NIRFAST 7.0

• For the final stage of the workflow, a tool Nirviz has been developed for visualizing 3D FEM solutions from Nirfast. These solution files contain multiple optical properties at each node in the mesh. The tool is able to switch between properties, displaying a volume rendering as well as three orthogonal slice views of the selected property. Many improvements have been made to Nirviz recently:
• Nirviz now properly allows the overlay of the FEM solution on the original DICOM images.
  1. Added the ability to threshold values.
  2. The ability to load default values for transparency, thresholding, and value range when viewing a solution. This is particularly useful for creating figures for a publication, as it allows multiple images to have the same scaling features.
  3. Keeping track of slice number.
  4. More robust transparency.
  5. Compiled on all platforms (Windows, Mac, Linux, 32 and 64-bit).
  6. Increased label size.
  7. Several bug fixes.
• Various mesh-creation tools have been added to Nirfast for creating a 3-dimentional finite element mesh from a segmented volume, and labeling the regions with optical properties. In particular, the tools allow the user to assess the quality of the mesh elements in a histogram or visual manner immediately after creating the mesh, using various quality criteria. This is useful in identifying any issues that may crop up either as a result of poor segmentation, choice of meshing parameters, or domain geometry issues that can lead to poor mesh quality. Additionally, changes have been made to Nirfast for improved source/detector placement from fiber fiducial markers. There is now the ability for a user to create a script specific to their system, denoting how sources and detectors are placed relative to the fiducial positions. This script will be automatically detected by Nirfast and included in the GUI in a seamless manner.
• A conjugate gradient based method has been developed to be able to handle data sets where memory limits would traditionally be a constraint on the size of the problem. This method avoids the computation of the entire sensitivity matrix (Jacobian), thus making a trade-off between memory and speed.
• Time resolved code has been added to Nirfast, allowing for the simulation of time-dependent data.
• You can now select which solver to use, or add your own solver to Nirfast, simply by creating a Matlab script. The script will automatically be detected by Nirfast, and integrated into the GUI. This makes it very easy to customize Nirfast.
• Various checks have been added to improve the robustness of Nirfast, including tests for mesh quality, mesh size, unused nodes, the range of optical properties, and more.
• Various bug fixes including better simple shape mesh creation.