A segmentation editing framework based on shape change statistics

Segmentation is a key task in medical image analysis because its accuracy significantly affects successive steps. Automatic segmentation methods often produce inadequate segmentations, which require the user to manually edit the produced segmentation slice by slice. Because editing is time-consuming, an editing tool that enables the user to produce accurate segmentations by only drawing a sparse set of contours would be needed. This paper describes such a framework as applied to a single object. Constrained by the additional information enabled by the manually segmented contours, the proposed framework utilizes object shape statistics to transform the failed automatic segmentation to a more accurate version. Instead of modeling the object shape, the proposed framework utilizes shape change statistics that were generated to capture the object deformation from the failed automatic segmentation to its corresponding correct segmentation. An optimization procedure was used to minimize an energy function that consists of two terms, an external contour match term and an internal shape change regularity term. The high accuracy of the proposed segmentation editing approach was confirmed by testing it on a simulated data set based on 10 in-vivo infant magnetic resonance brain data sets using four similarity metrics. Segmentation results indicated that our method can provide efficient and adequately accurate segmentations (Dice segmentation accuracy increase of 10%), with very sparse contours (only 10%), which is promising in greatly decreasing the work expected from the user

Zoom invariant vision of figural shape: The mathematics of cores

Believing that figural zoom invariance and the cross-figural boundary linking implied by medial loci are important aspects of object shape, we present the mathematics of and algorithms for the extraction of medial loci directly from image intensities. The medial loci called cores are defined as generalized maxima in scale space of a form of medial information that is invariant to translation, rotation, and in particular, zoom. These loci are very insensitive to image disturbances, in strong contrast to previously available medial loci, as demonstrated in a companion paper. Core-related geometric properties and image object representations are laid out which, together with the aforementioned insensitivities, allow the core to be used effectively for a variety of image analysis objectives.

Non-Euclidean, convolutional learning on cortical brain surfaces

In recent years there have been many studies indicating that multiple cortical features, extracted at each surface vertex, are promising in the detection of various neurodevelopmental and neurodegenerative diseases. However, with limited datasets, it is challenging to train stable classifiers with such high-dimensional surface data. This necessitates a feature reduction that is commonly accomplished via regional volumetric morphometry from standard brain atlases. However, current regional summaries are not specific to the given age or pathology that is studied, which runs the risk of losing relevant information that can be critical in the classification process. To solve this issue, this paper proposes a novel data-driven approach by extending convolutional neural networks (CNN) for use on non-Euclidean manifolds such as cortical surfaces. The proposed network learns the most powerful features and brain regions from the extracted large dimensional feature space; thus creating a new feature space in which the dimensionality is reduced and feature distributions are better separated. We demonstrate the usability of the proposed surface-CNN framework in an example study classifying Alzheimers disease patients versus normal controls. The high performance in the cross-validation diagnostic results shows the potential of our proposed prediction system

Quantitative measurement of blood flow in paediatric brain tumours. A comparative study of dynamic susceptibility contrast and multi-timepoint arterial spin-labelled MRI

OBJECTIVE: Arterial spin-labelling (ASL) MRI uses intrinsic blood water to quantify the cerebral blood flow (CBF), removing the need for the injection of a gadolinium-based contrast agent used for conventional perfusion imaging such as dynamic susceptibility contrast (DSC). Owing to the non-invasive nature of the technique, ASL is an attractive option for use in paediatric patients. This work compared DSC and multi-timepoint ASL measures of CBF in paediatric brain tumours. METHODS: Patients (n = 23; 20 low-grade tumours and 3 high-grade tumours) had DSC and multi-timepoint ASL with and without vascular crushers (VC). VC removes the contribution from larger vessel blood flow. Mean perfusion metrics were extracted from control and T(1)-enhanced tumour regions of interest (ROIs): arterial arrival time (AAT) and CBF from the ASL images with and without VC, relative cerebral blood flow (rCBF), relative cerebral blood volume, delay time (DT) and mean transit time (MTT) from the DSC images. RESULTS: Significant correlations existed for: AAT and DT (r = 0.77, p = 0.0002) and CBF and rCBF (r = 0.56, p = 0.02) in control ROIs for ASL-noVC. No significant correlations existed between DSC and ASL measures in the tumour region. Significant differences between control and tumour ROI were found for MTT (p < 0.001) and rCBF (p < 0.005) measures. CONCLUSION: Significant correlations between ASL-noVC and DSC measures in the normal brain suggest that DSC is most sensitive to macrovascular blood flow. The absence of significant correlations within the tumour ROI suggests that ASL is sensitive to different physiological mechanisms compared with DSC measures. ADVANCES IN KNOWLEDGE: ASL provides information which is comparable with that of DSC in healthy tissues, but appears to reflect a different physiology in tumour tissues

Post-operative pediatric cerebellar mutism syndrome and its association with hypertrophic olivary degeneration

Background: The dentato-thalamo-cortical (DTC) pathway is recognized as the anatomical substrate for postoperative pediatric cerebellar mutism (POPCMS), a well-recognized complication affecting up to 31% of children undergoing posterior fossa brain tumour resection. The proximal structures of the DTC pathway also form a segment of the Guillain and Mollaret triangle, a neural network which when disrupted causes hypertrophic olivary degeneration (HOD) of the inferior olivary nucleus (ION). We hypothesize that there is an association between the occurrence of POPCMS and HOD and aim to evaluate this on MR imaging using qualitative and quantitative analysis of the ION in children with and without POPCMS. Methods: In this retrospective study we qualitatively analysed the follow up MR imaging in 48 children who underwent posterior fossa tumour resection for presence of HOD. Quantitative analysis of the ION was possible in 28 children and was performed using semi-automated segmentation followed by feature extraction and feature selection techniques and relevance of the features to POPCMS were evaluated. The diagnosis of POPCMS was made independently based on clinical and nursing assessment notes. Results: There was significant association between POPCMS and bilateral HOD (P=0.002) but not unilateral HOD. Quantitative analysis showed that hyperintensity in the left ION was the most relevant feature in children with POPCMS. Conclusions: Bilateral HOD can serve as a reliable radiological indicator in establishing the diagnosis of POPCMS particularly in equivocal cases. The strong association of signal change due to HOD in the left ION suggests that injury to the right proximal efferent cerebellar pathway plays an important role in the causation of POPCMS. Keywords: Cerebellar mutism syndrome (CMS); hypertrophic olivary degeneration; posterior fossa syndrome (PFS); postoperative pediatric cerebellar mutism syndrom

PARP inhibitors affect growth, survival and radiation susceptibility of human alveolar and embryonal rhabdomyosarcoma cell lines

PARP inhibitors (PARPi) are used in a wide range of human solid tumours but a limited evidence is reported in rhabdomyosarcoma (RMS), the most frequent childhood soft-tissue sarcoma. The cellular and molecular effects of Olaparib, a specific PARP1/2 inhibitor, and AZD2461, a newly synthesized PARP1/2/3 inhibitor, were assessed in alveolar and embryonal RMS cells both as single-agent and in combination with ionizing radiation (IR)

Linking object boundaries at scale: a common mechanism for size and shape judgments

AbstractThe area over which boundary information contributes to the determination of the center of an extended object was inferred from results of a bisection task. The object to be bisected was a rectangle with two long sinusoidally modulated sides, i.e. a wiggly rectangle. The spatial frequency and amplitude of the edge modulation were varied. Two object widths were tested. The modulation of the perceived center approximately equaled that of the edges at very low edge modulation frequencies and decreased in amplitude with increasing edge modulation frequency. The edge modulation had a greater modulating effect on the perceived center for the narrower object than for the wider object. This scaling with object width didn't follow perfect zoom invariance but was precisely matched by the scaling of the bisection threshold with width, strongly supporting the idea that the same mechanism determines both the location of the perceived center for these stimuli and its variance. We propose that this mechanism is the linking of object boundaries at a scale determined by the object width

Averages of Fourier coefficients of Siegel modular forms and representation of binary quadratic forms by quadratic forms in four variables

Let $-d$ be a a negative discriminant and let $T$ vary over a set of representatives of the integral equivalence classes of integral binary quadratic forms of discriminant $-d$. We prove an asymptotic formula for $d \to \infty$ for the average over $T$ of the number of representations of $T$ by an integral positive definite quaternary quadratic form and obtain results on averages of Fourier coefficients of linear combinations of Siegel theta series. We also find an asymptotic bound from below on the number of binary forms of fixed discriminant $-d$ which are represented by a given quaternary form. In particular, we can show that for growing $d$ a positive proportion of the binary quadratic forms of discriminant $-d$ is represented by the given quaternary quadratic form.Comment: v5: Some typos correcte

Longitudinal assessment of ataxia in children following surgical resection of posterior fossa tumours

OBJECTIVES To report the natural history of ataxia in the first two years following surgical resection of a posterior fossa tumour (PFT). METHODS 20 children (mean age 9.9 years, range 5-15 years) who had undergone resection of a posterior fossa tumour were assessed using the Scale for the Assessment and Rating of Ataxia (SARA), Brief Ataxia Rating Scale (BARS) and the Pediatric Evaluation of Disability Index (PEDI) at the following time points; initial post-operative period, then at 3 months, 1 and 2 years post operatively. RESULTS The assessments demonstrated a rapid improvement in ataxia between initial and 3 months post-operative assessments, quantified by both the SARA and BARS (mean reduction in scores 4.8, 4.6 respectively). There were additional gradual improvements at 1 year (mean reduction SARA 0.6, BARS 0.2) and 2 years post operatively (mean reduction SARA 0.9, BARS 0.9). Return of function behaved similarly, quantified by a rapid increase in PEDI scores between initial and 3 month assessments (mean increase in score 26) and gradual increases at 1 and 2 years (mean increase 2, 2.5 respectively). There was a trend for children with medulloblastoma to demonstrate higher ataxia scores than children with low grade gliomas (mean initial post-operative scores 13.4 and 8.5 respectively). CONCLUSIONS The largest change in ataxia scores and functional mobility scores (PEDI) is demonstrated within the first 3 months post operatively. Ongoing gradual improvement in ataxia and mobility function was observed at 2 years. These results have implications for management of children with PFT