Credit / Blame / Contact - Tobias Wood - tobias.wood@kcl.ac.uk

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

If you find the tools useful the author would love to hear from you.

This is the updated version of QUIT based on ITK http://www.itk.org The previous version is here http://github.com/spinicist/old_quit

A collection of programs for processing quantitative MRI data, in particular DESPOT and mcDESPOT.

Many thanks to Samuel Hurley for many, many suggestions. Thanks to Anna Combes, Amy McDowell and Sjoerd Vos for finding bugs.

As of version 1.0 there is now a Wiki at http://github.com/spinicist/QUIT/wiki. It will be filled out gradually.

1. A C++11 compliant compiler (GCC 4.8.0+, Clang 3.1+)
2. CMake version 3.2 or higher (http://www.cmake.org)
3. Eigen version 3.2.4 or higher (http://eigen.tuxfamily.org)
4. ITK version 4.7.2 (http://www.itk.org)

WARNING - You will require a recent compiler for DESPOT as it uses C++11 features. GCC 4.8.0 is a MINIMUM as earlier versions do not support C++11 threads. Clang 3.1 will also work. You can find out the version of your system gcc by running "gcc -v".

There are two suggested methods to build the tools. If you are unfamiliar with CMake and command-line building use method 1. If you are familiar with them then you can use method 2.

1. Download and untar/unzip QUIT. In a terminal window, change directory to where you unpacked QUIT. Then type './easy_build.sh'. This will download Eigen & ITK into subdirectories, and then compile QUIT in a '/Build' subdirectory.
2. Download and compile ITK & Eigen. Download and unpack QUIT. Create a build directory, e.g. 'QUIT/Build'. Then run CMake as standard, e.g. 'ccmake ../' from within 'QUIT/Build'. Specify the directories of ITK and Eigen. It is likely that CMake will report an error on the first 'Configure' attempt if it cannot locate Eigen. After configuring and generating, run 'make -j'.

There are some example scripts for processing pipelines in the /Scripts directory. These print usage instructions if you call them with no arguments. They take a set of filenames as input, and you will need to modify the scripts with your particular flip-angles and TRs.

Each product has some basic usage instructions that will be printed with either the -h or --help options, e.g. “qimcdespot -h". The programs will then prompt you to enter flip-angles, TRs, etc. as they require based on your input options.

Once you are used to the input format, I recommend writing down the input in a plain text file, and then using either the redirect operator (“<“) or a HEREDOC (“<<“)to pass the input to your program. If you do this, you can suppress the prompts to enter input with the “-n” option. So to run DESPOT1-HIFI you would type:

qidespot1hifi -m mask_file.nii -n spgr_file.nii irspgr_file.nii < in.txt

where “in.txt” is a file containing:

# A # symbol means a comment
3 18   # SPGR flip-angles
0.0083 # SPGR TR in SECONDS, not milli-seconds
5      # IR-SPGR readout flip-angle
0.0083 # IR-SPGR readout TR
92     # IR-SPGR echo train length
0.45   # IR-SPGR TI in SECONDS

Because QUIT is based on ITK, in theory it supports multiple image formats. However I have only tested it with NIFTI.

NOTE - This section will migrate to the Wiki eventually.

In alphabetical order:

1. qiaffine - Applies simple affine transformations (currently rotations only) directly to NIFTI headers. It was written specifically for fixing pre-clinical data where orientations differ in definition to clinical.
2. qiafi - Calculates a B1+ map from Actual Flip-angle Imaging data. See Yarnykh, MRM 2007 & Yarnykh, MRM 2010.
3. qicomplex - Converts between magnitude/phase/real/imaginary/complex data. Exists because of a bug in fslcomplex.
4. qidespot1 - Calculates a T1 map using the DESPOT1/VFA method. Includes weighted least-squares (see Chang MRM 2008) and non-linear least-squares fitting as well as the classic least-squares algorithm (there are multiple references for this, e.g. Gupta JMR 1977)
5. qidespot1hifi - Calculates a T1 and B1+ map simultaneously. See Deoni JMRI 2007. Thanks to Michael Thrippleton for corrected equations.
6. qidespot2 - Calculates a T2 map. Only useful for band-free data, i.e. 1.5T or below.
7. qidespot2fm - Calculates a T2 and f0 (off-resonance) map simultaneously. See Deoni JMRI 2009.
8. qimcdespot - Calculates myelin water fraction maps. See Deoni MRM 2012.
9. qimultiecho - Calculates T2 or T2* maps from multi-echo data. See Pei MRM 2015.
10. qinewimage - Creates images. Used for tests.
11. qisignal - Calculates synthetic images using different signal equations. Used for tests.
12. qissfpbands - Removes band artefacts from bSSFP images. See Xiang, MRM 2014.
13. qiunwrap - Laplacian Phase Unwrapping. Experimental. See Schweser MRM 2013.

There will be more in future.