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Imaging Toolkit

Fast Imaging Library

This library of functions provides a number of algorithms to reconstruct accelerated MR data, including

• UNFOLD
• Parallel Imaging Methods
  1. SENSE, Variable Density SENSE, regularized SPACE RIP, and GRAPPA

as well as a number of associated MR image reconstruction algorithms, including

• Homodyne processing of partial-Fourier data
• Gradient field inhomogeneity correction (gradwarp)
• Nyquist Ghost correction

The complete package includes a reference manual (PDF and HTML), a binary library file, and demos in both C and Matlab (via MEX). To get started, follow the "Quick Start Guide" given in the manual.

Please direct support and other inquires to: ncigt-imaging-toolkit at bwh.harvard.edu

IGT Applications

The library is currently used for reconstruction of EPI data by the BWH Functional Neuroimaging Lab in z-shimmed applications.

Previously, this imaging toolkit was used in two projects within the IGT Center:

• Temperature Monitoring
• Prostate Biopsy Tracking

Downloads

• License
• Reference Manual

Version 1.08 (Released Sep 21, 2012)

Change Log:

• added 'char' style to .nd data format
• added in a scale factor during geste recon, to correct for the ifft scaling.
• modified the 3-nav-line ghost correction routines to support both single- and double-precision data. Added a MEX file to call NGC from Matlab.
• modified the Siemens meas.dat data reader to a stream format
• reduced threshold for line fitting in ngc_compute_phase_shift

Version 1.06 (Released Apr 27, 2012)

Change Log:

• fixed a bug in self_ref_b1_via_geyser, which would crash if the number of coils to process exceeded the number of concurrent processing threads.
• fixed a bug in apply_vbc_coefs, where the output data size array was incomplete for data with ndim > 4.
• added a 64-bit Mac variant to the release package.

Version 1.05 (Released Mar 8, 2012)

Change Log:

• reworked the virtual body coil code. VBC parameters are now available for re-use (e.g. with other volumes) and phase is aligned across slices
• fixed a bug in geste_interleave_frames (size of combo DATA_OBJ was not updated properly w/ rectangular images.)
• changed function name est_b1_via_geyser to self_ref_b1_via_geyser, to improve consistency with other coil sensitivity estimation functions
• added functions to support standard 3-nav-line EPI ghost correction
• cleaned up Siemens data reading code, for more consistency between multi-slice and single-slice data.
• added option to output an image mosaic of slices in demos/display/

Version 1.01 (Released Jul 14, 2011)

Change Log:

• added an option to output phase images in demos/display/
• updated display demos to use the same data-to-RGB code base
• fixed a bug in geste_calibrate__all_slices
• fixed a bug in sprip_lsqr_recon. now properly handles readout data of arbitrary length.
• fixed a bug in SVDLIBC: code was exiting before convergence in a few cases on 64-bit machines. Converted all 'long' to 'int' (to match 4-byte 32-bit definition) and problem resolved.
• fixed a bug in align_image_phase, regarding improper pthread management
• new functions:
  1. read data and header information from Siemens data files
  2. a function to compute the gridding matrix for resampling EPI ramp sampled data

Version 0.98 (Released Oct 15, 2010)
[rereleased Mar 28, 2011, after server upgrade]

Change Log:

• modified apply_ramp, so that phase envelope is symmetric about the center of k-space. e.g. the phase index now runs from (1-N/2)..(N/2) instead of (1..N)
• modified the phase_align function so that phase correction is split equally across both input data sets. This ensures GESTE is now suitable for temperature mapping applications.
• added nd2png demo, to convert .nd data files to .png images
• converted rampsamp correction function to use DATA_OBJ inputs
• reworked vbc code to handle multi-slice input data
• reworked geste code to better handle multi-slice input data
• added read_data_from_Pfile function to simplify access to raw GE k-space data files.

Version 0.96 (Released Mar 5, 2010)

Change Log:

• OF NOTE: changed name of 'COORD' struct to 'XCOORD', for Siemens ICE compatibility
• cleaned up win32 compiler warnings
• added Nyquist Ghost Elimination via Spatial and Temporal Encoding (GESTE) functions
• added display demo for showing images of .nd data in Windows
• fixed memory leak in find_tag (DICOM util)
• added fft manager init check to catch segfaults on uninitialized buffers
• split GRAPPA reconstruction code into two parts, so that GRAPPA reconstruction parameters can now be easily reused.
• fixed a bug in the project_mask function, so that it now works with rectangular matrices

Version 0.9 (Released Aug 3, 2009)

Change Log:

• added functions to support phase alignment between images
• added functions to support virtual body coil estimation
• converted CWP SVD code to use double precision. Fixed bug that prevented economy-sized SVD.
• added code for fast left-singular-vector calcuation (lsv) useful for rank-1 estimation of matrices
• fixed malloc bug in correct_rampsamp function
• converted unfold_filter to use multiple threads
• additional C-code demos added

Version 0.8 (Released Apr 14, 2009)