MRI). Unfortunately, images obtained using FSE often contain artifacts. These are caused primarily by patient motion and transversal magnetisation decay, the latter being characterised by the time constant T2. This paper presents a study of the effect of data acquisition order on the severity of these effects.

    View details for Web of Science ID 000253467001198

    View details for PubMedID 18002390

  • Improved bulk rotation detection and correction in MRI 2007 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-16 Bones, P. J., Maclaren, J. R. 2007: 2106-2109


    Bulk motion occurring during the acquisition of magnetic resonance images (MRI) remains a significant limitation in image quality. The paper presents an extension to TRELLIS, a recently developed method of detecting and correcting for bulk motion. Accurate determination of the relative orientations of overlapping strips of k-space is demonstrated. Reconstructions for both simulated and actual MRI acquisitions are presented.

    View details for Web of Science ID 000253467001211

    View details for PubMedID 18002403

  • Quantifying and correcting motion artifacts in MRI Conference on Image Reconstruction from Incomplete Data IV Bones, P. J., Maclaren, J. R., Millane, R. P., Watts, R. SPIE-INT SOC OPTICAL ENGINEERING. 2006

    View details for DOI 10.1117/12.681684

    View details for Web of Science ID 000241970900008

  • Correction of translational motion artifacts in magnetic resonance imaging PROCEEDINGS OF THE FIFTH IASTED INTERNATIONAL CONFERENCE ON VISUALIZATION, IMAGING, AND IMAGE PROCESSING Maclaren, J. R., Bones, P. J., Millane, R. P., Watts, R. 2005: 448-452
  • Determination of myosin filament positions and orientations in electron micrographs of muscle cross-sections IMAGE RECONSTRUCTION FROM INCOMPLETE DATA III Bodvarsson, B., Klim, S., Mortensen, S., Morkebjerg, M., Chen, J., Maclaren, J. R., Yoon, C. H., Luther, P. K., Squire, J. M., Bainbridge-Smith, A., Bones, P. J., Millane, R. P. 2004; 5562: 97-108

    View details for DOI 10.1117/12.562357

    View details for Web of Science ID 000225600000012

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