NIS Java Interfaces

The CCN and NCC labs are developing a standard set of graphical user interfaces for both NIS software as well as for third-party software that is extensively used by the CCN and NCC labs (e.g. AIR). The graphical user interfaces are being developed with the Java FisWidgets package. You need to install FisWidgets (as well as Java and Swing, and, optionally for AirAlign, the Jama Package) to use these interfaces. Also needed are AIR, imgio, and tools java packages. All of these products are in the public domain.

Please note: almost all of these Java programs are front ends to C or C++ programs distributed with the NIS or other packages. Unless you install the appropriate backend package(s), these graphical interfaces will not run. See the requirements listed below for details as to what programs are needed, and, how to specify what directories they are installed in. Please see the Related links section of the NIS package homepage for details about where to get the various packages used.

Index to Java Interfaces

Interfaces for NIS meta-fiswidgets (interfaces joining togther multiple fiswidgets)
- NisToolChest -- Toolchest with all NIS tools. screenshot
  Requirements: those of individual components.
- NisSingle -- Sample CCN lab single subject analysis stream. screenshot
  Requirements: those of individual components.
Interfaces for NIS modules
- CellCount -- compute counts of all combinations of factor levels from a given design file. screenshot, help file
  Requirements: none.
- FormatConvert -- convert between analyze and pgh format. screenshot, help file
  Requirements: pgh2air.csh, air2pgh1.csh, and decompress.csh scripts.
- GroupTransform -- prepare individual subject data for group analysis. screenshot, help file
  Requirements: AIR package; nisreslice, nisnorm, and nismooth programs.
- MakeDesign -- create design file for input to nisanova from Psyscope (or plaintext) datafile. screenshot, help file
  Requirements: none.
- Nisanova -- perform analysis of variance. screenshot, help file
  Requirements: nisanova program.
- Niscontrast -- perform different contrast analyses on datasets. screenshot, help file
  Requirements: niscontrast program.
- Niscorrect -- Polynomial detrend, baseline correction, and outlier correction of timeseries data. screenshot, help file
  Requirements: niscorrect program (distributed with NIS). Location specified by NIS_PATH key in .fisproperties file.
- Niscrit -- given probability and design file, return F threshold. screenshot, help file
  Requirements: niscrit program.
- Nisfilter -- convolves input pgh txyz dataset voxelwise with input filter. screenshot, help file
  Requirements: nisfilter program (distributed with NIS).
- Nishemo -- generates model hemodynamic functions: gaussian, poisson, gamma, and identity. screenshot, help file
  Requirements: nishemo program (distributed with NIS).
- Nismaps -- calculate voxelwise means, variance, signal-to-noise-ratio maps. screenshot, help file
  Requirements: nismaps program.
- Nisnorm -- perform mean normalization of images. screenshot, help file
  Requirements: nisnorm program.
- Nisoverlay -- overlay statistical map on anatomical image. screenshot, help file
  Requirements: nisoverlay program.
- Nisroi -- given an image, alpha threshold, and contiguity threshold, identify regions of interest. screenshot, help file
  Requirements: nisroi program.
- Nisthresh -- removes the image background by automatic thresholding. screenshot, help file
  Requirements: nisthresh program (distributed with NIS).
- Nistime -- given an ROI map and functional dataset, calculate mean timeseries data on an ROI basis. screenshot, help file
  Requirements: nistime program.
- Overlap -- computes table of pixel counts and percent overlap between two ROI images. screenshot, help file
  Requirements: overlap program (distributed with NIS).
- RoiApp -- Simple region-of-interest viewing tool. screenshot, output screenshot, help file
  Requirements: none.
- RoiDesign -- Plot mean contrasts by region of interest and factor combinations. screenshot, output screenshot, help file
  Requirements: none.
Interfaces for AIR modules (you need to install AIR to use these)
- AirAlign -- Interface to the AIR alignlinear program. screenshot, output screenshot, help file
  Requirements:
  - nisair program (distributed with NIS). Location specified by NIS_PATH key in .fisproperties file.
  - alignlinear program (distributed with AIR) is required for serial execution. Location specified in the compilation of nisair.
  - alignpvm program (distributed with NIS) is required for parallel execution. Location specified in the compilation of nisair and PVM architecture specification.
  - If you want a graph of the motion parameters to be plotted, you need to install the Jama package (see above).