ricardorios46 / quit Goto Github PK

Credit / Blame / Contact - Tobias Wood - [email protected]

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.

A collection of programs for processing quantitative MRI data, originally DESPOT but now a wider variety of techniques.

Many thanks to Samuel Hurley, Erika Raven, Anna Combes, Amy McDowell and Sjoerd Vos.

Documentation is available at http://quit.readthedocs.io (and the in Docs folder in .rst format).

Pre-compiled executables are provided for Linux and Mac OS X in a .tar.gz archive from http://github.com/spinicist/QUIT/releases. Download the archive and extract it with tar -xzf qi-platform.tar.gz. Then, move the resulting qi file to somewhere on your $PATH, for instance /usr/local/bin. That's it.

• MacOS Catalina or higher users should use curl to download the binary, i.e. type curl -L https://github.com/spinicist/QUIT/releases/download/v3.0/qi-macos.tar.gz This is because Safari now sets the quarantine attribute of all downloads, which prevents them being run as the binary is unsigned. It is possible to remove the quarantine flag with xattr, but downloading with curl is more straightforward.
• The Linux executable is compiled on Ubuntu 22.04 with GLIBC version 2.35 and a statically linked libc++. This means it will hopefully run on most modern Linux distributions. Let me know if it doesn't.

For instructions on how to compile from source, please see the developer page in the documentation.

QUIT now comes with nipype wrappers. Install with pip install qipype.

QUIT comes as a single executable file with multiple commands, similar to git or bart. Type qi to see a list of all the available commands. The majority of commands require an input 4D Nifti file containing the image data to fit, and a .json file containing the sequence parameters (e.g. TR). See examples for each command at https://quit.readthedocs.io.

An example iPython notebook is available here in a separate repo https://github.com/spinicist/qipype-binder. Workflows for CEST and MPM are provided in qipype.workflows.

If you can't find an answer to a problem in the documentation or help strings, you can open an issue, or find the developer on Twitter (@spinicist).