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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.
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C. Pierpaoli, L. Walker, M. O. Irfanoglu, A. Barnett, P. Basser, L-C. Chang, C. Koay, S. Pajevic, G. Civilization 3 complete for mac. 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:
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- 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.
Please make sure you untar your downloaded files from command line. After installation, if you receive permission issues when running a command, please change the permissions of the entire folder using chmod command.
1.1. LINUX
- Download
- Extract to a folder.
- In a terminal type the following echo $0
- after typing echo shell command, if terminal returns tcsh type tcsh ./install_tcsh.tcsh
- after typing echo shell command, if terminal returns bash type bash ./install_bash.sh OR bash ./install_bash.bash
If you are installing TORTOISE VER3.1.4 or 3.2, you may follow the above steps or:
- please then type bash install_TORTOISE.bash
Now, TORTOISE has been added to your path and you can just run any TORTOISE command by typing it in the terminal.
1.2. MAC
- Extract to a folder. Please make sure that you have downloaded the .tar.gz file and the file is not automatically being zipped by mac while downloading. If so, please click on your browser type on the top left corner, go to preferences, select general and uncheck the box that reads ‘open “safe” files after downloading.
- In a terminal type the following echo $0
- after typing echo shell command, if terminal returns tcsh type tcsh ./install_tcsh.tcsh
- after typing echo shell command, if terminal returns bash type bash ./install_bash.sh OR bash ./install_bash.bash
If you are installing TORTOISE VER3.1.4 or 3.2 you may follow the above steps or:
- please then type bash install_TORTOISE.bash
Now, TORTOISE has been added to your path and you can just run any TORTOISE command by typing it in the terminal.
1.3. WINDOWS
The support for windows version of TORTOISE has been discontinued. This is because , windows 10 now fully supports Ubuntu subsystem which can be downloaded from windows store. With this installed, in a command line, the users can type bash and be able to use the TORTOISE linux version. Please follow the steps detailed under linux installation above, if using Windows OS.
Note: If TORTOISE is added to your path using the above instructions for the different OS listed, you can run the various executables listed in the upcoming sections by just typing them in the terminal. If TORTOISE is not added to your path, then you will have to go to the folder where the executables exist and run with a ./ before running command of interest.
1.4. TORTOISE GUI
Along with command line feature, there is a TORTOISE GUI available in a separate folder when you download the TORTOISE software onto your selected OS. You will find inside the TORTOISE_GUI folder a executable by name TortoiseGui.py. Please refer to section 12 of this documentation for information on the GUI features.
To run TORTOISE GUI, PYQT5 needs to be installed using instructions below:
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In Ubuntu, type as a sudo user:
In MAC, with brew installed , type:
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With PyQt5 installed, you can run the GUI with :
python3 TortoiseGui.py