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FastMap is a GUI application that employs Qt libraries to provide enhanced functionality relative to its predecessor, the “jip toolkit”. Qt provides a broad range of GUI widgets, multi-platform support, multi-threading, high-level access to the file system (query, create, delete, etc) and to system calls (spawning processes, setting environment variables, changing working directories, etc.). Because Qt is widely used, there is a large shared code base and lots of online user support.

Fastmap has evolved to include 

  1. two image spaces
  • the time-series space forms the basis for time-series analysis
  • the anatomy space provides a template space for alignment, atlases, etc.
  1. time-series analyses on a separate graph window (voxel-based or ROI-based)
  • fMRI GLM analyses for rapid responses (standard HRF approach, IRF fitting)
  • phMRI GLM analyses using gamma-variate and sigmoidal responses
  • PET reference region kinetic analysis using pseudo-GLM approaches (MRTM, MRTM2)
  • PET reference region kinetic analysis using forward-model nonlinear methods with single or multiple compartments but fixed/global k4
  • PET SUV
  • T2 mapping and ADC mapping
  • T1 mapping for inversion-recovery magnitude images
  • DTI tensor-based analysis with tract tracing by tensor deflection
  • mixed and random effects second order GLM based upon the summary statistics approach
  1. preprocessing
  • alignment/normalization to a template, with a flexible user-based approach to defining templates
  • transformation of overlays (ROIs) between spaces
  • isotropic spatial smoothing (3D, 2D)
  • reslicing to reformat one file to match a second file with the same coordinates
  • partial volume correction for PET, using geometric transfer matrices
  • brain extraction based upon progressive dilation from a seed voxel
  • cropping to decrease the FOV


Download the software

https://www.nitrc.org/projects/fastmap


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), particularly R01NS112295 and R21NS090169 from NINDS, 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. 


License

Copyright (c) The General Hospital Corporation;

All rights reserved.


This agreement ("Software License") covers downloads and distribution of the Functional Analysis Software Toolkit for MRI and PET (FastMap), maintained by The General Hospital Corporation. Your downloading, copying, modifying, distributing, displaying, or use of any software and/or data from FastMap 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