Registration of 3D fetal neurosonography and MRI

Computational methods for the analysis of early-pregnancy brain ultrasonography: a systematic review

BACKGROUND

Early screening of the brain is becoming routine clinical practice. Currently, this screening is performed by manual measurements and visual analysis, which is time-consuming and prone to errors. Computational methods may support this screening. Hence, the aim of this systematic review is to gain insight into future research directions needed to bring automated early-pregnancy ultrasound analysis of the human brain to clinical practice.

METHODS

We searched PubMed (Medline ALL Ovid), EMBASE, Web of Science Core Collection, Cochrane Central Register of Controlled Trials, and Google Scholar, from inception until June 2022. This study is registered in PROSPERO at CRD42020189888. Studies about computational methods for the analysis of human brain ultrasonography acquired before the 20th week of pregnancy were included. The key reported attributes were: level of automation, learning-based or not, the usage of clinical routine data depicting normal and abnormal brain development, public sharing of program source code and data, and analysis of the confounding factors.

FINDINGS

Our search identified 2575 studies, of which 55 were included. 76% used an automatic method, 62% a learning-based method, 45% used clinical routine data and in addition, for 13% the data depicted abnormal development. None of the studies shared publicly the program source code and only two studies shared the data. Finally, 35% did not analyse the influence of confounding factors.

INTERPRETATION

Our review showed an interest in automatic, learning-based methods. To bring these methods to clinical practice we recommend that studies: use routine clinical data depicting both normal and abnormal development, make their dataset and program source code publicly available, and be attentive to the influence of confounding factors. Introduction of automated computational methods for early-pregnancy brain ultrasonography will save valuable time during screening, and ultimately lead to better detection, treatment and prevention of neuro-developmental disorders.

FUNDING

The Erasmus MC Medical Research Advisor Committee (grant number: FB 379283).

BEAN: Brain Extraction and Alignment Network for 3D Fetal Neurosonography

Brain extraction (masking of extra-cerebral tissues) and alignment are fundamental first steps of most neuroimage analysis pipelines. The lack of automated solutions for 3D ultrasound (US) has therefore limited its potential as a neuroimaging modality for studying fetal brain development using routinely acquired scans. In this work, we propose a convolutional neural network (CNN) that accurately and consistently aligns and extracts the fetal brain from minimally pre-processed 3D US scans. Our multi-task CNN, Brain Extraction and Alignment Network (BEAN), consists of two independent branches: 1) a fully-convolutional encoder-decoder branch for brain extraction of unaligned scans, and 2) a two-step regression-based branch for similarity alignment of the brain to a common coordinate space. BEAN was tested on 356 fetal head 3D scans spanning the gestational range of 14 to 30 weeks, significantly outperforming all current alternatives for fetal brain extraction and alignment. BEAN achieved state-of-the-art performance for both tasks, with a mean Dice Similarity Coefficient (DSC) of 0.94 for the brain extraction masks, and a mean DSC of 0.93 for the alignment of the target brain masks. The presented experimental results show that brain structures such as the thalamus, choroid plexus, cavum septum pellucidum, and Sylvian fissure, are consistently aligned throughout the dataset and remain clearly visible when the scans are averaged together. The BEAN implementation and related code can be found under www.github.com/felipemoser/kelluwen.

A review of image processing methods for fetal head and brain analysis in ultrasound images

BACKGROUND AND OBJECTIVE

Examination of head shape and brain during the fetal period is paramount to evaluate head growth, predict neurodevelopment, and to diagnose fetal abnormalities. Prenatal ultrasound is the most used imaging modality to perform this evaluation. However, manual interpretation of these images is challenging and thus, image processing methods to aid this task have been proposed in the literature. This article aims to present a review of these state-of-the-art methods.

METHODS

In this work, it is intended to analyze and categorize the different image processing methods to evaluate fetal head and brain in ultrasound imaging. For that, a total of 109 articles published since 2010 were analyzed. Different applications are covered in this review, namely analysis of head shape and inner structures of the brain, standard clinical planes identification, fetal development analysis, and methods for image processing enhancement.

RESULTS

For each application, the reviewed techniques are categorized according to their theoretical approach, and the more suitable image processing methods to accurately analyze the head and brain are identified. Furthermore, future research needs are discussed. Finally, topics whose research is lacking in the literature are outlined, along with new fields of applications.

CONCLUSIONS

A multitude of image processing methods has been proposed for fetal head and brain analysis. Summarily, techniques from different categories showed their potential to improve clinical practice. Nevertheless, further research must be conducted to potentiate the current methods, especially for 3D imaging analysis and acquisition and for abnormality detection.

A Systematic Review of Methodology Used in Studies Aimed at Creating Charts of Fetal Brain Structures

Ultrasound-based assessment of the fetal nervous system is routinely recommended at the time of the mid-trimester anatomy scan or at different gestations based on clinical indications. This review evaluates the methodological quality of studies aimed at creating charts for fetal brain structures obtained by ultrasound, as poor methodology could explain substantial variability in percentiles reported. Electronic databases (MEDLINE, EMBASE, Cochrane Library, and Web of Science) were searched from January 1970 to January 2021 to select studies on singleton fetuses, where the main aim was to construct charts on one or more clinically relevant structures obtained in the axial plane: parieto-occipital fissure, Sylvian fissure, anterior ventricle, posterior ventricle, transcerebellar diameter, and cisterna magna. Studies were scored against 29 predefined methodological quality criteria to identify the risk of bias. In total, 42 studies met the inclusion criteria, providing data for 45,626 fetuses. Substantial heterogeneity was identified in the methodological quality of included studies, and this may explain the high variability in centiles reported. In 80% of the studies, a high risk of bias was found in more than 50% of the domains scored. In conclusion, charts to be used in clinical practice and research should have an optimal study design in order to minimise the risk of bias and to allow comparison between different studies. We propose to use charts from studies with the highest methodological quality.

Quality control of fetal biometric evaluation and Doppler ultrasound

In recent years quality control in obstetric ultrasound has become recommended and an essential component of obstetric scanning. This is to minimize the inaccuracy and variability related to fetal measurements, to provide an effective quality assurance system to sonographers to certify their practice and decrease the impact of medical litigations. For a quality control system in obstetric ultrasound to be useful clinically, multiple strategies need to be employed: certified training, practical standardization exercise, image storing, qualitative and quantitative quality control. Qualitative quality control consists of the evaluation of images obtained for fetal biometry and Doppler scans using an objective score against predefined criteria. Quantitative quality control consists of analyzing quantitatively the performance of a sonographer and the impact on measurements values. Quantitative analysis could be performed either using estimates of intraobserver or interobserver reproducibility of plane acquisition and caliper placements.

Self-Supervised Ultrasound to MRI Fetal Brain Image Synthesis

Fetal brain magnetic resonance imaging (MRI) offers exquisite images of the developing brain but is not suitable for second-trimester anomaly screening, for which ultrasound (US) is employed. Although expert sonographers are adept at reading US images, MR images which closely resemble anatomical images are much easier for non-experts to interpret. Thus in this article we propose to generate MR-like images directly from clinical US images. In medical image analysis such a capability is potentially useful as well, for instance for automatic US-MRI registration and fusion. The proposed model is end-to-end trainable and self-supervised without any external annotations. Specifically, based on an assumption that the US and MRI data share a similar anatomical latent space, we first utilise a network to extract the shared latent features, which are then used for MRI synthesis. Since paired data is unavailable for our study (and rare in practice), pixel-level constraints are infeasible to apply. We instead propose to enforce the distributions to be statistically indistinguishable, by adversarial learning in both the image domain and feature space. To regularise the anatomical structures between US and MRI during synthesis, we further propose an adversarial structural constraint. A new cross-modal attention technique is proposed to utilise non-local spatial information, by encouraging multi-modal knowledge fusion and propagation. We extend the approach to consider the case where 3D auxiliary information (e.g., 3D neighbours and a 3D location index) from volumetric data is also available, and show that this improves image synthesis. The proposed approach is evaluated quantitatively and qualitatively with comparison to real fetal MR images and other approaches to synthesis, demonstrating its feasibility of synthesising realistic MR images.

International standards for fetal brain structures based on serial ultrasound measurements from Fetal Growth Longitudinal Study of INTERGROWTH-21st Project

OBJECTIVE

To create prescriptive growth standards for five fetal brain structures, measured using ultrasound, in healthy, well-nourished women at low risk of impaired fetal growth and poor perinatal outcome, taking part in the Fetal Growth Longitudinal Study (FGLS) of the INTERGROWTH-21^st Project.

METHODS

This was a complementary analysis of a large, population-based, multicenter, longitudinal study. The sample analyzed was selected randomly from the overall FGLS population, ensuring an equal distribution among the eight diverse participating sites and of three-dimensional (3D) ultrasound volumes across pregnancy (range: 15-36 weeks' gestation). We measured, in planes reconstructed from 3D ultrasound volumes of the fetal head at different timepoints in pregnancy, the size of the parieto-occipital fissure (POF), Sylvian fissure (SF), anterior horn of the lateral ventricle, atrium of the posterior horn of the lateral ventricle (PV) and cisterna magna (CM). Fractional polynomials were used to construct the standards. Growth and development of the infants were assessed at 1 and 2 years of age to confirm their adequacy for constructing international standards.

RESULTS

From the entire FGLS cohort of 4321 women, 451 (10.4%) were selected at random. After exclusions, 3D ultrasound volumes from 442 fetuses born without a congenital malformation were used to create the charts. The fetal brain structures of interest were identified in 90% of cases. All structures, except the PV, showed increasing size with gestational age, and the size of the POF, SF, PV and CM showed increasing variability. The 3^rd , 5^th , 50^th , 95^th and 97^th smoothed centiles are presented. The 5^th centiles for the POF and SF were 3.1 mm and 4.7 mm at 22 weeks' gestation and 4.6 mm and 9.9 mm at 32 weeks, respectively. The 95^th centiles for the PV and CM were 8.5 mm and 7.5 mm at 22 weeks and 8.6 mm and 9.5 mm at 32 weeks, respectively.

CONCLUSIONS

We have produced prescriptive size standards for fetal brain structures based on prospectively enrolled pregnancies at low risk of abnormal outcome. We recommend these as international standards for the assessment of measurements obtained using ultrasound from fetal brain structures. © 2020 Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Analyzing the co-localization of substantia nigra hyper-echogenicities and iron accumulation in Parkinson's disease: A multi-modal atlas study with transcranial ultrasound and MRI

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Volumetric 3D analysis of hyper-echogenicities from transcranial ultrasound (TCS).

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First multi-modal analysis of TCS and QSM-MRI in Parkinson's disease.

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Computations of TCS-MRI registration and a novel multi-modal anatomical template.

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TCS hyper-echogenicities are co-localized with QSM iron accumulations.

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Co-localizations occur in the SNc and VTA, but nowhere else in the midbrain.

Background

Transcranial B-mode sonography (TCS) can detect hyperechogenic speckles in the area of the substantia nigra (SN) in Parkinson's disease (PD). These speckles correlate with iron accumulation in the SN tissue, but an exact volumetric localization in and around the SN is still unknown. Areas of increased iron content in brain tissue can be detected in vivo with magnetic resonance imaging, using quantitative susceptibility mapping (QSM).

Methods

In this work, we i) acquire, co-register and transform TCS and QSM imaging from a cohort of 23 PD patients and 27 healthy control subjects into a normalized atlas template space and ii) analyze and compare the 3D spatial distributions of iron accumulation in the midbrain, as detected by a signal increase (TCS+ and QSM+) in both modalities.

Results

We achieved sufficiently accurate intra-modal target registration errors (TRE<1 mm) for all MRI volumes and multi-modal TCS-MRI co-localization (TRE<4 mm) for 66.7% of TCS scans. In the caudal part of the midbrain, enlarged TCS+ and QSM+ areas were located within the SN pars compacta in PD patients in comparison to healthy controls. More cranially, overlapping TCS+ and QSM+ areas in PD subjects were found in the area of the ventral tegmental area (VTA).

Conclusion

Our findings are concordant with several QSM-based studies on iron-related alterations in the area SN pars compacta. They substantiate that TCS+ is an indicator of iron accumulation in Parkinson's disease within and in the vicinity of the SN. Furthermore, they are in favor of an involvement of the VTA and thereby the mesolimbic system in Parkinson's disease.

Probabilistic Learning Coherent Point Drift for 3D Ultrasound Fetal Head Registration

Quantification of brain growth is crucial for the assessment of fetal well being, for which ultrasound (US) images are the chosen clinical modality. However, they present artefacts, such as acoustic occlusion, especially after the 18^th gestational week, when cranial calcification appears. Fetal US volume registration is useful in one or all of the following cases: to monitor the evolution of fetometry indicators, to segment different structures using a fetal brain atlas, and to align and combine multiple fetal brain acquisitions. This paper presents a new approach for automatic registration of real 3D US fetal brain volumes, volumes that contain a considerable degree of occlusion artefacts, noise, and missing data. To achieve this, a novel variant of the coherent point drift method is proposed. This work employs supervised learning to segment and conform a point cloud automatically and to estimate their subsequent weight factors. These factors are obtained by a random forest-based classification and are used to appropriately assign nonuniform membership probability values of a Gaussian mixture model. These characteristics allow for the automatic registration of 3D US fetal brain volumes with occlusions and multiplicative noise, without needing an initial point cloud. Compared to other intensity and geometry-based algorithms, the proposed method achieves an error reduction of 7.4% to 60.7%, with a target registration error of only 6.38 ± 3.24 mm. This makes the herein proposed approach highly suitable for 3D automatic registration of fetal head US volumes, an approach which can be useful to monitor fetal growth, segment several brain structures, or even compound multiple acquisitions taken from different projections.

Automatic and efficient MRI-US segmentations for improving intraoperative image fusion in image-guided neurosurgery

Knowledge of the exact tumor location and structures at risk in its vicinity are crucial for neurosurgical interventions. Neuronavigation systems support navigation within the patient's brain, based on preoperative MRI (preMRI). However, increasing tissue deformation during the course of tumor resection reduces navigation accuracy based on preMRI. Intraoperative ultrasound (iUS) is therefore used as real-time intraoperative imaging. Registration of preMRI and iUS remains a challenge due to different or varying contrasts in iUS and preMRI. Here, we present an automatic and efficient segmentation of B-mode US images to support the registration process. The falx cerebri and the tentorium cerebelli were identified as examples for central cerebral structures and their segmentations can serve as guiding frame for multi-modal image registration. Segmentations of the falx and tentorium were performed with an average Dice coefficient of 0.74 and an average Hausdorff distance of 12.2 mm. The subsequent registration incorporates these segmentations and increases accuracy, robustness and speed of the overall registration process compared to purely intensity-based registration. For validation an expert manually located corresponding landmarks. Our approach reduces the initial mean Target Registration Error from 16.9 mm to 3.8 mm using our intensity-based registration and to 2.2 mm with our combined segmentation and registration approach. The intensity-based registration reduced the maximum initial TRE from 19.4 mm to 5.6 mm, with the approach incorporating segmentations this is reduced to 3.0 mm. Mean volumetric intensity-based registration of preMRI and iUS took 40.5 s, including segmentations 12.0 s.

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We demonstrate that our segmentation-based registration increases accuracy, robustness, and speed of multi-modal image registration of preoperative MRI and intraoperative ultrasound images for improving intraoperative image guided neurosurgery.

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For this we provide a fast and efficient segmentation of central anatomical structures of the perifalcine region on ultrasound images.

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We demonstrate the advantages of our method by comparing the results of our segmentation-based registration with the initial registration provided by the navigation system and with an intensity-based registration approach.

Multiple-correlation similarity for block-matching based fast CT to ultrasound registration in liver interventions

In this work we present a fast approach to perform registration of computed tomography to ultrasound volumes for image guided intervention applications. The method is based on a combination of block-matching and outlier rejection. The block-matching uses a correlation based multimodal similarity metric, where the intensity and the gradient of the computed tomography images along with the ultrasound volumes are the input images to find correspondences between blocks in the computed tomography and the ultrasound volumes. A variance and octree based feature point-set selection method is used for selecting distinct and evenly spread point locations for block-matching. Geometric consistency and smoothness criteria are imposed in an outlier rejection step to refine the block-matching results. The block-matching results after outlier rejection are used to determine the affine transformation between the computed tomography and the ultrasound volumes. Various experiments are carried out to assess the optimal performance and the influence of parameters on accuracy and computational time of the registration. A leave-one-patient-out cross-validation registration error of 3.6 mm is achieved over 29 datasets, acquired from 17 patients.

Fetal neuroimaging: an update on technical advances and clinical findings

This paper is based on a literature review from 2011 to 2016. The paper is divided into two main sections. The first section relates to technical advances in fetal imaging techniques, including fetal motion compensation, imaging at 3.0 T, 3-D T2-weighted MRI, susceptibility-weighted imaging, computed tomography, morphometric analysis, diffusion tensor imaging, spectroscopy and fetal behavioral assessment. The second section relates to clinical updates, including cerebral lamination, migrational anomalies, midline anomalies, neural tube defects, posterior fossa anomalies, sulcation/gyration and hypoxic-ischemic insults.

Fetal Central Nervous System Anomalies Detected by Magnetic Resonance Imaging: A Two-Year Experience

BACKGROUND

Magnetic resonance imaging (MRI) is gradually becoming more common for thorough visualization of the fetus than ultrasound (US), especially for neurological anomalies, which are the most common indications for fetal MRI and are a matter of concern for both families and society.

OBJECTIVES

We investigated fetal MRIs carried out in our center for frequency of central nervous system anomalies. This is the first such report in southern Iran.

MATERIALS AND METHODS

One hundred and seven (107) pregnant women with suspicious fetal anomalies in prenatal ultrasound entered a cross-sectional retrospective study from 2011 to 2013. A 1.5 T Siemens Avanto scanner was employed for sequences, including T2 HASTE and Trufisp images in axial, coronal, and sagittal planes to mother's body, T2 HASTE and Trufisp relative to the specific fetal body part being evaluated, and T1 flash images in at least one plane based on clinical indication. We investigated any abnormality in the central nervous system and performed descriptive analysis to achieve index of frequency.

RESULTS

Mean gestational age ± standard deviation (SD) for fetuses was 25.54 ± 5.22 weeks, and mean maternal age ± SD was 28.38 ± 5.80 years Eighty out of 107 (74.7%) patients who were referred with initial impression of borderline ventriculomegaly. A total of 18 out of 107 (16.82%) patients were found to have fetuses with CNS anomalies and the remainder were neurologically normal. Detected anomalies were as follow: 3 (16.6%) fetuses each had the Dandy-Walker variant and Arnold-Chiari II (with myelomeningocele). Complete agenesis of corpus callosum, partial agenesis of corpus callosum, and aqueductal stenosis were each seen in 2 (11.1%) fetuses. Arnold-Chiari II without myelomeningocele, anterior spina bifida associated with neurenteric cyst, arachnoid cyst, lissencephaly, and isolated enlarged cisterna magna each presented in one (5.5%) fetus. One fetus had concomitant schizencephaly and complete agenesis of the corpus callosum.

CONCLUSIONS

MRI is superior to ultrasound and physical exam of live births in detection of CNS anomalies. In this investigation within a single referral center in southern Iran, anomalies included Dandy-Walker variant and Arnold-Chiari II as the most common findings. Other findings with lower incidence were complete and partial agenesis of corpus callosum, aqueductal stenosis, anterior spina bifida, schizencephaly, arachnoid cyst, lissencephaly, and isolated enlarged cisterna magna.

Learning-based prediction of gestational age from ultrasound images of the fetal brain

We propose an automated framework for predicting gestational age (GA) and neurodevelopmental maturation of a fetus based on 3D ultrasound (US) brain image appearance. Our method capitalizes on age-related sonographic image patterns in conjunction with clinical measurements to develop, for the first time, a predictive age model which improves on the GA-prediction potential of US images. The framework benefits from a manifold surface representation of the fetal head which delineates the inner skull boundary and serves as a common coordinate system based on cranial position. This allows for fast and efficient sampling of anatomically-corresponding brain regions to achieve like-for-like structural comparison of different developmental stages. We develop bespoke features which capture neurosonographic patterns in 3D images, and using a regression forest classifier, we characterize structural brain development both spatially and temporally to capture the natural variation existing in a healthy population (N=447) over an age range of active brain maturation (18-34weeks). On a routine clinical dataset (N=187) our age prediction results strongly correlate with true GA (r=0.98,accurate within±6.10days), confirming the link between maturational progression and neurosonographic activity observable across gestation. Our model also outperforms current clinical methods by ±4.57 days in the third trimester-a period complicated by biological variations in the fetal population. Through feature selection, the model successfully identified the most age-discriminating anatomies over this age range as being the Sylvian fissure, cingulate, and callosal sulci.

Automatic deformable MR-ultrasound registration for image-guided neurosurgery

In this work, we present a novel algorithm for registration of 3-D volumetric ultrasound (US) and MR using Robust PaTch-based cOrrelation Ratio (RaPTOR). RaPTOR computes local correlation ratio (CR) values on small patches and adds the CR values to form a global cost function. It is therefore invariant to large amounts of spatial intensity inhomogeneity. We also propose a novel outlier suppression technique based on the orientations of the RaPTOR gradients. Our deformation is modeled with free-form cubic B-splines. We analytically derive the derivatives of RaPTOR with respect to the transformation, i.e., the displacement of the B-spline nodes, and optimize RaPTOR using a stochastic gradient descent approach. RaPTOR is validated on MR and tracked US images of neurosurgery. Deformable registration of the US and MR images acquired, respectively, preoperation and postresection is of significant clinical significance, but challenging due to, among others, the large amount of missing correspondences between the two images. This work is also novel in that it performs automatic registration of this challenging dataset. To validate the results, we manually locate corresponding anatomical landmarks in the US and MR images of tumor resection in brain surgery. Compared to rigid registration based on the tracking system alone, RaPTOR reduces the mean initial mTRE over 13 patients from 5.9 to 2.9 mm, and the maximum initial TRE from 17.0 to 5.9 mm. Each volumetric registration using RaPTOR takes about 30 sec on a single CPU core. An important challenge in the field of medical image analysis is the shortage of publicly available dataset, which can both facilitate the advancement of new algorithms to clinical settings and provide a benchmark for comparison. To address this problem, we will make our manually located landmarks available online.

Magnetic microbubble-mediated ultrasound-MRI registration based on robust optical flow model

Background

As a dual-modality contrast agent, magnetic microbubbles (MMBs) can not only improve contrast of ultrasound (US) image, but can also serve as a contrast agent of magnetic resonance image (MRI). With the help of MMBs, a new registration method between US image and MRI is presented.

Methods

In this method, MMBs were used in both ultrasound and magnetic resonance imaging process to enhance the most important information of interest. In order to reduce the influence of the speckle noise to registration, semi-automatic segmentations of US image and MRI were carried out by using active contour model. After that, a robust optical flow model between US image segmentation (floating image) and MRI segmentation (reference image) was built, and the vector flow field was estimated by using the Coarse-to-fine Gaussian pyramid and graduated non-convexity (GNC) schemes.

Results

Qualitative and quantitative analyses of multiple group comparison experiments showed that registration results using all methods tested in this paper without MMBs were unsatisfactory. On the contrary, the proposed method combined with MMBs led to the best registration results.

Conclusion

The proposed algorithm combined with MMBs contends with larger deformation and performs well not only for local deformation but also for global deformation. The comparison experiments also demonstrated that ultrasound-MRI registration using the above-mentioned method might be a promising method for obtaining more accurate image information.

Deformable registration of preoperative MR, pre-resection ultrasound, and post-resection ultrasound images of neurosurgery

PURPOSE

Sites that use ultrasound (US) in image-guided neurosurgery (IGNS) of brain tumors generally have three sets of imaging data: preoperative magnetic resonance (MR) image, pre-resection US, and post-resection US. The MR image is usually acquired days before the surgery, the pre-resection US is obtained after the craniotomy but before the resection, and finally, the post-resection US scan is performed after the resection of the tumor. The craniotomy and tumor resection both cause brain deformation, which significantly reduces the accuracy of the MR-US alignment.

METHOD

Three unknown transformations exist between the three sets of imaging data: MR to pre-resection US, pre- to post-resection US, and MR to post-resection US. We use two algorithms that we have recently developed to perform the first two registrations (i.e., MR to pre-resection US and pre- to post-resection US). Regarding the third registration (MR to post-resection US), we evaluate three strategies. The first method performs a registration between the MR and pre-resection US, and another registration between the pre- and post-resection US. It then composes the two transformations to register MR and post-resection US; we call this method compositional registration. The second method ignores the pre-resection US and directly registers the MR and post-resection US; we refer to this method as direct registration. The third method is a combination of the first and second: it uses the solution of the compositional registration as an initial solution for the direct registration method. We call this method group-wise registration.

RESULTS

We use data from 13 patients provided in the MNI BITE database for all of our analysis. Registration of MR and pre-resection US reduces the average of the mean target registration error (mTRE) from 4.1 to 2.4 mm. Registration of pre- and post-resection US reduces the average mTRE from 3.7 to 1.5 mm. Regarding the registration of MR and post-resection US, all three strategies reduce the mTRE. The initial average mTRE is 5.9 mm, which reduces to 3.3 mm with the compositional method, 2.9 mm with the direct technique, and 2.8 mm with the group-wise method.

CONCLUSION

Deformable registration of MR and pre- and post-resection US images significantly improves their alignment. Among the three methods proposed for registering the MR to post-resection US, the group-wise method gives the lowest TRE values. Since the running time of all registration algorithms is less than 2 min on one core of a CPU, they can be integrated into IGNS systems for interactive use during surgery.

Resting State fMRI in the moving fetus: a robust framework for motion, bias field and spin history correction

There is growing interest in exploring fetal functional brain development, particularly with Resting State fMRI. However, during a typical fMRI acquisition, the womb moves due to maternal respiration and the fetus may perform large-scale and unpredictable movements. Conventional fMRI processing pipelines, which assume that brain movements are infrequent or at least small, are not suitable. Previous published studies have tackled this problem by adopting conventional methods and discarding as much as 40% or more of the acquired data. In this work, we developed and tested a processing framework for fetal Resting State fMRI, capable of correcting gross motion. The method comprises bias field and spin history corrections in the scanner frame of reference, combined with slice to volume registration and scattered data interpolation to place all data into a consistent anatomical space. The aim is to recover an ordered set of samples suitable for further analysis using standard tools such as Group Independent Component Analysis (Group ICA). We have tested the approach using simulations and in vivo data acquired at 1.5 T. After full motion correction, Group ICA performed on a population of 8 fetuses extracted 20 networks, 6 of which were identified as matching those previously observed in preterm babies.