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New Method Development

Division of Psychiatric Neuroimaging

PNI is actively involved in the development and testing of new analytic tools and methods for analyzing neuroimaging data. Below are some of our active development projects. More information, reliability and validity, as well as some sample data will be available soon.


BRAINSTRIP is a semi-automated brain extraction tool, implemented as a plug-in to MIPAV. The main developers of this tool are Pierre-Louis Bazin and Dzung Pham of the MedIC lab. The program implements the algorithm by Goldszal at al. (1998). PNI is involved in the testing of this software, as well as establishing the reliability and validity of the method. The plug-in algorithm and evaluations are currently in press. For testing, you can download the software from the MedIC Site.

GRAT (Group ROI Analysis Toolbox)

The GRAT is under active development. It is a plug-in to SPM that utilizes the MarsBaR routines to extract region of interest time course for groups of subjects, calculates average time courses and percent voxels activated, as well as mean and maximum amplitudes. It also includes plotting routines to co-plot time-course data with task parameters. This project is still under construction.

ABSEG (Atlas-Based Segmentation)

ABSEG was developed by Adam Dziorny as a plug-in to MIPAV, re-implementing an algorithm for whole brain segmentation based on Atlas priors by Bruce Fischl at MGH. The software provides a tool for the automated labeling of neuroanatomical structures in the human brain. This algorithm combines spatial and intensity information to improve registration to manually created atlases. This tool is still undergoing testing.


DEMONS was originally developed by Thirion et al. (1998) as an image registration method using optical flow techniques. It was re-implemented by the MedIC lab as a method to assess longitudinal atrophy in patients at increased risk for developing AD. The use of DEMONS as a method to reliably assess these differences is still undergoing tesing. DEMONS is also implemented as a plug-in to MIPAV.


With the onset of voxel-based morphometric analyses a few years ago, several applications of these methods have become possible. PNI is developing new methods to extend the use of VBM and VBM-like methods to the assessment of differences across groups in different imaging modalities, such as diffusion weighted imaging, and fractional anisotropy images. In addition, we are also working on ways to conduct these voxel-based analyses with regional specificity to improve the quality of the registration in the hypothesized areas of interest, and increase statistical power.


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