3D Motion Correction Research Articles

CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals.

Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multi-stage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.

Downward myocardial creep during stress PET imaging is inversely associated with mortality

PurposeThe myocardial creep is a phenomenon in which the heart moves from its original position during stress-dynamic PET myocardial perfusion imaging (MPI) that can confound myocardial blood flow measurements. Therefore, myocardial motion correction is important to obtain reliable myocardial flow quantification. However, the clinical importance of the magnitude of myocardial creep has not been explored. We aimed to explore the prognostic value of myocardial creep quantified by an automated motion correction algorithm beyond traditional PET-MPI imaging variables.MethodsConsecutive patients undergoing regadenoson rest-stress [82Rb]Cl PET-MPI were included. A newly developed 3D motion correction algorithm quantified myocardial creep, the maximum motion at stress during the first pass (60 s), in each direction. All-cause mortality (ACM) served as the primary endpoint.ResultsA total of 4,276 patients (median age 71 years; 60% male) were analyzed, and 1,007 ACM events were documented during a 5-year median follow-up. Processing time for automatic motion correction was < 12 s per patient. Myocardial creep in the superior to inferior (downward) direction was greater than the other directions (median, 4.2 mm vs. 1.3–1.7 mm). Annual mortality rates adjusted for age and sex were reduced with a larger downward creep, with a 4.2-fold ratio between the first (0 mm motion) and 10th decile (11 mm motion) (mortality, 7.9% vs. 1.9%/year). Downward creep was associated with lower ACM after full adjustment for clinical and imaging parameters (adjusted hazard ratio, 0.93; 95%CI, 0.91–0.95; p < 0.001). Adding downward creep to the standard PET-MPI imaging model significantly improved ACM prediction (area under the receiver operating characteristics curve, 0.790 vs. 0.775; p < 0.001), but other directions did not (p > 0.5).ConclusionsDownward myocardial creep during regadenoson stress carries additional information for the prediction of ACM beyond conventional flow and perfusion PET-MPI. This novel imaging biomarker is quantified automatically and rapidly from stress dynamic PET-MPI.

MP-RAVE: IR-Prepared T1 -Weighted Radial Stack-of-Stars 3D GRE imaging with retrospective motion correction.

To describe an inversion-recovery T1 -weighted radial stack-of-stars 3D gradient echo (GRE) sequence with comparable image quality to conventional MP-RAGE and to demonstrate how the radial acquisition scheme can be utilized for additional retrospective motion correction to improve robustness to head motion. The proposed sequence, named MP-RAVE, has been derived from a previously described radial stack-of-stars 3D GRE sequence (RAVE) and includes a 180° inversion recovery pulse that is generated once for every stack of radial views. The sequence is combined with retrospective 3D motion correction to improve robustness. The effectiveness has been evaluated in phantoms and healthy volunteers and compared to conventional MP-RAGE acquisition. MP-RAGE and MP-RAVE anatomical images were rated "good" to "excellent" in overall image quality, with artifact level between "mild" and "no artifacts", and with no statistically significant difference between methods. During head motion, MP-RAVE showed higher inherent robustness with artifacts confined to local brain regions. In combination with motion correction, MP-RAVE provided noticeably improved image quality during different head motion and showed statistically significant improvement in image sharpness. MP-RAVE provides comparable image quality and contrast to conventional MP-RAGE with improved robustness to head motion. In combination with retrospective 3D motion correction, MP-RAVE can be a useful alternative to MP-RAGE, especially in non-cooperative or pediatric patients.

Effectuality study of a 3D motion correction algorithm in C-arm CTs of severely impaired image quality during transarterial chemoembolization

BackgroundTo evaluate effectivity of a 3D-motion correction algorithm in C-Arm CTs (CACT) with limited image quality (IQ) during transarterial chemoembolization (TACE).MethodsFrom 1/2015–5/2021, 644 CACTs were performed in patients during TACE. Of these, 27 CACTs in 26 patients (18 m, 8f; 69.7 years ± 10.7 SD) of limited IQ were included. Post-processing of the original raw-data sets (CACTOrg) included application of a 3D-motion correction algorithm and bone segmentation (CACTMC_no_bone). Four radiologists (R1-4) compared the images by choosing their preferred dataset and recommending repeat acquisition in case of severe IQ-impairment. R1,2 performed additional grading of intrahepatic vessel visualization, presence/extent of movement artifacts, and overall IQ.ResultsR1,2 demonstrated excellent interobserver agreement for overall IQ (ICC 0.79,p < 0.01) and the five-point vessel visualization scale before and after post-processing of the datasets (ICC 0.78,p < 0.01). Post-processing caused significant improvement, with overall IQ improving from 2.63 (CACTOrg) to 1.39 (CACTMC_no_bone;p < 0.01) and a decrease in the mean distance of identifiable, subcapsular vessels to the liver capsule by 4 mm (p < 0.01). This proved especially true for datasets with low parenchymal and high hepatic artery contrast. A good interobserver agreement (ICC = 0.73) was recorded concerning the presence of motion artifacts, with significantly less discernible motion after post-processing (CACTOrg:1.31 ± 1.67, CACTMC_no_bone:1.00 ± 1.34, p < 0.01). Of the 27 datasets, ≥ 23 CACTMC_no_bone were preferred, with identical datasets chosen by the readers to show benefit from the algorithm.ConclusionApplication of a 3D-motion correction algorithm significantly improved IQ in diagnostically limited CACTs during TACE, with the potential to decrease repeat acquisitions.

A Novel Radiomics-Based Tumor Volume Segmentation Algorithm for Lung Tumors in FDG-PET/CT after 3D Motion Correction-A Technical Feasibility and Stability Study.

Positron emission tomography (PET) provides important additional information when applied in radiation therapy treatment planning. However, the optimal way to define tumors in PET images is still undetermined. As radiomics features are gaining more and more importance in PET image interpretation as well, we aimed to use textural features for an optimal differentiation between tumoral tissue and surrounding tissue to segment-target lesions based on three textural parameters found to be suitable in previous analysis (Kurtosis, Local Entropy and Long Zone Emphasis). Intended for use in radiation therapy planning, this algorithm was combined with a previously described motion-correction algorithm and validated in phantom data. In addition, feasibility was shown in five patients. The algorithms provided sufficient results for phantom and patient data. The stability of the results was analyzed in 20 consecutive measurements of phantom data. Results for textural feature-based algorithms were slightly worse than those of the threshold-based reference algorithm (mean standard deviation 1.2%—compared to 4.2% to 8.6%) However, the Entropy-based algorithm came the closest to the real volume of the phantom sphere of 6 ccm with a mean measured volume of 26.5 ccm. The threshold-based algorithm found a mean volume of 25.0 ccm. In conclusion, we showed a novel, radiomics-based tumor segmentation algorithm in FDG-PET with promising results in phantom studies concerning recovered lesion volume and reasonable results in stability in consecutive measurements. Segmentation based on Entropy was the most precise in comparison with sphere volume but showed the worst stability in consecutive measurements. Despite these promising results, further studies with larger patient cohorts and histopathological standards need to be performed for further validation of the presented algorithms and their applicability in clinical routines. In addition, their application in other tumor entities needs to be studied.

Simultaneous multi-slice combined with PROPELLER.

Simultaneous multi-slice (SMS) imaging is an advantageous method for accelerating MRI scans, allowing reduced scan time, increased slice coverage, or high temporal resolution with limited image quality penalties. In this work we combine the advantages of SMS acceleration with the motion correction and artifact reduction capabilities of the PROPELLER technique. A PROPELLER sequence was developed with support for CAIPIRINHA and phase optimized multiband radio frequency pulses. To minimize the time spent on acquiring calibration data, both in-plane-generalized autocalibrating partial parallel acquisition (GRAPPA) and slice-GRAPPA weights for all PROPELLER blade angles were calibrated on a single fully sampled PROPELLER blade volume. Therefore, the proposed acquisition included a single fully sampled blade volume, with the remaining blades accelerated in both the phase and slice encoding directions without additional auto calibrating signal lines. Comparison to 3D RARE was performed as well as demonstration of 3D motion correction performance on the SMS PROPELLER data. We show that PROPELLER acquisitions can be efficiently accelerated with SMS using a short embedded calibration. The potential in combining these two techniques was demonstrated with a high quality 1.0 × 1.0 × 1.0 mm3 resolution T2 -weighted volume, free from banding artifacts, and capable of 3D retrospective motion correction, with higher effective resolution compared to 3D RARE. With the combination of SMS acceleration and PROPELLER imaging, thin-sliced reformattable T2 -weighted image volumes with 3D retrospective motion correction capabilities can be rapidly acquired with low sensitivity to flow and head motion. Magn Reson Med 80:496-506, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Retrospective 3D motion correction using spherical navigator echoes

PurposeTo develop and evaluate a rapid spherical navigator echo (SNAV) motion correction technique, then apply it for retrospective correction of brain images. MethodsThe pre-rotated, template matching SNAV method (preRot-SNAV) was developed in combination with a novel hybrid baseline strategy, which includes acquired and interpolated templates. Specifically, the SNAV templates are only rotated around X- and Y-axis; for each rotated SNAV, simulated baseline templates that mimic object rotation about the Z-axis were interpolated.The new method was first evaluated with phantom experiments. Then, a customized SNAV-interleaved gradient echo sequence was used to image three volunteers performing directed head motion. The SNAV motion measurements were used to retrospectively correct the brain images. Experiments were performed using a 3.0T whole-body MRI scanner and both single and 8-channel head coils. ResultsPhantom rotations and translations measured using the hybrid baselines agreed to within 0.9° and 1mm compared to those measured with the original preRot-SNAV method. Retrospective motion correction of in vivo images using the hybrid preRot-SNAV effectively corrected for head rotation up to 4° and 4mm. ConclusionsThe presented hybrid approach enables the acquisition of pre-rotated baseline templates in as little as 2.5s, and results in accurate measurement of rotations and translations. Retrospective 3D motion correction successfully reduced motion artifacts in vivo.

Accelerated isotropic resolution 3D image-based navigators for coronary MR angiography

Background Motion remains a primary challenge for MR coronary angiography. In our previous protocol, we performed retrospective 3D motion correction based on a set of orthogonal 2D image-based navigators (iNAV) [1]. Recent work examined the use of anisotropic-resolution 3D Cartesian iNAVs every heartbeat [2]. Capitalizing on the efficiency of non-Cartesian imaging and iterative reconstruction, we sought an improved 3D iNAVs acquisition with isotropic resolution, to facilitate wholeheart motion correction with translational or more advanced models. In this work, we propose a method providing 3D motion correction on a per-heartbeat basis using a variable-density 3D cones iNAV acquisition [3].

High temporal resolution retrospective motion correction with radial parallel imaging

A method for motion correction in multicoil imaging applications, involving both data collection and reconstruction, is presented. A bit-reversed radial acquisition scheme, in conjunction with a rapid self-calibrated parallel imaging method, Generalized auto-calibrating partial parallel acquisition (GRAPPA) operator for wider radial bands (GROWL), is used to achieve motion correction at a high temporal resolution. View-by-view in-plane motion correction is achieved in 2D imaging, while 3D motion correction is achieved for every two consecutive slice-encoding planes in 3D imaging. In the proposed technique, GROWL contributes in two aspects: First, a central k-space circle/cylinder used as the motion-free reference is generated from a small number of radial lines/planes; Second, undersampled k-space regions resulting from rotation and inconsistent (e.g. intraview and nonrigid body) motion can be filled in. When compared with navigator-based motion correction methods, the proposed method does not prolong scan time and can be applied to short-TR sequences. Magn Reson Med, 2011. © 2011 Wiley-Liss, Inc.

Temporal changes of human cone photoreceptors observed in vivo with SLO/OCT

In this study we use our previously introduced scanning laser ophthalmoscope (SLO) / transverse scanning optical coherence tomography (TS-OCT) instrument to investigate long term changes in cone photoreceptors. The instrument is capable to provide 3D information of the human cone photoreceptors with negligible eye motion artifacts due to an implemented 3D motion correction on a cellular level. This allows for an in vivo investigation of exactly the same location on the retina with cellular resolution over several days. Temporal changes in the backscattered intensity are observed and quantified within the junction between inner and outer segments of cone photoreceptors, the cone outer segments, the end tips of cone photoreceptors and the retinal pigment epithelium. Furthermore, the length of individual cone outer segments is measured and observed over time. We show, to the best of our knowledge for the first time, that bright reflection spots which are located within the outer segment of cone photoreceptors change their position when observed over extended time periods. The average measured bright reflection spot motion speed corresponds well to the expected cone growth speed. We believe that this observation can be associated with the first direct in vivo imaging of the cone renewal process.

In vivo investigation of human cone photoreceptors with SLO/OCT in combination with 3D motion correction on a cellular level

We present a further improvement of our SLO/OCT imaging system which enables to practically eliminate all eye motion artifacts with a correction accuracy approaching sub-cellular dimensions. Axial eye tracking is achieved by using a hardware based, high speed tracking system that consists of a rapid scanning optical delay line in the reference arm of the interferometer. A software based algorithm is employed to correct for transverse eye motion in a post-processing step. The instrument operates at a frame rate of 40 en-face fps with a field of view of approximately 1 degrees x 1 degrees. Dynamic focusing enables the recording of 3D volumes of the human retina with cellular resolution throughout the entire imaging depth. Several volumes are stitched together to increase the total field of view. Different features of the three dimensional structure of cone photoreceptors are investigated in detail and at different eccentricities from the fovea.

Brain surface motion imaging to predict adhesions between meningiomas and the brain surface

"Brain surface motion imaging" (BSMI) is the subtraction of pulse-gated, 3D, heavily T2-weighted image of two different phases of cerebrospinal fluid (CSF) pulsation, which enables the assessment of the dynamics of brain surface pulsatile motion. The purpose of this study was to evaluate the feasibility of this imaging method for providing presurgical information about adhesions between meningiomas and the brain surface. Eighteen cases with surgically resected meningioma in whom BSMI was presurgically obtained were studied. BSMI consisted of two sets of pulse-gated, 3D, heavily T2-weighted, fast spin echo scans. Images of the systolic phase and the diastolic phase were obtained, and subtraction was performed with 3D motion correction. We analyzed the presence of band-like texture surrounding the tumor and judged the degree of motion discrepancy as "total," "partial," or "none." The correlation between BSMI and surgical findings was evaluated. For cases with partial adhesions, agreements in the locations of the adhesions were also evaluated. On presurgical BSMI, no motion discrepancy was seen in eight cases, partial in six cases, and total in four cases. These presurgical predictions about adhesions and surgical findings agreed in 13 cases (72.2%). The locations of adhesions agreed in five of six cases with partial adhesions. In the current study, BSMI could predict brain and meningioma adhesions correctly in 72.2% of cases, and adhesion location could also be predicted. This imaging method appears to provide presurgical information about brain/meningioma adhesions.

Impact of motion correction on the quantitative analysis of DCE-MR Images

Dynamic magnetic resonance imaging (DCE-MRI) carried out with contrast media such as Gd-chelate complex (Gd-DTPA) allows the non-invasive assessment of microcirculatory characteristics of malignant lesions. Quantitative estimation of lesion parameters from the passage of the contrast media requires the use of pharmacokinetic two-compartment model. The input to the model is the time-intensity plot from a region of interest (ROI) covering the lesion extent. The lengthy imaging process, elasticity of the organs and patient movement result in complex deformations in the subject requiring 3D motion correction for ROI alignment. This paper presents results on applying the Thirion Demon’s 3D elastic matching procedure in the ITK framework on the two-compartment lesion parameters. Registration, meanwhile involves interpolation and smoothing operations thereby affecting the time-intensity plots. We explore the trade-offs that arise between registration and lesion parameter estimation. Experiments on synthesized and real deformation are presented.

Free‐breathing radial acquisitions of the heart

There is considerable interest in performing free-breathing acquisitions of the heart in order to obtain high-quality images without the need for multiple, long breathholds. In this article a 3D motion-correction method is described that is based on image registration of in-plane data and through-plane slice tracking. A number of fast radial undersampled images are acquired, each of which is free of motion artifacts. Initially, in-plane translational and rotational motion between each image was corrected before combining the data to give a fully sampled image. At the next stage, correction of in-plane deformation, in addition to translations and rotations, was performed in the image domain. Through-plane translational motion was compensated using a navigator echo to move the acquisition plane. Using this method, information on the motion of the heart was captured at the same time as acquiring the image data. No motion model, assumptions about the motion, or training data are required. The method is demonstrated on phantom data and cardiac images acquired on free-breathing volunteers.

Physiological self-regulation of regional brain activity using real-time functional magnetic resonance imaging (fMRI): methodology and exemplary data

A brain–computer interface (BCI) based on real-time functional magnetic resonance imaging (fMRI) is presented which allows human subjects to observe and control changes of their own blood oxygen level-dependent (BOLD) response. This BCI performs data preprocessing (including linear trend removal, 3D motion correction) and statistical analysis on-line. Local BOLD signals are continuously fed back to the subject in the magnetic resonance scanner with a delay of less than 2 s from image acquisition. The mean signal of a region of interest is plotted as a time-series superimposed on color-coded stripes which indicate the task, i.e., to increase or decrease the BOLD signal. We exemplify the presented BCI with one volunteer intending to control the signal of the rostral–ventral and dorsal part of the anterior cingulate cortex (ACC). The subject achieved significant changes of local BOLD responses as revealed by region of interest analysis and statistical parametric maps. The percent signal change increased across fMRI-feedback sessions suggesting a learning effect with training. This methodology of fMRI-feedback can assess voluntary control of circumscribed brain areas. As a further extension, behavioral effects of local self-regulation become accessible as a new field of research.

Motion correction of parametric fMRI data from multi‐slice single‐shot multi‐echo acquisitions

Fast parametric imaging using multi-echo techniques has been proven to yield quantitative parameter maps with high stability for functional MRI (fMRI). Due to the different contrasts and signal-to-noise ratios (SNRs) in the various images, motion correction of the echo images or the resulting parameter maps is not a straightforward process. 3D motion correction of parametric imaging data has not yet been examined thoroughly. However, motion correction is an essential step in fMRI data processing. In this study several possible motion detection methods were tested and compared. Motion parameters can be estimated from the different echo images as well as from the parameter maps. The accuracy of the different methods was examined in simulations and in in vivo experiments. Motion parameters should be estimated from the I(0)-parameter maps and subsequently applied to the T(*)(2)-parameter maps.