Overview

The JIP Toolkit was developed primarily for analysis of preclinical fMRI data, because the widely available neuro-imaging packages proved to be consistently bad at such tasks, although they may have become more flexible in recent years. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable

  1. automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step,
  2. visualization of 4-dimensional data using either mosaic or tri-planar display, and integration of general linear models for graphical display of time series analysis,
  3. a simple and flexible 1st-order GLM for fMRI time series analysis,
  4. a GLM for PET analysis within the framework of the simplified reference tissue model,
  5. a 2nd-order GLM analysis following the Worsley 2002 scheme,
  6. a tool for performing smoothing, registration, mapping (etc). using a command interpreter,
  7. MRI templates to place your data into standardized neuro-imaging spaces.


Platforms


All tools use the Linux/Unix environment. The current distribution includes executables for

  • Linux i686 (32-bit),
  • Linux x86_64 (64-bit),
  • Darwin for Mac OS X (universal binary), and
  • Cygwin/X (32-bit) for Windows.

The code is distributed as open source to enable creation of executables for other systems. For any system, the essential components are Linux or Unix plus X11 graphic capabilities.


Download the software

http://www.nitrc.org/projects/jip



Acknowledgement of Support


Like most software developed for scientific research, this work was funded indirectly through projects that required or benefited from its functionality. Support was derived from NIH grants to the developer of this software (Joseph B. Mandeville) and from grants to collaborators. Additional funding came from the Athinoula A. Martinos Center for Biomedical Imaging, a collaboration of the Massachusetts General Hospital, the Massachusetts Institute of Technology, and the Harvard Medical School. Explicit support for the distribution of this software came from the National Institute for Biomedical Imaging and Bioengineering (NIBIB @ NIH) through grant R03EB008134. 


License


Copyright (c) The General Hospital Corporation

All rights reserved.


This agreement ("Software License") covers downloads of the JIP fMRI Analysis Toolkit maintained by The General Hospital Corporation. Your downloading, copying, modifying, distributing, displaying, or use of any software and/or data from the JIP fMRI Analysis Toolkit constitutes acceptance of all of the terms and conditions of this Agreement. If you do not agree to such terms and conditions, you have no right to download, copy, modify, distribute, display, or use the Software.


1. As used in this Software License,

"you" means the individual downloading and/or using, reproducing, modifying, and/or displaying the Software and the institution or entity which employs or is otherwise affiliated with such individual in connection therewith; The General Hospital Corporation d/b/a Massachusetts General Hospital ("Hospital") hereby grants you with respect to Hospital's rights in the software, and data, if any, which is the subject of this software license (collectively, the "Software"), a royalty-free, non-exclusive license under Hospital's copyright rights, to redistribute, reproduce, modify, and display the Software (in source or binary forms), provided that: 


(a) you accept and adhere to all of the terms and conditions of this Software License; 


(b) redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer;


(c) redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with distribution;


2. The Software is provided "AS IS" and neither Hospital nor any contributor to the software (each a "Contributor") shall have any obligation to provide maintenance, support, updates, enhancements or modifications thereto. HOSPITAL AND ALL CONTRIBUTORS SPECIFICALLY DISCLAIM ALL EXPRESS AND IMPLIED WARRANTIES OF ANY KIND INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL HOSPITAL OR ANY CONTRIBUTOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, EXEMPLARY OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY ARISING IN ANY WAY RELATED TO THE SOFTWARE, EVEN IF HOSPITAL OR ANY CONTRIBUTOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. TO THE MAXIMUM EXTENT NOT PROHIBITED BY LAW OR REGULATION, YOU FURTHER ASSUME ALL LIABILITY FOR YOUR USE, REPRODUCTION, DISPLAY, LICENSE OR DISTRIBUTION OF THE SOFTWARE AND AGREE TO INDEMNIFY AND HOLD HARMLESS HOSPITAL AND ALL CONTRIBUTORS FROM AND AGAINST ANY AND ALL CLAIMS, SUITS, ACTIONS, DEMANDS AND JUDGMENTS ARISING THEREFROM. 


3. None of the names, logos or trademarks of Hospital or any of Hospital's affiliates or any of the Contributors, or any funding agency, may be used to endorse or promote products produced in whole or in part by operation of the Software or derived from or based on the Software without specific prior written permission from the applicable party.  In the case of Hospital, permission needs to be obtained from its Public Affairs Office.


4. You agree to provide acknowledgement to Hospital when you publish and present results of your use of the Software in peer-reviewed journals in accordance with standard academic practice. 


5. This Software License does not grant any rights with respect to third party software, except those rights that Hospital has been authorized by a third party to grant to you, and accordingly you are solely responsible for obtaining any permissions from third parties that you need to use, reproduce, distribute, modify, and display the Software. 


6. The Software has been designed for research purposes only and has not been reviewed or approved

by the Food and Drug Administration or by any other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. You further agree to use, reproduce, and display the Software in compliance with all applicable governmental laws, regulations and orders, including without limitation those relating to export and import control.


Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard