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In a broad range of fields it may be desirable to reuse a supervised classification algorithm and apply it to a new data set. However, generalization of such an algorithm and thus achieving a similar classification performance is only possible when the training data used to build the algorithm is similar to new unseen data one wishes to apply it to. It is often unknown in advance how an algorithm will perform on new unseen data, being a crucial reason for not deploying an algorithm at all. Therefore, tools are needed to measure the similarity of data sets. In this paper, we propose the Data Representativeness Criterion (DRC) to determine how representative a training data set is of a new unseen data set. We present a proof of principle, to see whether the DRC can quantify the similarity of data sets and whether the DRC relates to the performance of a supervised classification algorithm. We compared a number of magnetic resonance imaging (MRI) data sets, ranging from subtle to severe difference is acquisition parameters. Results indicate that, based on the similarity of data sets, the DRC is able to give an indication as to when the performance of a supervised classifier decreases. The strictness of the DRC can be set by the user, depending on what one considers to be an acceptable underperformance.

Pooling of multicenter brain imaging data is a trend in studies on ageing related brain diseases. This poses challenges to MR-based brain segmentation. The performance across different field strengths of three widely used automated methods for brain volume measurements was assessed in the present study. Ten subjects (mean age: 64 years) were scanned on 1.5T and 3T MRI on the same day. We determined robustness across field strength (i.e., whether measured volumes between 3T and 1.5T scans in the same subjects were similar) for SPM12, Freesurfer 5.3.0 and FSL 5.0.7. As a frame of reference, 3T MRI scans from 20 additional subjects (mean age: 71 years) were segmented manually to determine accuracy of the methods (i.e., whether measured volumes corresponded with expert-defined volumes). Total brain volume (TBV) measurements were robust across field strength for Freesurfer and FSL (mean absolute difference as % of mean volume ≤ 1%), but less so for SPM (4%). Gray matter (GM) and white matter (WM) volume measurements were robust for Freesurfer (1%; 2%) and FSL (2%; 3%) but less so for SPM (5%; 4%). For intracranial volume (ICV), SPM was more robust (2%) than FSL (3%) and Freesurfer (9%). TBV measurements were accurate for SPM and FSL, but less so for Freesurfer. For GM volume, SPM was accurate, but accuracy was lower for Freesurfer and FSL. For WM volume, Freesurfer was accurate, but SPM and FSL were less accurate. For ICV, FSL was accurate, while SPM and Freesurfer were less accurate. Brain volumes and ICV could be measured quite robustly in scans acquired at different field strengths, but performance of the methods varied depending on the assessed compartment (e.g., TBV or ICV). Selection of an appropriate method in multicenter brain imaging studies therefore depends on the compartment of interest.

Background and Purposes. The 320-detector row CT scanner enables visualization of whole-brain hemodynamic information (dynamic CT angiography (CTA) derived from CT perfusion scans). However, arterial image quality in dynamic CTA (dCTA) is inferior to arterial image quality in standard CTA. This study evaluates whether the arterial image quality can be improved by using a total bolus extraction (ToBE) method. Materials and Methods. DCTAs of 15 patients, who presented with signs of acute cerebral ischemia, were derived from 320-slice CT perfusion scans using both the standard subtraction method and the proposed ToBE method. Two neurointerventionalists blinded to the scan type scored the arterial image quality on a 5-point scale in the 4D dCTAs in consensus. Arteries were divided into four categories: (I) large extradural, (II) intradural (large, medium, and small), (III) communicating arteries, and (IV) cerebellar and ophthalmic arteries. Results. Quality of extradural and intradural arteries was significantly higher in the ToBE dCTAs than in the standard dCTAs (extradural P=0.001, large intradural P<0.001, medium intradural P<0.001, and small intradural P<0.001). Conclusion. The 4D dCTAs derived with the total bolus extraction (ToBE) method provide hemodynamic information combined with improved arterial image quality as compared to standard 4D dCTAs.

Many methods have been proposed for tissue segmentation in brain MRI scans. The multitude of methods proposed complicates the choice of one method above others. We have therefore established the MRBrainS online evaluation framework for evaluating (semi)automatic algorithms that segment gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) on 3T brain MRI scans of elderly subjects (65–80 y). Participants apply their algorithms to the provided data, after which their results are evaluated and ranked. Full manual segmentations of GM, WM, and CSF are available for all scans and used as the reference standard. Five datasets are provided for training and fifteen for testing. The evaluated methods are ranked based on their overall performance to segment GM, WM, and CSF and evaluated using three evaluation metrics (Dice, H95, and AVD) and the results are published on the MRBrainS13 website. We present the results of eleven segmentation algorithms that participated in the MRBrainS13 challenge workshop at MICCAI, where the framework was launched, and three commonly used freeware packages: FreeSurfer, FSL, and SPM. The MRBrainS evaluation framework provides an objective and direct comparison of all evaluated algorithms and can aid in selecting the best performing method for the segmentation goal at hand.

In the medical image analysis field, organizing challenges with associated workshops at international conferences began in 2007 and has grown to include over 150 challenges. Several of these challenges have had a major impact in the field. However, whereas well-designed challenges have the potential to unite and focus the field on creating solutions to important problems, poorly designed and documented challenges can equally impede a field and lead to pursuing incremental improvements in metric scores with no theoretic or clinical significance. This is supported by a critical assessment of challenges at the international MICCAI conference. In this assessment the main observation was that small changes to the underlying challenge data can drastically change the ranking order on the leaderboard. Related to this is the practice of leaderboard climbing, which is characterized by participants focusing on incrementally improving metric results rather than advancing science or solving the driving problem of a challenge. In this abstract we look beyond the leaderboard of a challenge and instead look at the conclusions that can be drawn from a challenge with respect to the research problem that it is addressing. Research study design is well described in other research areas and can be translated to challenge design when viewing challenges as research studies on algorithm performance that address a research problem. Based on the two main types of scientific research study design, we propose two main challenge types, which we think would benefit other research areas as well: 1) an insight challenge that is based on a qualitative study design and 2) a deployment challenge that is based on a quantitative study design. In addition we briefly touch upon related considerations with respect to statistical significance versus practical significance, generalizability and data saturation.

Generalization of voxelwise classifiers is hampered by differences between MRI-scanners, e.g. different acquisition protocols and field strengths. To address this limitation, we propose a Siamese neural network (MRAI-NET) that extracts acquisition-invariant feature vectors. These can consequently be used by task-specific methods, such as voxelwise classifiers for tissue segmentation. MRAI-NET is tested on both simulated and real patient data. Experiments show that MRAI-NET outperforms voxelwise classifiers trained on the source or target scanner data when a small number of labeled samples is available.

In this paper we aim to refine the concept of grand challenges in medical image analysis, based on statistical principles from quantitative and qualitative experimental research. We identify two types of challenges based on their generalization objective: 1) a deployment challenge and 2) an insight challenge. A deployment challenge's generalization objective is to find algorithms that solve a medical image analysis problem, which thereby requires the use of a quantitative experimental design. An insight challenge's generalization objective is to gain a broad understanding of what class of algorithms might be effective for a class of medical image analysis problems, in which case a qualitative experimental design is sufficient. Both challenge types are valuable, but problems arise when a challenge's design and objective are inconsistent, as is often the case when a challenge does not carefully consider these concepts. Therefore, in this paper, we propose a theoretical framework, based on statistical principles, to guide researchers in challenge design, documentation, and assessment. Experimental results are given that explore the factors that effect the practical implementation of this theoretical framework.

In a broad range of fields it may be desirable to reuse a supervised classification algorithm and apply it to a new data set. However, generalization of such an algorithm and thus achieving a similar classification performance is only possible when the training data used to build the algorithm is similar to new unseen data one wishes to apply it to. It is often unknown in advance how an algorithm will perform on new unseen data, being a crucial reason for not deploying an algorithm at all. Therefore, tools are needed to measure the similarity of data sets. In this paper, we propose the Data Representativeness Criterion (DRC) to determine how representative a training data set is of a new unseen data set. We present a proof of principle, to see whether the DRC can quantify the similarity of data sets and whether the DRC relates to the performance of a supervised classification algorithm. We compared a number of magnetic resonance imaging (MRI) data sets, ranging from subtle to severe difference is acquisition parameters. Results indicate that, based on the similarity of data sets, the DRC is able to give an indication as to when the performance of a supervised classifier decreases. The strictness of the DRC can be set by the user, depending on what one considers to be an acceptable underperformance.

There has recently been great progress in automatic segmentation of medical images with deep learning algorithms. In most works observer variation is acknowledged to be a problem as it makes training data heterogeneous but so far no attempts have been made to explicitly capture this variation. Here, we propose an approach capable of mimicking different styles of segmentation, which potentially can improve quality and clinical acceptance of automatic segmentation methods. In this work, instead of training one neural network on all available data, we train several neural networks on subgroups of data belonging to different segmentation variations separately. Because a priori it may be unclear what styles of segmentation exist in the data and because different styles do not necessarily map one-on-one to different observers, the subgroups should be automatically determined. We achieve this by searching for the best data partition with a genetic algorithm. Therefore, each network can learn a specific style of segmentation from grouped training data. We provide proof of principle results for open-sourced prostate segmentation MRI data with simulated observer variations. Our approach provides an improvement of up to 23% (depending on simulated variations) in terms of Dice and surface Dice coefficients compared to one network trained on all data.

Automatic segmentation in MR brain images is important for quantitative analysis in large-scale studies with images acquired at all ages. This paper presents a method for the automatic segmentation of MR brain images into a number of tissue classes using a convolutional neural network. To ensure that the method obtains accurate segmentation details as well as spatial consistency, the network uses multiple patch sizes and multiple convolution kernel sizes to acquire multi-scale information about each voxel. The method is not dependent on explicit features, but learns to recognise the information that is important for the classification based on training data. The method requires a single anatomical MR image only. The segmentation method is applied to five different data sets: coronal T2-weighted images of preterm infants acquired at 30 weeks postmenstrual age (PMA) and 40 weeks PMA, axial T2- weighted images of preterm infants acquired at 40 weeks PMA, axial T1-weighted images of ageing adults acquired at an average age of 70 years, and T1-weighted images of young adults acquired at an average age of 23 years. The method obtained the following average Dice coefficients over all segmented tissue classes for each data set, respectively: 0.87, 0.82, 0.84, 0.86 and 0.91. The results demonstrate that the method obtains accurate segmentations in all five sets, and hence demonstrates its robustness to differences in age and acquisition protocol.