Nisnorm

Performs mean normalization on a set of neuroimaging scans. Each image in the set is normalized to a specified target value or to the first image in the set, such that the mean signal intensity in all the images is equivalent.

Invocation

java Nisnorm

Nisnorm window

Information to be entered

• Input file/directory
  Text file with filenames of images to be normalized, or the name of a directory with such images. This program will try to uncompress the images if they are compressed.
• Output directory
  Directory where the output images will be placed. This program will try to create this directory if it doesn't already exist.
• Threshold
  Calculates mean based only on voxels whose mean signal intensity is above threshold. Provides a means of ignoring background pixels.
• Normalize to first image in list/directory
  Choose this option if you want to normalize all the images to the mean intensity value of the first image in the specified set.
• Normalize to target mean value
  Choose this if you want to normalize all the images to the specified target mean value.
• Compress input images when finished
  Check this box if you want input images to be compressed (gzipped) after processing so as to save disk space.
• Options...
  Select other normalization options
  • Additive vs. Multiplicative adjustment
    Additive adjustment will bring each image to the desired target mean intensity by adding a constant value to each pixel. Multiplicative adjustment will bring each image to the desired target mean intensity by multiplying the value of each pixel by a constant value.
  • Use output stem
    The default is to prepend an 'n' to each input image filename in creating the filename of the output image, so that the normalized version of "func_00427.img" would be named "nfunc_00427.img" (for example). Check this box if you want to specify the output stem instead (a stem of "norm_" would result in an output filename of "norm_00427.img" in this example). Checking this box will also force the output image sequence to start on 1 and increase by 1 for each subsequent image in the filelist, which is useful if the input images come from different directories but have some identical image stems and numbers, or if images have been inserted or deleted and a contiguous sequence is desired.
  • Verbose mode
    Checking this box will print details about each image (including adjustment factor and target intensity) as it is normalized.

• Menubar
• Toolbar
• Output window