Welcome to TORTOISE documentation!


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TORTOISE is comprised of the following tools:

  • DIFFPREP [1]- Distortion and motion correction module: Link text Command Line and Link text GUI
  • DR-BUDDI [2] - EPI distortion correction module, run after DIFFPREP processing and if 2 or 4 opposite phase encode direction data present
  • DIFFCALC [3]- Tensor fitting and post processing correction module

In its newest form, DIFFPREP and DR-BUDDI modules have been revived from TORTOISE 2.5.1 and repackaged. DIFFPREP is primarily used in importing raw images, performing motion+eddy and EPI distortion corrections, as well as reorientation to a template space (if provided). Importantly, DIFFPREP has now been re-designed to run fully in C++ and does not require an IDL license or VM (yay!)– it is even executable from the command line. Some of the new features incorporated into the new DIFFPREP (and few in common with DR-BUDDI are as follows):

  • Batch capability for import and processing the data
  • Raw images converted to NIFTI format
  • No IDL license requirement
  • Gibbs ringing artifact removal
  • Data denoising
  • Improved image-based EPI distortion algorithm
  • A detailed log of import and processing procedures


Practical Recommendations for dMRI Data Acquisitions

We list several general and scanner specific recommendations here for dMRI data acquisition.



Please refer the change log that documents the features incorporated in the new versions of the software

***version 3.2 change log details have been updated. Please refer the section before using the new version.****


TORTOISE version 3.1.3 Main Documentation

- Please use this documentation as a general reference for version v3.1.1, v3.1.2, v3.1.4 and v3.2.
- exception of version 3.2, the previous versions have similar features. There are syntax changes (tags may have been removed or added, from one version to the next) for certain commands. In such cases, it would be beneficial to refer the help file that gets printed out in the terminal, upon typing the command.
-Major feature changes between versions are documented in the change log.