Index to Programs

• nisair -- is a wrapper to run the AIR alignlinear program on multiple image files (can run in parallel using PVM).
• nisanova -- performs a general analysis of variance on functional neuroimaging datasets. It outputs statistical parametric maps based on the F-ratios of each pixel in all of the main effects and interactions of the experimental design. It is based, in large part, on the |STAT anova package written by Gary Perlman. man page
• niscontrast -- performs different contrast analyses on functional neuroimaging datasets. The program can either be used as a posthoc test on data that have already been thresholded for omnibus significance level, or be run as a focused contrast (i.e., on raw data). man page
• niscrit -- given a probability and a design file, it returns the F threshold for each factor and their interactions.
• nisexpand -- magnifies the number of pixels in an image. man page
• nisgetmean -- returns the mean value of an ANALYZE image.
• nismaps -- calculates voxelwise mean and variance of a timeseries of ANALYZE images.
• nismask -- Takes an ROI image and a .plist file and produces an image where the value of each pixel indicates what ROI that pixel belongs to; a pixel value of zero means that pixel does not belong to any ROI.
• nisnorm -- performs mean normalization on functional neuroimaging datasets. Each image is adjusted to a reference image (the first input) or to a given value such that the means of all the images in the dataset are identical. man page
• nisoverlay -- overlays a thresholded functional image map onto a corresponding structural image. It automatically expands the functional image to the same dimension as the structural image (but only in the X and Y axes and only if the corresponding dimensions are integer multiples of one another).
• nisroi -- given an image, an alpha threshold, and a contiguity threshold, returns an image and supporting files (.txt, .plist) that collect individual voxels into larger regions containing only significant voxels.
• nisthresh -- removes the image background by automatic thresholding. man page
• nistime -- given an ROI file and a list of files (time points), calculates the mean activation level within each ROI at each time point. Also provides the option to calculate the activation level for each pixel within each ROI at each time point.
• overlap -- computes table of pixel counts and percent overlap between two ROI images.
• plist_split -- takes a .plist file and separates all the ROIs each into its own .plist file.