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NIH Pediatric Neuroimaging - Diffusion Tensor MRI Center
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Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble

The current release is TORTOISE V2.1.0, available on the download page

Click here for version update information.

To get started with TORTOISE: Quick Start Guide


Please register to the TORTOISEDTI Google group for questions and help at:!forum/tortoisedti




*See note at bottom of the page


Second TORTOISE Hands-on Course

September 29th, 2014

NIH campus, Natcher Hall Rooms C1/C2

Kindly Hosted by the AFNI Bootcamp

TORTOISE Course Details

8:30 am - 8:35 am          Welcome Address

8:35 am - 8:50 am          Diffusion Tensor Imaging (DTI) Acquisition tips and tricks 

                                     Speaker: Joelle Sarlls


8:50am - 9:50 am       - General Considerations on the Diffusion Processing Pipeline

                                     - The advantages of a good processing Pipeline

                                     - Concept of Artifacts and Artifacts Remediation

                                     - Diffusion Consequences of EPI Distortions

                                     Speaker: Carlo Pierpaoli


9:50 am - 10:15 am      - Introduction to TORTOISE

                                      - ACPC Reorientation of an Anatomical Image with MIPAV

                                   Speakers: M. Okan Irfanoglu, Amritha Nayak

10:15 am - 10:30am          Break

10:30am - 11:15am        Overview of DIFFPREP

                                   Speaker: M. Okan Irfanoglu

11:15 am - 12:00pm      Overview of DIFFCALC

                                     Speaker: Carlo Pierpaoli

12:00 am - 12:15 pm      The latest and the greatest in TORTOISE: DR-BUDDI

                                     Speaker: Okan Irfanoglu

12:15 pm - 12:30 pm      Q & A

Step-by-step instruction manual can be downloaded from: afni_tut_instructions.pdf 
The dataset to be used in the bootcamp can be found at:


For more details please visit :


Why TORTOISE? Our software is not for rabbit type people; if you need to process diffusion data at the scanner console you do not want to use our software.

Why obsessive? We have realized that DTI is a wonderful quantitative technique which is unfortunately susceptible to all sorts of artifacts and confounds. We spent a lot of time trying to obtain reliable DTI measurements, which has made ourselves and our software a little obsessive. Why indolent? Our emphasis has been on developing conceptually rigorous routines more than optimizing the speed and user-friendliness of the software.

TORTOISE was presented at the ISMRM meeting in Stockholm, Sweden in 2010. Please reference the following abstract if you use TORTOISE in your work.

C. Pierpaoli, L. Walker, M. O. Irfanoglu, A. Barnett, P. Basser, L-C. Chang, C. Koay, S. Pajevic, G. Rohde, J. Sarlls, and M. Wu, 2010, TORTOISE: an integrated software package for processing of diffusion MRI data, ISMRM 18th annual meeting, Stockholm, Sweden, #1597 (pdf)

The TORTOISE software package is for processing diffusion MRI data, and it contains three main modules:

  • DIFF_PREP - software for image resampling, motion, eddy current distortion, and EPI distortion correction using a structural image as target, and for re-orientation of data to a common space
  • DIFF_CALC - software for tensor fitting, error analysis, directionally encoded color map visualization and ROI analysis
  • DR-BUDDI- software for EPI distortion correction using pairs of diffusion data sets acquired with opposite phase encoding (blip-up blip-down acquisitions). 

In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.

Some common questions and answers about our software packages are listed in the FAQ.

If you are interested in contributing to these wiki pages, please contact us in order to create an account for you.

*This picture is adapted from an image we downloaded from the web. We would like to give credit to the original author(s) who we have been unable to identify. Please contact us at if you know the origins of this picture.

For internal NIH collaborators only