MIA - A free and open source software for gray scale medical image analysis

BraNet: a mobil application for breast image classification based on deep learning algorithms

Mobile health apps are widely used for breast cancer detection using artificial intelligence algorithms, providing radiologists with second opinions and reducing false diagnoses. This study aims to develop an open-source mobile app named "BraNet" for 2D breast imaging segmentation and classification using deep learning algorithms. During the phase off-line, an SNGAN model was previously trained for synthetic image generation, and subsequently, these images were used to pre-trained SAM and ResNet18 segmentation and classification models. During phase online, the BraNet app was developed using the react native framework, offering a modular deep-learning pipeline for mammography (DM) and ultrasound (US) breast imaging classification. This application operates on a client-server architecture and was implemented in Python for iOS and Android devices. Then, two diagnostic radiologists were given a reading test of 290 total original RoI images to assign the perceived breast tissue type. The reader's agreement was assessed using the kappa coefficient. The BraNet App Mobil exhibited the highest accuracy in benign and malignant US images (94.7%/93.6%) classification compared to DM during training I (80.9%/76.9%) and training II (73.7/72.3%). The information contrasts with radiological experts' accuracy, with DM classification being 29%, concerning US 70% for both readers, because they achieved a higher accuracy in US ROI classification than DM images. The kappa value indicates a fair agreement (0.3) for DM images and moderate agreement (0.4) for US images in both readers. It means that not only the amount of data is essential in training deep learning algorithms. Also, it is vital to consider the variety of abnormalities, especially in the mammography data, where several BI-RADS categories are present (microcalcifications, nodules, mass, asymmetry, and dense breasts) and can affect the API accuracy model.

Dental morphology in Homo habilis and its implications for the evolution of early Homo

The phylogenetic position of Homo habilis is central to debates over the origin and early evolution of the genus Homo. A large portion of the species hypodigm consists of dental remains, but they have only been studied at the often worn enamel surface. We investigate the morphology of the H. habilis enamel-dentine junction (EDJ), which is preserved in cases of moderate tooth wear and known to carry a strong taxonomic signal. Geometric morphometrics is used to characterise dentine crown shape and size across the entire mandibular and maxillary tooth rows, compared with a broad comparative sample (n = 712). We find that EDJ morphology in H. habilis is for the most part remarkably primitive, supporting the hypothesis that the H. habilis hypodigm has more in common with Australopithecus than later Homo. Additionally, the chronologically younger specimen OH 16 displays a suite of derived features; its inclusion in H. habilis leads to excessive levels of variation.

Extended-volume image-derived models of coronary microcirculation

OBJECTIVE

Recent advances in tissue clearing and high-throughput imaging have enabled the acquisition of extended-volume microvasculature images at a submicron resolution. The objective of this study was to extract information from this type of images by integrating a sequence of 3D image processing steps on Terabyte scale datasets.

METHODS

We acquired coronary microvasculature images throughout an entire short-axis slice of a 3-month-old Wistar-Kyoto rat heart. This dataset covered 13 × 10 × 0.6 mm at a resolution of 0.933 × 0.933 × 1.866 μm and occupied 700 Gigabytes of disk space. We used chunk-based image segmentation, combined with an efficient graph generation technique, to quantify the microvasculature in the large-scale images. Specifically, we focused on the microvasculature with a vessel diameter up to 15 μm.

RESULTS

Morphological data for the complete short-axis ring were extracted within 16 h using this pipeline. From the analyses, we identified that microvessel lengths in the rat coronary microvasculature varied from 6 to 300 μm. However, their distribution was heavily skewed toward shorter lengths, with a mode of 16.5 μm. In contrast, vessel diameters ranged from 3 to 15 μm and had an approximately normal distribution of 6.5 ± 2 μm.

CONCLUSION

The tools and techniques from this study will serve other investigations into the microcirculation, and the wealth of data from this study will enable the analysis of biophysical mechanisms using computer models.

Deep Learning-Based Image Registration in Dynamic Myocardial Perfusion CT Imaging

Registration of dynamic CT image sequences is a crucial preprocessing step for clinical evaluation of multiple physiological determinants in the heart such as global and regional myocardial perfusion. In this work, we present a deformable deep learning-based image registration method for quantitative myocardial perfusion CT examinations, which in contrast to previous approaches, takes into account some unique challenges such as low image quality with less accurate anatomical landmarks, dynamic changes of contrast agent concentration in the heart chambers and tissue, and misalignment caused by cardiac stress, respiration, and patient motion. The introduced method uses a recursive cascade network with a ventricle segmentation module, and a novel loss function that accounts for local contrast changes over time. It was trained and validated on a dataset of n = 118 patients with known or suspected coronary artery disease and/or aortic valve insufficiency. Our results demonstrate that the proposed method is capable of registering dynamic cardiac perfusion sequences by reducing local tissue displacements of the left ventricle (LV), whereas contrast changes do not affect the registration and image quality, in particular the absolute CT (HU) values of the entire CT sequence. In addition, the deep learning-based approach presented reveals a short processing time of a few seconds compared to conventional image registration methods, demonstrating its application potential for quantitative CT myocardial perfusion measurements in daily clinical routine.

Generative Adversarial Networks in Medical Image Processing

BACKGROUND

The emergence of generative adversarial networks (GANs) has provided new technology and framework for the application of medical images. Specifically, a GAN requires little to no labeled data to obtain high-quality data that can be generated through competition between the generator and discriminator networks. Therefore, GANs are rapidly proving to be a state-of-the-art foundation, achieving enhanced performances in various medical applications.

METHODS

In this article, we introduce the principles of GANs and their various variants, deep convolutional GAN, conditional GAN, Wasserstein GAN, Info-GAN, boundary equilibrium GAN, and cycle-GAN.

RESULTS

All various GANs have found success in medical imaging tasks, including medical image enhancement, segmentation, classification, reconstruction, and synthesis. Furthermore, we summarize the data processing methods and evaluation indicators. Finally, we note the limitations of existing methods and the existing challenges that need to be addressed in this field.

CONCLUSION

Although GANs are in the initial stage of development in medical image processing, it will have a great prospect in the future.

Accessory cusp expression at the enamel-dentine junction of hominin mandibular molars

Studies of hominin dental morphology frequently consider accessory cusps on the lower molars, in particular those on the distal margin of the tooth (C6 or distal accessory cusp) and the lingual margin of the tooth (C7 or lingual accessory cusp). They are often utilized in studies of hominin systematics, where their presence or absence is assessed at the outer enamel surface (OES). However, studies of the enamel-dentine junction (EDJ) suggest these traits may be more variable in development, morphology and position than previously thought. Building on these studies, we outline a scoring procedure for the EDJ expression of these accessory cusps that considers the relationship between these accessory cusps and the surrounding primary cusps. We apply this scoring system to a sample of Plio-Pleistocene hominin mandibular molars of Paranthropus robustus, Paranthropus boisei, Australopithecus afarensis, Australopithecus africanus, Homo sp., Homo habilis and Homo erectus from Africa and Asia (n = 132). We find that there are taxon-specific patterns in accessory cusp expression at the EDJ that are consistent with previous findings at the OES. For example, P. robustus M₁s and M₂s very often have a distal accessory cusp but no lingual accessory cusp, while H. habilis M₁s and M₂s show the opposite pattern. The EDJ also reveals a number of complicating factors; some apparent accessory cusps at the enamel surface are represented at the EDJ only by shouldering on the ridges associated with the main cusps, while other accessory cusps appear to have little or no EDJ expression at all. We also discuss the presence of double and triple accessory cusps, including the presence of a double lingual accessory cusp on the distal ridge of the metaconid in the type specimen of H. habilis (OH 7–M₁) that is not clear at the OES due to occlusal wear. Overall, our observations, as well as our understanding of the developmental underpinnings of cusp patterning, suggest that we should be cautious in our comparisons of accessory cusps for taxonomic interpretations.

The morphology of the Late Pleistocene hominin remains from the site of La Cotte de St Brelade, Jersey (Channel Islands)

Thirteen permanent fully erupted teeth were excavated at the Paleolithic site of La Cotte de St Brelade in Jersey in 1910 and 1911. These were all found in the same location, on a ledge behind a hearth in a Mousterian occupation level. They were originally identified as being Neanderthal. A fragment of occipital bone was found in a separate locality in a later season. Recent dating of adjacent sediments gives a probable age of <48 ka. The purpose of this article is to provide an updated description of the morphology of this material and consider its likely taxonomic assignment from comparison with Neanderthal and Homo sapiens samples. One of the original teeth has been lost, and we identify one as nonhominin. At least two adult individuals are represented. Cervix shape and the absence of common Neanderthal traits in several teeth suggest affinities with H. sapiens in both individuals, while crown and root dimensions and root morphology of all the teeth are entirely consistent with a Neanderthal attribution, pointing toward a possible shared Neanderthal and H. sapiens ancestry (the likely date of this material corresponds with the time in which both Neanderthals and H. sapiens were present in Europe). The occipital fragment is stratigraphically more recent and does not exhibit any diagnostic Neanderthal features.

Using point clouds to investigate the relationship between trabecular bone phenotype and behavior: An example utilizing the human calcaneus

OBJECTIVES

The objective of this study is to demonstrate a new method for analyzing trabecular bone volume fraction and degree of anisotropy in three dimensions.

METHODS

We use a combination of automatic mesh registration, point-cloud correspondence registration, and P-value corrected univariate statistical tests to compare bone volume fraction and degree of anisotropy on a point by point basis across the entire calcaneus of two human groups with different subsistence strategies.

RESULTS

We found that the patterns of high and low bone volume fraction and degree of anisotropy distribution between the Black Earth (hunter-gatherers) and Norris Farms (mixed-strategy agriculturalists) are very similar, but differ in magnitude. The hunter-gatherers exhibit higher levels of bone volume fraction and less anisotropic trabecular bone organization. Additionally, patterns of bone volume fraction and degree of anisotropy in the calcaneus correspond well with biomechanical expectations of relative forces experienced during walking and running.

CONCLUSIONS

We conclude that comparing site-specific, localized differences in trabecular bone variables such as bone volume fraction and degree of anisotropy in three-dimensions is a powerful analytical tool. This method makes it possible to determine where similarities and differences between groups are located within the whole skeletal element of interest. The visualization of multiple variables also provides a way for researchers to see how the trabecular bone variables interact within the morphology, and allows for a more nuanced understanding of how they relate to one another and the broader mechanical environment.

Distinct mandibular premolar crown morphology in Homo naledi and its implications for the evolution of Homo species in southern Africa

Homo naledi displays a combination of features across the skeleton not found in any other hominin taxon, which has hindered attempts to determine its placement within the hominin clade. Using geometric morphometrics, we assess the morphology of the mandibular premolars of the species at the enamel-dentine junction (EDJ). Comparing with specimens of Paranthropus, Australopithecus and Homo (n = 97), we find that the H. naledi premolars from the Dinaledi chamber consistently display a suite of traits (e.g., tall crown, well-developed P₃ and P₄ metaconid, strongly developed P₃ mesial marginal ridge, and a P₃ > P₄ size relationship) that distinguish them from known hominin groups. Premolars from a second locality, the Lesedi Chamber, are consistent with this morphology. We also find that two specimens from South Africa, SK 96 (usually attributed to Paranthropus) and Stw 80 (Homo sp.), show similarities to the species, and we discuss a potential evolutionary link between H. naledi and hominins from Sterkfontein and Swartkrans.

Endostructural morphology in hominoid mandibular third premolars: Geometric morphometric analysis of dentine crown shape

In apes, the mandibular third premolar (P₃) is adapted for a role in honing the large upper canine. The role of honing was lost early in hominin evolution, releasing the tooth from this functional constraint and allowing it to respond to subsequent changes in masticatory demands. This led to substantial morphological changes, and as such the P₃ has featured prominently in systematic analyses of the hominin clade. The application of microtomography has also demonstrated that examination of the enamel-dentine junction (EDJ) increases the taxonomic value of variations in crown morphology. Here we use geometric morphometric techniques to analyze the shape of the P₃ EDJ in a broad sample of fossil hominins, modern humans, and extant apes (n = 111). We test the utility of P₃ EDJ shape for distinguishing among hominoids, address the affinities of a number of hominin specimens of uncertain taxonomic attribution, and characterize the changes in P₃ EDJ morphology across our sample, with particular reference to features relating to canine honing and premolar 'molarization'. We find that the morphology of the P₃ EDJ is useful in taxonomic identification of individual specimens, with a classification accuracy of up to 88%. The P₃ EDJ of canine-honing apes displays a tall protoconid, little metaconid development, and an asymmetrical crown shape. Plio-Pleistocene hominin taxa display derived masticatory adaptations at the EDJ, such as the molarized premolars of Australopithecus africanus and Paranthropus, which have well-developed marginal ridges, an enlarged talonid, and a large metaconid. Modern humans and Neanderthals display a tall dentine body and reduced metaconid development, a morphology shared with premolars from Mauer and the Cave of Hearths. Homo naledi displays a P₃ EDJ morphology that is unique among our sample; it is quite unlike Middle Pleistocene and recent Homo samples and most closely resembles Australopithecus, Paranthropus and early Homo specimens.

Mandibular molar root and pulp cavity morphology in Homo naledi and other Plio-Pleistocene hominins

The craniomandibular morphology of Homo naledi shows variable resemblances with species across Homo, which confounds an easy assessment of its phylogenetic position. In terms of skull shape, H. naledi has its closest affinities with Homo erectus, while mandibular shape places it closer to early Homo. From a tooth crown perspective, the smaller molars of H. naledi make it distinct from early Homo and H. erectus. Here, we compare the mandibular molar root morphology of six H. naledi individuals from the Dinaledi Chamber to those of African and Eurasian Plio-Pleistocene fossil hominins (totalling 183 mandibular first, second and third molars). The analysis of five root metric variables (cervical plane area, root length, root cervix volume, root branch volume, and root surface area) derived from microCT reconstructions reveals that the molar roots of H. naledi are smaller than those of Homo habilis, Homo rudolfensis, and H. erectus, but that they resemble those of three Homo sp. specimens from Swartkrans and Koobi Fora in size and overall appearance. Moreover, though H. naledi molar roots are similar in absolute size to Pleistocene Homo sapiens, they differ from H. sapiens in having a larger root volume for a given cervical plane area and less taurodont roots; the root cervix-to-branch proportions of H. naledi are comparable to those of Australopithecus africanus and species of Paranthropus. H. naledi also shares a metameric root volume pattern (M₂ > M₃ > M₁) with Australopithecus and Paranthropus but not with any of the other Homo species (M₂ > M₁ > M₃). Our findings therefore concur with previous studies that found that H. naledi shares plesiomorphic features with early Homo, Australopithecus, and Paranthropus. While absolute molar root size aligns H. naledi with Homo from North and South Africa, it is distinguishable from these in terms of root volumetric proportions.

CoreSlicer: a web toolkit for analytic morphomics

BACKGROUND

Analytic morphomics, or more simply, "morphomics," refers to the measurement of specific biomarkers of body composition from medical imaging, most commonly computed tomography (CT) images. An emerging body of literature supports the use of morphomic markers measured on single-slice CT images for risk prediction in a range of clinical populations. However, uptake by healthcare providers been limited due to the lack of clinician-friendly software to facilitate measurements. The objectives of this study were to describe the interface and functionality of CoreSlicer- a free and open-source web-based interface aiming to facilitate measurement of analytic morphomics by clinicians - and to validate muscle and fat measurements performed in CoreSlicer against reference software.

RESULTS

Measurements of muscle and fat obtained in CoreSlicer show high agreement with established reference software. CoreSlicer features a full set of DICOM viewing tools and extensible plugin interface to facilitate rapid prototyping and validation of new morphomic markers by researchers. We present published studies illustrating the use of CoreSlicer by clinicians with no prior knowledge of medical image segmentation techniques and no formal training in radiology, where CoreSlicer was successfully used to predict operative risk in three distinct populations of cardiovascular patients.

CONCLUSIONS

CoreSlicer enables extraction of morphomic markers from CT images by non-technically skilled clinicians. Measurements were reproducible and accurate in relation to reference software.

Evo-devo models of tooth development and the origin of hominoid molar diversity

The detailed anatomical features that characterize fossil hominin molars figure prominently in the reconstruction of their taxonomy, phylogeny, and paleobiology. Despite the prominence of molar form in human origins research, the underlying developmental mechanisms generating the diversity of tooth crown features remain poorly understood. A model of tooth morphogenesis-the patterning cascade model (PCM)-provides a developmental framework to explore how and why the varying molar morphologies arose throughout human evolution. We generated virtual maps of the inner enamel epithelium-an indelibly preserved record of enamel knot arrangement-in 17 living and fossil hominoid species to investigate whether the PCM explains the expression of all major accessory cusps. We found that most of the variation and evolutionary changes in hominoid molar morphology followed the general developmental rule shared by all mammals, outlined by the PCM. Our results have implications for the accurate interpretation of molar crown configuration in hominoid systematics.

MIA-Clustering: a novel method for segmentation of paleontological material

Paleontological research increasingly uses high-resolution micro-computed tomography (μCT) to study the inner architecture of modern and fossil bone material to answer important questions regarding vertebrate evolution. This non-destructive method allows for the measurement of otherwise inaccessible morphology. Digital measurement is predicated on the accurate segmentation of modern or fossilized bone from other structures imaged in μCT scans, as errors in segmentation can result in inaccurate calculations of structural parameters. Several approaches to image segmentation have been proposed with varying degrees of automation, ranging from completely manual segmentation, to the selection of input parameters required for computational algorithms. Many of these segmentation algorithms provide speed and reproducibility at the cost of flexibility that manual segmentation provides. In particular, the segmentation of modern and fossil bone in the presence of materials such as desiccated soft tissue, soil matrix or precipitated crystalline material can be difficult. Here we present a free open-source segmentation algorithm application capable of segmenting modern and fossil bone, which also reduces subjective user decisions to a minimum. We compare the effectiveness of this algorithm with another leading method by using both to measure the parameters of a known dimension reference object, as well as to segment an example problematic fossil scan. The results demonstrate that the medical image analysis-clustering method produces accurate segmentations and offers more flexibility than those of equivalent precision. Its free availability, flexibility to deal with non-bone inclusions and limited need for user input give it broad applicability in anthropological, anatomical, and paleontological contexts.

New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens

Fossil evidence points to an African origin of Homo sapiens from a group called either H. heidelbergensis or H. rhodesiensis. However, the exact place and time of emergence of H. sapiens remain obscure because the fossil record is scarce and the chronological age of many key specimens remains uncertain. In particular, it is unclear whether the present day 'modern' morphology rapidly emerged approximately 200 thousand years ago (ka) among earlier representatives of H. sapiens or evolved gradually over the last 400 thousand years. Here we report newly discovered human fossils from Jebel Irhoud, Morocco, and interpret the affinities of the hominins from this site with other archaic and recent human groups. We identified a mosaic of features including facial, mandibular and dental morphology that aligns the Jebel Irhoud material with early or recent anatomically modern humans and more primitive neurocranial and endocranial morphology. In combination with an age of 315 ± 34 thousand years (as determined by thermoluminescence dating), this evidence makes Jebel Irhoud the oldest and richest African Middle Stone Age hominin site that documents early stages of the H. sapiens clade in which key features of modern morphology were established. Furthermore, it shows that the evolutionary processes behind the emergence of H. sapiens involved the whole African continent.

Homology, homoplasy and cusp variability at the enamel-dentine junction of hominoid molars

Evolutionary studies of mammalian teeth have generally concentrated on the adaptive and functional significance of dental features, whereas the role of development on phenotypic generation and as a source of variation has received comparatively little attention. The present study combines an evolutionary biological framework with state-of-the-art imaging techniques to examine the developmental basis of variation of accessory cusps. Scholars have long used the position and relatedness of cusps to other crown structures as a criterion for differentiating between developmentally homologous and homoplastic features, which can be evaluated with greater accuracy at the enamel-dentine junction (EDJ). Following this approach, we collected digital models of the EDJ and outer enamel surface of more than 1000 hominoid teeth to examine whether cusp 5 of the upper molars (UM C5) and cusps 6 and 7 of the lower molars (LM C6 and LM C7) were associated each with a common developmental origin across species. Results revealed that each of these cusps can develop in a variety of ways, in association with different dental tissues (i.e. oral epithelium, enamel matrix) and dental structures (i.e. from different cusps, crests and cingula). Both within and between species variability in cusp origin was highest in UM C5, followed by LM C7, and finally LM C6. The lack of any species-specific patterns suggests that accessory cusps in hominoids are developmentally homoplastic and that they may not be useful for identifying phylogenetic homology. An important and unanticipated finding of this study was the identification of a new taxonomically informative feature at the EDJ of the upper molars, namely the post-paracone tubercle (PPT). We found that the PPT was nearly ubiquitous in H. neanderthalensis and the small sample of Middle Pleistocene African and European humans (MPAE) examined, differing significantly from the low frequencies observed in all other hominoids, including Pleistocene and recent H. sapiens. We emphasize the utility of the EDJ for human evolutionary studies and demonstrate how features that look similar at the external surface may be the product of different developmental patterns. This study also highlights the importance of incorporating both developmental and morphological data into evolutionary studies in order to gain a better understanding of the evolutionary significance of dental and skeletal features.

An Open Benchmark Challenge for Motion Correction of Myocardial Perfusion MRI

Cardiac magnetic resonance perfusion examinations enable noninvasive quantification of myocardial blood flow. However, motion between frames due to breathing must be corrected for quantitative analysis. Although several methods have been proposed, there is a lack of widely available benchmarks to compare different algorithms. We sought to compare many algorithms from several groups in an open benchmark challenge. Nine clinical studies from two different centers comprising normal and diseased myocardium at both rest and stress were made available for this study. The primary validation measure was regional myocardial blood flow based on the transfer coefficient (Ktrans), which was computed using a compartment model and the myocardial perfusion reserve (MPR) index. The ground truth was calculated using contours drawn manually on all frames by a single observer, and visually inspected by a second observer. Six groups participated and 19 different motion correction algorithms were compared. Each method used one of three different motion models: rigid, global affine, or local deformation. The similarity metric also varied with methods employing either sum-of-squared differences, mutual information, or cross correlation. There were no significant differences in Ktrans or MPR compared across different motion models or similarity metrics. Compared with the ground truth, only Ktrans for the sum-of-squared differences metric, and for local deformation motion models, had significant bias. In conclusion, the open benchmark enabled evaluation of clinical perfusion indices over a wide range of methods. In particular, there was no benefit of nonrigid registration techniques over the other methods evaluated in this study. The benchmark data and results are available from the Cardiac Atlas Project ( www.cardiacatlas.org).

3D printing: clinical applications in orthopaedics and traumatology

Advances in image processing have led to the clinical use of 3D printing technology, giving the surgeon a realistic physical model of the anatomy upon which he or she will operate.

Relying on CT images, the surgeon creates a virtual 3D model of the target anatomy from a series of bi-dimensional images, translating the information contained in CT images into a more usable format.

3D printed models can play a central role in surgical planning and in the training of novice surgeons, as well as reducing the rate of re-operation.

Cite this article: Auricchio F, Marconi S. 3D printing: clinical applications in orthopaedics and traumatology. EFORT Open Rev 2016;1:121–127. DOI: 10.1302/2058-5241.1.000012.

Object-based representation and analysis of light and electron microscopic volume data using Blender

Background

Rapid improvements in light and electron microscopy imaging techniques and the development of 3D anatomical atlases necessitate new approaches for the visualization and analysis of image data. Pixel-based representations of raw light microscopy data suffer from limitations in the number of channels that can be visualized simultaneously. Complex electron microscopic reconstructions from large tissue volumes are also challenging to visualize and analyze.

Results

Here we exploit the advanced visualization capabilities and flexibility of the open-source platform Blender to visualize and analyze anatomical atlases. We use light-microscopy-based gene expression atlases and electron microscopy connectome volume data from larval stages of the marine annelid Platynereis dumerilii. We build object-based larval gene expression atlases in Blender and develop tools for annotation and coexpression analysis. We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity.

Conclusions

We demonstrate the power and flexibility of Blender for visualizing and exploring complex anatomical atlases. The resources we have developed for Platynereis will facilitate data sharing and the standardization of anatomical atlases for this species. The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0652-7) contains supplementary material, which is available to authorized users.

Free breathing myocardial perfusion data sets for performance analysis of motion compensation algorithms

Background

Perfusion quantification by using first-pass gadolinium-enhanced myocardial perfusion magnetic resonance imaging (MRI) has proved to be a reliable tool for the diagnosis of coronary artery disease that leads to reduced blood flow to the myocardium. The image series resulting from such acquisition usually exhibits a breathing motion that needs to be compensated for if a further automatic analysis of the perfusion is to be executed. Various algorithms have been presented to facilitate such a motion compensation, but the lack of publicly available data sets hinders a proper, reproducible comparison of these algorithms.

Material

Free breathing perfusion MRI series of ten patients considered clinically to have a stress perfusion defect were acquired; for each patient a rest and a stress study was executed. Manual segmentations of the left ventricle myocardium and the right-left ventricle insertion point are provided for all images in order to make a unified validation of the motion compensation algorithms and the perfusion analysis possible. In addition, all the scripts and the software required to run the experiments are provided alongside the data, and to enable interested parties to directly run the experiments themselves, the test bed is also provided as a virtual hard disk.

Findings

To illustrate the utility of the data set two motion compensation algorithms with publicly available implementations were applied to the data and earlier reported results about the performance of these algorithms could be confirmed.

Conclusion

The data repository alongside the evaluation test bed provides the option to reliably compare motion compensation algorithms for myocardial perfusion MRI. In addition, we encourage that researchers add their own annotations to the data set, either to provide inter-observer comparisons of segmentations, or to make other applications possible, for example, the validation of segmentation algorithms.

[PET and SPECT in epilepsy]

Epilepsy is one of the most frequent chronic neurological disorders, affecting 1-2% of the population. Patients with complex partial drug resistant episodes may benefit from a surgical treatment consisting in the excision of the epileptogenic area. Localization of the epileptogenic area was classically performed with video-EEG and magnetic resonance (MR). Recently, functional neuroimaging studies of Nuclear Medicine, positron emission tomography (PET) and single photon emission tomography (SPECT) have demonstrated their utility in the localization of the epileptogenic area prior to surgery. Ictal SPECT with brain perfusion tracers show an increase in blood flow in the initial ictal focus, while PET with (18)FDG demonstrates a decrease of glucose metabolism in the interictal functional deficit zone. In this review, the basic principles and methodological characteristics of the SPECT and PET in epilepsy are described. The ictal SPECT injection mechanism, different patterns of perfusion based on the time of ictal, postictal or interictal injection are detailed and the different diagnostic sensitivities of each one of these SPECT are reviewed. Different methods of analysis of the images with substraction and fusion systems with the MR are described. Similarly, the injection methodology, quantification and evaluation of the images of the PET in epilepsy are described. Finally, the main clinical indications of SPECT and PET in temporal and extratemporal epilepsy are detailed.