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Fastmap

FastMap is a Functional Analysis software tool for MRI and PET, designed by Joseph Mandeville. 

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 site

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
fastmap download