The Buffalo Neuroimaging Analysis Center (BNAC) uses a variety of software programs in the course of analyzing MRI datasets, including but not limited to:

  • Validated software developed at the BNAC, designed by expert computer scientists
  • The FSL software library (including SIENA/X)
  • Analyze
  • SPM
  • VBM
  • Java Image Manipulation (JIM)
  • DispImage
  • FreeSurfer
  • A.I.R.
  • LCD
  • LCModel
  • ITK
  • VTK
  • 3D-Slicer
  • MEDx

The BNAC does not rely on any single program for all analyses, but rather selects the best tool(s) for each particular task. Taken together, these programs provide all the capabilities requested and considerably more:

  • Image visualization requirements are met by JIM and Analyze. Furthermore, images can be simultaneously viewed orthogonally or visualized volumetrically in 3D. If necessary, more specific requirements are met using custom VTK programming

Post-processing requirements are met by a variety of validated BNAC software algorithms, and by JIM, Analyze, FSL, AIR, and FreeSurfer, etc.

  • Additional post-processing capabilities include correction of scanner inhomogeneity, image co-registration, matching of cross-sectional and longitudinal histograms, and “unwrapping” (removal of warping artifacts)
  • Histogram analysis is provided by validated BNAC algorithms, JIM, and Analyze. The BNAC can also perform more advanced histogram measurements, including entrophy and joint-histogram analysis
  • All requested ROI types and operations are provided by both JIM and Analyze. Validated BNAC algorithms , as well as FreeSurfer are capable of automatically creating certain types of ROI using pattern matching, machine learning, and warping techniques. Specifically, highly accurate region-specific ROIscan be generated.

In addition, the BNAC has the capability to perform many other analyses, including measurement of voxel-wise longitudinal change for numerous features.