Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

This website has been deprecated and exists as an archive only.

The TORTOISE website has been moved to https://tortoise.nibib.nih.gov.

For any information about TORTOISE generation V3.x.x, please refer to the new website.

3.2.7.2 iRESTORE Options

When iRESTORE is selected, the user is able to set additional parameters using the iRESTORE Options menu.

Tensor options with iRESTORE selected

Click the help button for additional details of each parameter. The parameters are briefly described below the figure.

iRESTORE options dialogue
  • Threshold value of reduced chi-square - iRESTORE is only run if the data fails to reach a "quality" threshold, which can be user define. This threshold, based on the chi-square goodness of fit measure, is automatically computed for your data based on the formula provided in the "help". However, if the user wishes to be more or less stringent, the value can be set manually here.
  • Threshold value of confidence interval - By default, iRESTORE rejects data points based on the size of the residuals. This value determines if the point is considered outside the acceptable range.
  • Maximum number of bias -
  • Do not check the b0 images - Default value = do not check. The non-diffusion weighted (b0) images generally show different variance properties than the diffusion weighted images. As such, RESTORE is not optimized to identify outliers in the b0 images. We recommend leaving this at the default value. All voxels of all b0 images will be included in the tensor fitting.
  • B-value threshold - The b-value of each volume is determined from the b-matrix. Due to imaging gradients, rotations of the b-matrix from motion correction, or acquisition of non-zero low b-value images, means that the b-value of the b0 image may not be exactly 0. The user can input a minimum value below which images are not considered for outlier detection. Default value is 100.
  • Check the remaining directions after outlier identifications - this is a newer feature of RESTORE that checks that the b-matrix is not ill-defined after removal of data points (i.e. ensures that enough data remains in all diffusion encoding directions). Default value is "on", and we recommend that this check be performed.
  • Redundancy coefficient - Determines the minimum amount of data required in each encoding direction. More details of this coefficient can be found in Chang, et al.1
  • Write log file to record parameters used in robust fitting - a log file can be written to keep track of parameters used.