Jesica Makanyanga

Grading Crohn disease activity with MRI: interobserver variability of MRI features, MRI scoring of severity, and correlation with Crohn disease endoscopic index of severity.

OBJECTIVE The purpose of this article is to assess the interobserver variability for scoring MRI features of Crohn disease activity and to correlate two MRI scoring systems to the Crohn disease endoscopic index of severity (CDEIS). MATERIALS AND METHODS Thirty-three consecutive patients with Crohn disease undergoing 3-T MRI examinations (T1-weighted with IV contrast medium administration and T2-weighted sequences) and ileocolonoscopy within 1 month were independently evaluated by four readers. Seventeen MRI features were recorded in 143 bowel segments and were used to calculate the MR index of activity and the Crohn disease MRI index (CDMI) score. Multirater analysis was performed for all features and scoring systems using intraclass correlation coefficient (icc) and kappa statistic. Scoring systems were compared with ileocolonoscopy with CDEIS using Spearman rank correlation. RESULTS Thirty patients (median age, 32 years; 21 women and nine men) were included. MRI features showed fair-to-good interobserver variability (intraclass correlation coefficient or kappa varied from 0.30 to 0.69). Wall thickness in millimeters, presence of edema, enhancement pattern, and length of the disease in each segment showed a good interobserver variability between all readers (icc = 0.69, κ = 0.66, κ = 0.62, and κ = 0.62, respectively). The MR index of activity and CDMI scores showed good reproducibility (icc = 0.74 and icc = 0.78, respectively) and moderate CDEIS correlation (r = 0.51 and r = 0.59, respectively). CONCLUSION The reproducibility of individual MRI features overall is fair to good, with good reproducibility for the most commonly used features. When combined into the MR index of activity and CDMI score, overall reproducibility is good. Both scores show moderate agreement with CDEIS.

Respiratory motion correction in dynamic MRI using robust data decomposition registration - application to DCE-MRI.

Motion correction in Dynamic Contrast Enhanced (DCE-) MRI is challenging because rapid intensity changes can compromise common (intensity based) registration algorithms. In this study we introduce a novel registration technique based on robust principal component analysis (RPCA) to decompose a given time-series into a low rank and a sparse component. This allows robust separation of motion components that can be registered, from intensity variations that are left unchanged. This Robust Data Decomposition Registration (RDDR) is demonstrated on both simulated and a wide range of clinical data. Robustness to different types of motion and breathing choices during acquisition is demonstrated for a variety of imaged organs including liver, small bowel and prostate. The analysis of clinically relevant regions of interest showed both a decrease of error (15-62% reduction following registration) in tissue time-intensity curves and improved areas under the curve (AUC60) at early enhancement.

Automatic Detection and Segmentation of Crohn's Disease Tissues From Abdominal MRI

We propose an information processing pipeline for segmenting parts of the bowel in abdominal magnetic resonance images that are affected with Crohns disease. Given a magnetic resonance imaging test volume, it is first oversegmented into supervoxels and each supervoxel is analyzed to detect presence of Crohns disease using random forest (RF) classifiers. The supervoxels identified as containing diseased tissues define the volume of interest (VOI). All voxels within the VOI are further investigated to segment the diseased region. Probability maps are generated for each voxel using a second set of RF classifiers which give the probabilities of each voxel being diseased, normal or background. The negative log-likelihood of these maps are used as penalty costs in a graph cut segmentation framework. Low level features like intensity statistics, texture anisotropy and curvature asymmetry, and high level context features are used at different stages. Smoothness constraints are imposed based on semantic information (importance of each feature to the classification task) derived from the second set of learned RF classifiers. Experimental results show that our method achieves high segmentation accuracy with Dice metric values of 0.90 ± 0.04 and Hausdorff distance of 7.3 ± 0.8 mm. Semantic information and context features are an integral part of our method and are robust to different levels of added noise.

Current and Future Role of MR Enterography in the Management of Crohn Disease

OBJECTIVE The purpose of this article is to explore the future role of MRI in assessing the global disease burden of Crohn disease and monitoring treatment response. CONCLUSION MR enterography is increasingly used to evaluate disease activity in Crohn disease, and scoring methods have been validated. Current MRI protocols may be extended to allow the assessment of inflammation and fibrosis.

Small bowel strictures in Crohn’s disease: a quantitative investigation of intestinal motility using MR enterography

Intestinal stricturing and aberrant small bowel motility are common complications in patients with Crohns disease (CD) leading to significant morbidity. A retrospective study was performed quantifying small bowel motility within and upstream of strictures in CD patients using magnetic resonance enterography (MRE).

Dual registration of abdominal motion for motility assessment in free-breathing data sets acquired using dynamic MRI

At present, registration-based quantification of bowel motility from dynamic MRI is limited to breath-hold studies. Here we validate a dual-registration technique robust to respiratory motion for the assessment of small bowel and colonic motility. Small bowel datasets were acquired in breath-hold and free-breathing in 20 healthy individuals. A pre-processing step using an iterative registration of the low rank component of the data was applied to remove respiratory motion from the free breathing data. Motility was then quantified with an existing optic-flow (OF) based registration technique to form a dual-stage approach, termed Dual Registration of Abdominal Motion (DRAM). The benefit of respiratory motion correction was assessed by (1) assessing the fidelity of automatically propagated segmental regions of interest (ROIs) in the small bowel and colon and (2) comparing parametric motility maps to a breath-hold ground truth. DRAM demonstrated an improved ability to propagate ROIs through free-breathing small bowel and colonic motility data, with median error decreased by 90% and 55%, respectively. Comparison between global parametric maps showed high concordance between breath-hold data and free-breathing DRAM. Quantification of segmental and global motility in dynamic MR data is more accurate and robust to respiration when using the DRAM approach.

Assessment of wall inflammation and fibrosis in Crohn’s disease: value of T1-weighted gadolinium-enhanced MR imaging

MRI is increasingly advocated as a robust method for quantifying disease activity in Crohn’s disease. In particular, T1-weighted gadolinium-enhanced imaging shows considerable promise as a marker of inflammatory activity. However, interpretation of the literature must be made with an understanding of (i) the technical limitations of T1-weighted acquisition protocols and enhancement measurements; (ii) differences in standards of reference for disease activity employed between published studies; and (iii) important underlying macro and micro vascular changes in Crohn’s disease. This review will focus specifically on the value of T1-weighted gadolinium-enhanced imaging in the assessment of wall inflammation and fibrosis.

Active learning based segmentation of Crohn's disease using principles of visual saliency

We propose a active learning (AL) approach to segment Crohns disease (CD) affected regions in abdominal magnetic resonance (MR) images. Our label query strategy is inspired from the principles of visual saliency which has similar considerations for choosing the most salient region. These similarities are encoded in a graph using classification maps and low level features. The most informative node is determined using random walks. Experimental results on real patient datasets show the superior performance of our approach and highlight the importance of different features to determine a regions importance.

Aberrant Motility in Unaffected Small Bowel is Linked to Inflammatory Burden and Patient Symptoms in Crohn's Disease.

Background:Inflammation-related enteric dysmotility has been postulated as a cause for abdominal symptoms in Crohns disease (CD). We investigated the relationship between magnetic resonance imaging–quantified small bowel (SB) motility, inflammatory activity, and patient symptom burden. Methods:The Harvey–Bradshaw index (HBI) and fecal calprotectin were prospectively measured in 53 patients with CD (median age, 35; range, 18–78 years) the day before magnetic resonance enterography, which included a dynamic (cine), breath-hold motility sequence, repeated to encompass the whole SB volume. A validated registration-based motility quantitation technique produced motility maps, and regions of interest were drawn to include all morphologically normal SB (i.e., excluding diseased bowel). Global SB motility was correlated with calprotectin, HBI, and symptom components (well-being, pain, and diarrhea). Adjustment for age, sex, smoking, and surgical history was made using multivariate linear regression. Results:Median calprotectin was 336 (range, 0–1280). Median HBI, motility mean, and motility variance were 3 (range, 0–16), 0.33 (0.18–0.51), and 0.01 (0.0014–0.034), respectively. Motility variance was significantly negatively correlated with calprotectin (rho = −0.33, P = 0.015), total HBI (rho = −0.45, P < 0.001), well-being (rho = −0.4, P = 0.003), pain (rho = −0.27, P = 0.05), and diarrhea (rho = −0.4, P = 0.0025). The associations remained highly significant after adjusting for covariates. There was no association between mean motility and calprotectin or HBI (P > 0.05). Conclusions:Reduced motility variance in morphologically normal SB is associated with patient symptoms and fecal calprotectin levels, supporting the hypothesis that inflammation-related enteric dysmotility may explain refractory abdominal symptoms in CD.

A Model Development Pipeline for Crohn's Disease Severity Assessment from Magnetic Resonance Images

Crohns Disease affects the intestinal tract of a patient and can have varying severity which influences treatment strategy. The clinical severity score CDEIS Crohns Disease Endoscopic Index of severity ranges from 0 to 44 and is measured by endoscopy. In this paper we investigate the potential of non-invasive magnetic resonance imaging to assess this severity, together with the underlying question which features are most relevant for this estimation task. We propose a new general and modular pipeline that uses machine learning techniques to quantify disease severity from MR images and show its value on Crohns Disease severity assessment on 30 patients scored by 4 medical experts. With the pipeline, we can obtain a magnetic resonance imaging score which outperforms two existing reference scores MaRIA and AIS.