Welcome to the website for the Quantitative Imaging Toolkit (QIT). This wiki provides information about basic usage, core concepts, and a number of tutorials for using the toolkit. Download and installation instructions can be found here.
What is QIT?
QIT is a software package of computational tools for the modeling, analysis, and visualization of scientific imaging data. It was specifically developed for tractography and microstructure analysis of diffusion magnetic resonance imaging datasets, but it has capabilities that are generally useful for other imaging modalities as well. It supports many different data types, including multi-channel volumetric datasets, multi-label masks, curves, triangle meshes, geometric primitives, tabular data, and spatial transformations. QIT provides an application called
qitview for interactive 3D rendering and data analysis, as well as, a suite of command line tools available through a program named
qit that provides a way to do batch processing and scripting. In addition, QIT also provides ways to integrate of these tools into grid computing environments and scientific workflows.
How is QIT developed?
QIT was originally designed and developed by Ryan Cabeen for his Ph.D under advisement of David H. Laidlaw in the Department of Computer Science at Brown University. Currently, QIT is actively being developed under advisement of Dr. Arthur Toga at the USC Laboratory of Neuro Imaging Resource.
Comments, criticism, and concerns are appreciated and can be directed here.
How do I cite QIT?
If QIT was used in part of your research, please cite the following abstract in associated publications:
Cabeen, R. P., Laidlaw, D. H., and Toga, A. W. (2018). Quantitative Imaging Toolkit: Software for Interactive 3D Visualization, Data Exploration, and Computational Analysis of Neuroimaging Datasets. Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM), 2854.
How can I use QIT?
Quantitative Imaging Toolkit (QIT) (c) 2012-2018 Ryan Cabeen All rights reserved. The Software remains the property of Ryan Cabeen ("the Author"). The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the Author as a charitable foundation protects its assets for the benefit of its educational and research purposes, the Author makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the Author disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software. The Licensee agrees to indemnify the Author and hold the Author harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software. No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the Author. The permission of the Author is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received.
What does QIT use?
QIT was developed using a combination of Java (version 1.8 and above) and Python (version 2.7 and above). The package also uses the excellent open source resources listed below. In the QIT application directory, you can also find copies of their license files, as well as the separate jars for each library that are linked by QIT.
- Apache Commons CLI 1.2, released under the Apache v2 license
- Apache Commons IO 2.1, released under the Apache v2 license
- Apache Commons Lang 3.0.1, released under the Apache v2 license
- Gson, released under the Apache v2 license
- log4j 1.2.9, released under the Apache v2 license
- Guava 11.0.2, released under the Apache v2 license
- Jama 1.0.2, released into the public domain
- opencsv 2.3, released under the Apache v2 license
- reflections-0.9.8, released under the WTFPL license
- Jython 2.5.0, released under the Jython license
- jythonconsole-0.0.7, released under the LGPL v3 license
- Camino, released under the Artistic 2.0 license
- matrix-toolkits-java, released under the LGPL v3 license
- smile, released under the Apache 2.0 license
- jogl, released under the BSD license
- JPOP: Java parallel optimization package, released under the LGPL license
- object-explorer, released under Apache v2 license
- Logo, released under the Creative Commons license
The license documentation associated with each of these can be found in the software package under