Work Description

Title: Data for "Myelin Water Fraction Estimation Using Small-Tip Fast Recovery MRI" Open Access Deposited

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Methodology
  • MRI scans of a healthy volunteer were acquired on a GE Discovery MR750 3.0T scanner using a 32-channel Nova Medical head coil. Three scans were acquired: multi-echo spin echo (MESE) data with 32 echoes, a pair of Bloch-Siegert (BS) acquisitions, and 13 small-tip fast recovery (STFR) scans. The BS scans were used to estimate the transmit field inhomogeneity. Myelin water fraction (MWF) maps were computed from the MESE data using a regularized non-negative least squares (NNLS) algorithm, and from the STFR scans using parameter estimation via regression with kernels (PERK).
Description
  • File: P,jf06Sep2019,mese.7 The multi-echo spin echo (MESE) data was acquired using a 3D acquisition with an initial 90 degree excitation pulse followed by 32 refocusing (180 degree) pulses, resulting in 32 echoes with echo spacing of 10 ms. The repetition time of the sequence was 1200 ms. Each refocusing pulse was flanked by crusher gradients to impart 14 cycles of phase across the imaging volume. The initial excitation pulse had time-bandwidth product of 6, duration of 3 ms, and slab thickness of 0.9 cm, and each refocusing pulse had time-bandwidth product of 2, duration of 2 ms, and slab thickness of 2.1 cm. The scan took 36 min 11 s and covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9.

  • File: P,jf06Sep2019,b1.7 The Bloch-Siegert (BS) scans were acquired using a 3D acquisition. The excitation pulse of these scans had time-bandwidth product of 8 and duration of 1 ms. The pair of scans used +/-4 kHz off-resonant Fermi pulses between excitation and readout. The BS scans took 2 min 40 s in total and covered a FOV of 22 x 22 x 0.99 cm^3 with matrix size 200 x 50 x 9.

  • File: P,jf06Sep2019,mwf.7 The small-tip fast recovery (STFR) scans were acquired using a 3D acquisition. The first two and last two scans were pairs of spoiled gradient-recalled echo (SPGR) scans with echo time difference of 2.3 ms. (In the related paper, only the first set was used, i.e., only 11 of the 13 scans were used.) The remaining scans used scan parameters that were optimized to minimize the Cramer-Rao Lower Bound (CRLB) of estimates of myelin water fraction (MWF). The RF pulses had time-bandwidth product of 8 and duration of 1 ms. Each pair of SPGR scans took 58 s and the nine STFR scans took 3 min 36 s for a total scan time of 5 min 32 s (4 min 34 s if one pair of SPGR scans is ignored). The scans covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9.

  • File: meseslice5.mat Contains the 32 echoes of the MESE image data for the middle slice of the imaging volume. Saved using Mathworks MATLAB R2019a.

  • File: b1slice5.mat Contains the transmit field inhomogeneity map for the middle slice of the imaging volume.

  • File: recon.jld Key "img" contains the 11 STFR images for the middle slice of the imaging volume. Key "b0map" contains a field map estimated from the two SPGR scans. Key "mask" contains a mask of the voxels for which to estimate MWF. Key "T1img" contains a T1-weighted image for anatomical reference.

  • File: headmask.mat Contains a mask for visualizing just the brain (ignores the skull) for the middle slice of the imaging volume.

  • File: rois.mat Contains masks for various regions of interest (ROIs), used for computing statistics. Keys "mtopleft", "mtopright", "mbottomleft", and "mbottomright" refer to the corresponding locations on the anatomical reference image (see related paper). Key "mic" refers to the internal capsules, and key "mgm" refers to a gray matter ROI.

  • The raw data files (P-files) can be read into the Julia programming language using the Julia version of the Michigan Image Reconstruction Toolbox ( https://github.com/JeffFessler/MIRT.jl) or into MATLAB using TOPPE ( https://github.com/toppeMRI/toppe). The reconstructed slices used in the related paper are provided for convenience, and are stored in .mat files that can be loaded into Julia (using the package MAT.jl) or MATLAB, and a .jld file that can be loaded into Julia (using the package JLD.jl). The Julia code for processing the data to create MWF maps is hosted publicly on GitHub at  https://github.com/StevenWhitaker/STFR-MWF.

  • Files: toppe-master.zip and MIRT.jl-master.zip are archived versions of the TOPPE and Michigan Image Reconstruction Toolbox code sets from GitHub as of 2/28/2020.
Creator
Depositor
  • stwhit@umich.edu
Contact information
Discipline
Funding agency
  • National Institutes of Health (NIH)
Keyword
Citations to related material
  • Whitaker, S. T., Nataraj, G., Nielsen, J.-F., & Fessler, J. A. (2020). Myelin water fraction estimation using small-tip fast recovery MRI. Magnetic Resonance in Medicine, 84(4), 1977–1990. https://doi.org/10.1002/mrm.28259
Resource type
Last modified
  • 11/18/2022
Published
  • 02/26/2020
Language
DOI
  • https://doi.org/10.7302/nw6e-1d66
License
To Cite this Work:
Whitaker, S. T., Nataraj, G., Nielsen, J., Fessler, J. A. (2020). Data for "Myelin Water Fraction Estimation Using Small-Tip Fast Recovery MRI" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/nw6e-1d66

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Files (Count: 11; Size: 12.2 GB)

Thumbnailthumbnail-column Title Original Upload Last Modified File Size Access Actions
README.txt 2020-02-26 2020-02-28 1.34 KB Embargo
P_jf06Sep2019_mese.7 2020-03-03 2020-03-03 8.34 GB Embargo
P_jf06Sep2019_b1.7 2020-02-27 2020-02-27 146 MB Embargo
P_jf06Sep2019_mwf.7 2020-03-03 2020-03-03 3.65 GB Embargo
meseslice5.mat 2020-02-27 2020-02-27 36.7 MB Embargo
b1slice5.mat 2020-02-27 2020-02-27 527 KB Embargo
recon.jld 2020-02-03 2020-02-03 3.98 MB Embargo
headmask.mat 2020-02-27 2020-02-27 5.32 KB Embargo
rois.mat 2020-02-27 2020-02-27 20.8 KB Embargo
toppe-master.zip 2020-02-28 2020-02-28 6.46 MB Embargo
MIRT.jl-master.zip 2020-02-28 2020-02-28 144 KB Embargo

Myelin Water Fraction Estimation Using Small-Tip Fast Recovery MRI

Steven T. Whitaker, Gopal Nataraj, Jon-Fredrik Nielsen, Jeffrey A. Fessler

# Overview
In this work, we optimized the scan parameters for a set of small-tip fast
recovery (STFR) MRI scans for estimating myelin water fraction (MWF).
The scans were optimized to minimize the Cramer-Rao Lower Bound (CRLB)
(or maximize the precision) of estimates of MWF. The optimized scans
were used to acquire an in vivo dataset, from which we estimated MWF using
parameter estimation via regression with kernels (PERK) using a
three-compartment tissue model with exchange. The STFR-based MWF estimates
were compared to multi-echo spin echo (MESE) MWF estimates obtained using
non-negative least squares (NNLS). The STFR-based MWF estimates were similar
to the MESE-based estimates, but were much less noisy.

# About This Repository
This repository contains the raw scan data from the in vivo scans. It also
contains the reconstructed images for the single slice we analyzed in the
paper, as well as data files for separately estimated parameters and binary
masks. See the detailed description for links to code repositories that can be
used to work with the data. In particular, look at the README for
https://github.com/StevenWhitaker/STFR-MWF for step-by-step instructions for
how to reproduce the results in the paper.

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