Feature space analysis: effects of MRI protocols

Whole volume brain extraction for multi-centre, multi-disease FLAIR MRI datasets

Automatic segmentation of the brain from magnetic resonance images (MRI) is a fundamental step in many neuroimaging processing frameworks. There are mature technologies for this task for T1- and T2-weighted MRI; however, a widely-accepted brain extraction method for Fluid-Attenuated Inversion Recovery (FLAIR) MRI has yet to be established. FLAIR MRI are becoming increasingly important for the analysis of neurodegenerative diseases and tools developed for this sequence would have clinical value. To maximize translation opportunities and for large scale research studies, algorithms for brain extraction in FLAIR MRI should generalize to multi-centre (MC) data. To this end, this work proposes a fully automated, whole volume brain extraction methodology for MC FLAIR MRI datasets. The framework is built using a novel standardization framework which reduces acquisition artifacts, standardizes the intensities of tissues and normalizes the spatial coordinates of brain tissue across MC datasets. Using the standardized datasets, an intuitive set of features based on intensity, spatial location and gradients are extracted and classified using a random forest (RF) classifier to segment the brain tissue class. A series of experiments were conducted to optimize classifier parameters, and to determine segmentation accuracy for standardized and unstandardized (original) data, as a function of scanner vendor, feature type and disease type. The models are trained, tested and validated on 156 image volumes (∼8000 image slices) from two multi-centre, multi-disease datasets, acquired with varying imaging parameters from 30 centres and three scanner vendors. The image datasets, denoted as CAIN and ADNI for vascular and dementia disease, respectively, represent a diverse collection of MC data to test the generalization capabilities of the proposed design. Results demonstrate the importance of standardization for segmentation of MC data, as models trained on standardized data yielded a drastic improvement in brain extraction accuracy compared to the original, unstandardized data (CAIN: DSC = 91% and ADNI: DSC = 86% vs. CAIN: 78% and ADNI: 65%). It was also found that models created from one scanner vendor based on unstandardized data yielded poor segmentation results in data acquired from other scanner vendors, which was improved through standardization. These results demonstrate that to create consistency in segmentations from multi-institutional datasets it is paramount that MC variability be mitigated to improve stability and to ensure generalization of machine learning algorithms for MRI.

T2 detection of tumor invasion within segmented components of glioblastoma multiforme

PURPOSE

To use T2-weighted images to detect tumor invasion when comparing normal individuals to groups of gliomablastoma multiforme (GBM) patients with varying levels of CXCR4, a chemokine receptor that promotes tumor migration.

MATERIALS AND METHODS

T2-weighted images were acquired preoperatively in 22 treatment-naïve GBM patients. Two groups were formed based on the expression levels of CXCR4. A third group of normal volunteers was used for comparison. Each image was segmented to obtain four different clusters for tissue types identified as white matter, basal ganglia, gray matter/edema and cerebrospinal fluid (CSF)/tumor. Signal intensity histograms were formed for each cluster and compared between groups.

RESULTS

In every cluster the GBM groups displayed significantly higher standard deviations of intensity distributions when compared to normal subjects. Significant differences in skewness were found between normal subjects and GBM patients in the white matter, basal ganglia, and CSF/tumor. Further, when the two groups of GBM patients were compared the CXCR4-high group was found to have a significant shift in the median intensity values in the cluster containing gray matter and peritumoral edema.

CONCLUSION

T2 signal intensity histograms in normal subjects differ significantly from those obtained from GBM groups, suggesting widespread dissemination of disease.

Part 1. Automated change detection and characterization in serial MR studies of brain-tumor patients

The goal of this study was to create an algorithm which would quantitatively compare serial magnetic resonance imaging studies of brain-tumor patients. A novel algorithm and a standard classify-subtract algorithm were constructed. The ability of both algorithms to detect and characterize changes was compared using a series of digital phantoms. The novel algorithm achieved a mean sensitivity of 0.87 (compared with 0.59 for classify-subtract) and a mean specificity of 0.98 (compared with 0.92 for classify-subtract) with regard to identification of voxels as changing or unchanging and classification of voxels into types of change. The novel algorithm achieved perfect specificity in seven of the nine experiments. The novel algorithm was additionally applied to a short series of clinical cases, where it was shown to identify visually subtle changes. Automated change detection and characterization could facilitate objective review and understanding of serial magnetic resonance imaging studies in brain-tumor patients.

A system for brain tumor volume estimation via MR imaging and fuzzy connectedness

This paper presents a method for the precise, accurate and efficient quantification of brain tumor (glioblastomas) via MRI that can be used routinely in the clinic. Tumor volume is considered useful in evaluating disease progression and response to therapy, and in assessing the need for changes in treatment plans. We use multiple MRI protocols including FLAIR, T1, and T1 with Gd enhancement to gather information about different aspects of the tumor and its vicinity. These include enhancing tissue, nonenhancing tumor, edema, and combinations of edema and tumor. We have adapted the fuzzy connectedness framework for tumor segmentation in this work and the method requires only limited user interaction in routine clinical use. The system has been tested for its precision, accuracy, and efficiency, utilizing 10 patient studies. The percent coefficient of variation (% CV) in volume due to operator subjectivity in specifying seeds for fuzzy connectedness segmentation is less than 1%. The mean operator and computer time required per study for estimating the volumes of both edema and enhancing tumor is about 16 min. The software package is designed to run under operator supervision. Delineation has been found to agree with the operators' visual inspection most of the time except in some cases when the tumor is close to the boundary of the brain. In the latter case, the scalp, surgical scar, or orbital contents are included in the delineation, and an operator has to exclude this manually. The methodology is rapid, robust, consistent, yielding highly reproducible measurements, and is likely to become part of the routine evaluation of brain tumor patients in our health system.