The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis

Abstract

The National Alliance for Medical Image Computing (NA-MIC), is a multi-institutional, interdisciplinary community of researchers, who share the recognition that modern health care demands improved technologies to ease suffering and prolong productive life. Organized under the National Centers for Biomedical Computing 7 years ago, the mission of NA-MIC is to implement a robust and flexible open-source infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. A measure of its success, NA-MIC is now applying this technology to diseases that have immense impact on the duration and quality of life: cancer, heart disease, trauma, and degenerative genetic diseases. The targets of this technology range from group comparisons to subject-specific analysis.

Figure 1

Chorea-acanthocytosis (ChAc) is an uncommon autosomal recessive disorder due to mutations of the VPS13A gene, which encodes for the membrane protein chorein. ChAc presents with progressive limb and orobuccal chorea, but there is often a marked dysexecutive syndrome. ChAc may first present with neuropsychiatric disturbance such as obsessive-compulsive disorder, suggesting a particular role for disruption to striatal structures involved in non-motor frontostriatal loops, such as the head of the caudate nucleus. We investigated morphometric changes in 13 patients with genetically or biochemically confirmed ChAc and 26 age and gender-matched controls. Subjects underwent MRI and manual segmentation of the caudate nucleus and putamen, and shape analysis using a non-parametric spherical harmonic technique. Both structures showed significant and marked reductions in volume compared with controls, with reduction greatest in the caudate nucleus. Both structures showed significant shape differences, particularly in the head of the caudate nucleus. No significant correlation was shown between the duration of illness and striatal volume or shape, suggesting that much structural change may have already taken place at the time of symptom onset. Our results suggest that striatal neuron loss may occur early in the disease process, and follows a dorsal–ventral gradient that may correlate with early neuropsychiatric and cognitive presentations of the disease. Left (top) and right (bottom) putamen changes, showing differences between ChAc patients and controls. On the left, uncorrected raw p value map; middle, FDR-corrected p value map; right, between-group displacement map. Legend to p value map shows that regions with p>0.05 are colored blue, with significant values on a spectrum from green (p=0.05) to red (p=0). Legend to displacement map shows displacement of the ChAc group from the control group in millimeters.

Figure 2

This figure illustrates the network of National Alliance for Medical Image Computing (NA-MIC) collaborations that span the diagnosis and therapy of schizophrenia, lupus, autism, chronic obstructive pulmonary disease (COPD), cancer of the liver, colon, and prostate, as well as musculoskeletal disorders. These are funded by 18 National Institutes of Health grants including eight R01/R21 funded through the ‘collaboration with National Center for Biomedical Computing (NCBC’) mechanism, three center grants headquartered at Brigham and Women's Hospital, and one clinical trial (for COPD) that has already used the NA-MIC kit software to process 2500+ CT scans. In addition, we actively collaborate with three internationally funded efforts.

Figure 3

This figure illustrates how the National Alliance for Medical Image Computing (NA-MIC) kit, which contains a modular set of interoperable free open source software packages, is managed under a collaborative, high quality software engineering methodology. The kit itself consists of the 3D slicer application software, a number of tools and toolkits such as Visualization Tool kit (VTK) and Insight Segmentation and Registration Tool kit (ITK), and a software engineering methodology that enables multi-platform implementations. DBP, driving biological projects.