DOI: 10.5281/zenodo.6406741
title: Time-encoded pseudo-continuous arterial spin labeling: increasing SNR in ASL dynamic angiography

description: This repository contains the raw K-space data and all MATLAB (The MathWorks, Natick, MA) code used for reconstruction, simulations, data analysis, and figure generation used in the article titled "Time-encoded pseudo-continuous arterial spin labeling: increasing SNR in ASL dynamic angiography". ## Referencing If you use any of the data or the code provided here, please cite: 1. Woods JG, Schauman SS, Chiew M, Chappell MA, Okell TW. Time-encoded pseudo-continuous arterial spin labeling: increasing SNR in ASL angiography. ArXiv. 2022. https://doi.org/10.48550/arXiv.2204.00664<br> 2. This Zenodo repository: Joseph G. Woods, S. Sophie Schauman, Mark Chiew, Michael A. Chappell & Thomas W. Okell. (2022). Time-encoded pseudo-continuous arterial spin labeling: increasing SNR in ASL dynamic angiography [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6406741 Note: this work was submitted for peer-review to Magnetic Resonance in Medicine in April 2022. If accepted, please reference the peer-reviewed version of the manuscript. If you use the reconstruction code provided here, please also cite: 1. Fessler JA, Sutton BP. Nonuniform fast fourier transforms using min-max interpolation. IEEE Transactions on Signal Processing. 2003;51(2):560-574. doi:10.1109/TSP.2002.807005<br> 2. Fessler JA. Michigan Image Reconstruction Toolbox. https://web.eecs.umich.edu/~fessler/code/. Accessed February 26, 2018.<br> 3. Schauman SS. Accelerated_TEASL. https://github.com/SophieSchau/Accelerated_TEASL. Accessed October 19, 2020.<br> 4. Chiew M. MR Linear Encoding Operators. https://users.fmrib.ox.ac.uk/~mchiew/Tools.html. Accessed March 30, 2020. ## Notes for use: All data processing is performed in MATLAB (tested with 2021a and 2021b on macOS 10.14 (Mojave) and 12 (Monterey)) The "code/" and "data/" folders should be placed within the same folder. The necessary file paths within each script in "code/" will be set up automatically. **Note**: the file paths use "/", so would need to be manually changed for use on Windows, which uses "\" in file paths. - For optimising the constant flip angles for the sequential and time-encoded protocols, **run Optimise_CFAs.m**.<br> - All code provided - For performing full reconstruction of in vivo K-space data, **run reconalldata.m**.<br> - All code provided<br> - Uses:<br> 1. Jeff Fessler's MIRT: http://web.eecs.umich.edu/~fessler/irt/fessler.tgz<br> 2. Mark Chiew's: xfm_NUFFT.m, etc: https://users.fmrib.ox.ac.uk/~mchiew/Tools.html<br> 3. Sophie Schauman's Accelerated_TEASL: https://github.com/SophieSchau/Accelerated_TEASL - For plotting in-vivo data, **run figures_invivo.m**.<br> - FSL's read_avw to read in NIFTIs (but can replace this with MATLAB's in-built niftiread instead).<br> - (Install FSL from here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)<br> - All other code provided - For performing simulation and plotting results, **run figures_simulation.m**.<br> - All code provided - Location of specific Figure generation code:<br> - Figure 1: no code - manually made.<br> - Figure 2: figures_invivo.m<br> - Figure 3: figures_simulation.m<br> - Figure 4: figures_invivo.m<br> - Figure 5: figures_invivo.m<br> - Figure 6: figures_invivo.m<br> - Figure 7: figures_invivo.m<br> - Figure 8: figures_invivo.m<br> - Figure 9A,C,D,E: figures_invivo.m<br> - Figure 9B: figures_simulation.m<br> - Supporting Information Figure S1: figures_simulation.m<br> - Supporting Information Figure S2: figures_invivo.m<br> - Supporting Information Figure S3: figures_invivo.m<br> - Supporting Information Figure S4: figures_invivo.m<br> - Supporting Information Figure S5: figures_invivo.m<br> - Supporting Information Figure S6: figures_invivo.m
description: TWO and JGW were supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (220204/Z/20/Z). JGW, SSS, and MAC were supported by funding from the EPSRC (EP/L016052/1 and EP/P012361/1). The Wellcome Centre for Integrative Neuroimaging is supported by core funding from the Wellcome Trust (203139/Z/16/Z).