2006 Scientific Report Highlight Summary
A Summary of 2006 NA-MIC Highlights
While NA-MIC had a productive year as evidenced by its collaborative wiki (700 pages total, 200 users, 650K page views and 15K edits), here we present just three highlights representing the diversity of the NA-MIC collaborative effort. These highlights demonstrate the world class software process used to create, implement, test and disseminate NA-MIC software (Cores 1,2,4,6); the on-going collaboration between the DPB scientists and algorithms (Cores 1 and 3); and the on-going efforts to transition the technology to researchers throughout the world (Cores 4,5,6).
Before proceeding to the descriptions of these highlights, we would like to point to one activity in particular that epitomizes NA-MICs culture of colloboration and technical excellence. In the first year of this NCBC, NA-MIC established what was then known as Programming Week. The original concept was to create teams consisting of members from multiple Cores, with experience levels ranging from expert to student. Each team identified technical challenges within NA-MIC's mandate, and worked together in an intensive period ranging from an afternoon to an entire week. The ultimate goal of each project was to move from research problem to solution; with the solution implemented in our open source NA-MIC Kit software suite.
The results of this experiment have been strongly positive. Participants have been energized by the diversity of the teams and the rapid transition of research to implementation. In particular, the open source software process resulted in technology transition measured in days or weeks versus months and years that conventional processes require. The enthusiastic reception of Programming Week has led NA-MIC to repeat this experiment several more times, with growing enthusiasm each time. We have also renamed this event to Project Week to better reflect the extent of its activities, and to emphasize NA-MICs inter-Core, collaborative efforts focused on solving problems and transitioning results.
According to the The Biomedical Information Science and Technology Initiative (BISTI) report:
One important element in the system is the creation of software-development groups: software and computer engineers who can take laboratory-based software and "harden" it-standardizing it for more general use, testing it under various conditions, documenting it, supporting it, and upgrading it as technology changes.
With this mandate in mind, NA-MIC has and continues to implement a world-class software process. At the core of this process is a minimally intrusive but effective set of procedures that have been developed over a period of more than a decade, and which have been extended through the NA-MIC initiative into new areas. The process revolves around testing of software on a continuous basis acrosss multiple computing platforms (i.e., a computing platform is defined here as a combination of hardware, operating system, and compiler). The results of these tests are reported continuously on quality dashboards (see http://public.kitware.com/dashboard.php and choose the various software tools from the top tabs). Such feedback enables developers to make changes to the code base insuring that the quality of the software remains high. As evidenced by this page, the various components making up the NA-MIC kit--ITK, VTK, Slicer3.0, CMake, KWWidgets and other NAMIC utilities--have all been placed under the auspices of the software process. The following paragraphs summarize the major accomplishments related to the software process in Year 2 of the NA-MIC effort.
- The next generation testing process, based on the DART server and CMake/CTest client, has been completed. DART now supports dynamic queries to a formal database with configurable presentation of testing results, and optimal storage strategies for managing the gigabytes of data arriving from testing clients around the world. CTest, which is an adjunct module to the CMake cross-platform build system, has been modified to integrate with the new DART server.
- CPack, a new software tool funded under the NA-MIC initiative, is another adjunct module to CMake. CPack is a cross-platform packaging and distribution utility that is an essential part of the NA-MIC software kit. CPack enables software to be easily packaged for distribution across computer platforms. Thus it is relatively easy to create binary and source code ditributions for Windows, Lunix, Unix and MacOSX systems. The ultimate effect is that the time to move from algorithm to software implementation to multi-platform distribution has been greatly reduced.
- CMake release 2.4 has been completed. CMake enables software to be compiled, linked and tested across multiple computer platforms. CMake is one of a few, and possibly only, build systems in the world today that can handle the complexity of configuring, building and linking the NA-MIC software kit across multiple computing platforms. Thus CMake enables NA-MIC developers to rapidly combine advanced software toolkits such as VTK, ITK, and KWWidgets into complex software applications such as Slicer3.0.
As evidence of the effectiveness of the process, software communities around the world are now adopting the NA-MIC process for their own development efforts. For example, the KDE Linux Desktop System, which is the world's largest open source software project in terms of lines of code, has adopted CMake as their official build tool. This choice was made by the KDE community after an intensive evaluation period which concluded that CMake is the only system in the world capable of managing KDE's complex build process. The KDE community is also enthusiastically embracing the testing quality dashboards.
Clinical Application of Diffusion Tensor Imaging
MIT computer scientists in collaboration with Harvard neuroscientists, have produced a robust method for identifying anatomically distinct fiber tracts in the human brian using clustering techniques applied to magnetic resonance diffusion tensor imaging (DTI). DTI is a relatively new technique that makes it possible to visualize and to quantify the organization and integrity of white matter fiber tracts in the brain, in vivo. As part of NA-MIC collaboration, the focus is on identifying fiber tracts that may be abnormal in schizophrenia, although such work can be applied to study both global and specific diffusion changes in white matter in various neurological and psychiatric disorders including Alzheimer's disease and multiple sclerosis. Of note here, MIT computer scientists have worked closely with schizophrenia researchers to develop and apply sophisticated computer vision algorithms in order to extract fiber bundles likely important in the pathophysiology of schizophrenia, including the fornix, uncinate fasciculus (the largest fiber tract connecting the frontal and temporal lobe), and the corpus callosum (largest white matter fiber tract in the brain and likely important in communication between the two hemispheres). The method developed can also be applied to surgical planning, to clinical psychiatry, as well as to neurological disorders and for identifying fiber bundles in the brain.
The paper, "A Method for Clustering White Matter Fiber Tracts", will appear in the May issue of the American Journal of Neuroradiology. This work was funded by NA-MIC. Illustrating the cross-disciplinary nature of NA-MIC, an MIT computer scientist is the first author on this paper with collaborators from Harvard and the Veterans Administration. Thus NA-MIC has successfully teamed computer scientists and software engineers to create industry quality software tools to solve driving biological problems.
The primary goal of the Dissemination Core 6 in the second year of the NA-MIC effort has been to focus on outreach to the broader research community. This was accomplished using several mechanisms. In addition to the training events reported by the Training Core 5, three workshops and two birds-of-a-feather meetings were held in collaboration with the Service Core 4. Three invited talks were presented about NA-MIC, and the wiki-based collaborative web presence was also approximately doubled in this time. Deatils of these events follow.
- Workshops: Two of the three workshops were focused exclusively on the broader research community. The first workshop was organized in response to a request by researchers at EPFL, Lausanne, Switzerland who were interested in advanced development using our software tools. 37 participants from 9 countries attended this 2.5-day hands-on event at EPFL. Details of this workshop are available at : http://www.na-mic.org/Wiki/index.php/Dissemination:EPFL_Workshop_2005
- The focus of the second workshop was open source software, a driving theme in the NA-MIC kit, and was held in conjunction with MICCAI 2005 in Palm Springs, CA. There were 80 registered attendees for this workshop, 37 submissions, 90 open reviews, and 21 submissions were selected for presentation. This workshop was organized jointly with the Insight Software Consortium and details are available here: http://www.na-mic.org/Wiki/index.php/Dissemination:MICCAI_Workshop_2005
- The topic for the third workshop was validation, which was held in conjunction with the NA-MIC all-hands meeting in Salt Lake City, Utah in January 2006. There were over 50 participants in this workshop, primarily from within NA-MIC and some outside collaborators. Details of this workshop are available here: http://www.na-mic.org/Wiki/index.php/AHM2006_ValidationWorkshop
- Invited Talks: Three invited talks were also given about NA-MIC at CSB, Stanford (Kikinis, Aug 2005), Schizophrenia and Big Science (ISBI, March 2006), NA-MIC Kit (Pieper, 2006).
- Birds-of-a-Feather Meetings: The “Programming Week” event that was started in the first year of NA-MIC to gauge the interest of participants in spending a week together working on NA-MIC projects was expanded in both scope and duration in the second year. The scope has been expanded to include algorithm brainstorming and clinical application work, and the event has been re-named “Project Week” to reflect this. The duration has been extended to 1.5 weeks per year – the last week of June at MIT, as well as half a week in conjunction with the all-hands meeting in January. The extension in duration has largely been to accommodate the desire of the participants to stay in touch with the community.
- Web Presence: The collaborative wiki (http://wiki.na-mic.org) has expanded to 700 pages and about 200 users. (In the first year, we had 350 pages and 150 users.) An interesting statistic is that since the inception of this wiki, there have been a total of 650K page views and 15K page edits, which translates to 4 edits per page, and 41 views per edit. In addition to the NA-MIC investigators use of these wiki pages, the usage by external collaborators continues to expand (NAC, NCIGT, and CIMIT were added this year, while NIH and BIRN continue to use it from last year.)