Database sharing:

Morphological Analyses

The QMC continues to provide extensive expertise in quantitative methods, software usage, and advanced microscopy to members of the Conte Center. Our software modules (NeuroGL, VIAS, PVIEW, NeuroStudio) are fully accessible through our website (http://www.mssm.edu/cnic) and members of the NYU and Rockefeller teams are using them regularly. We have on-site training of students and postdocs from these groups on a weekly basis, and several projects on-going on our equipment at MSSM. Efforts to transfer technology to the other sites are made. Quantitative morphology for dendrites as well as stereology using QMC procedures are currently implemented in Drs LeDoux and McEwen's group.

Training in other methods such as cell loading and quantitative electron microscopy is also continuing at MSSM. The QMC maintains overseeing quantitative datasets to ensure consistency of methods, quality and rigor of sampling, and uniformity across sites. Data are regularly presented and discussed in relevant group meetings at NYU or Rockefeller that are attended by the QMC leader.

Imaging Tools

The neuroimaging data processing and analysis software packages consist of 3 major modules of MATLAB, C, R programs and shell scripts (FNLproc, FNLstat and FNLlme),developed by the Neuroimaging and Neuropsychiatry Core (and now Project 2), and are available to the public and the members of research community through the website of the Functional Neuroimaging Lab (www.functionalneuroimaginglab.org) under the section of Methods Development. The 3 software modules have adapted several major brain imaging data processing and analysis tools (such as SPM, FSL and fmristat) at their essence, and customized, optimized and streamlined the major aspects that are crucial to improve sensitivity, specificity and accuracy in neuroimaging data processing and analysis, through advanced mathematical/statistical methods and improved numerical algorithms (which have gone through extensive testing and evaluation based on multiple data sets). Notable improvements and additions to the existing software tools in the field include: functional image reconstruction, physiological noise estimation, global temporal fluctuation estimation, realignment based on intracranial voxels, and modeling of variance components in functional neuroimaging data. More advanced and more powerful methods, algorithms and programs are continuously being developed by the core, and will be made publicly available through the same website once the new software is tested and evaluated. On-site training courses for trainees explaining the mathematical, statistical and computational principles, methods and algorithms plus the usage of the user interface and automated batch programs are provided on an ongoing basis, and didactic material is provided to a wider audience of trainees through an NIMH-sponsored (R25) training and educational program during every summer session. These programs, together with training and expertise, have been provided to colleagues from Rockefeller University, Memorial Sloan-Kettering Cancer Center, Johannes Gutenberg-Universitat/Mainz and University Hospital Munster (Germany).

The FNLDB database modules developed by the Neuroimaging and Neuropsychiatry Core (and now Project 2) are also made available to the public through the website of the Functional Neuroimaging Lab (www.functionalneuroimaginglab.org) under the section of Methods Development. On site training courses for students and postdocs explaining the use of the database interface are provided annually. The continuing beta testing involves members of the Functional Neuroimaging Lab. FNLDB is multi-user/account-based, provides for session control and has granular access control to database tables. It supplies a web interface, which is usable by novices. It implements features of a transactional database and uses a relational database. Currently FNLDB is installed on a standard APACHE webserver, with SSL, PERL and MYSQL modules/programs. This setup allows for server authentication and the encryption of the data transfers.