Time-encoded pseudo-continuous arterial spin labeling: increasing SNR in ASL dynamic angiography

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 dynamic angiography. Magnetic Resonance in Medicine. 2023; doi:10.1002/mrm.29491
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.6791097

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
2. Fessler JA. Michigan Image Reconstruction Toolbox. https://web.eecs.umich.edu/~fessler/code/. Accessed February 26, 2018.
3. Schauman SS. Accelerated_TEASL. https://github.com/SophieSchau/Accelerated_TEASL. Accessed October 19, 2020.
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 performing full reconstruction of in vivo K-space data, **run reconalldata.m**.
    - All code provided
    - Uses:
        1. Jeff Fessler's MIRT: http://web.eecs.umich.edu/~fessler/irt/fessler.tgz
        2. Mark Chiew's: xfm_NUFFT.m, etc: https://users.fmrib.ox.ac.uk/~mchiew/Tools.html
        3. Sophie Schauman's Accelerated_TEASL: https://github.com/SophieSchau/Accelerated_TEASL

- For plotting in-vivo data, **run figures_invivo.m**.
    - FSL's read_avw to read in NIFTIs (but can replace this with MATLAB's in-built niftiread instead).
        - (Install FSL from here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)
    - All other code provided

- For performing simulation and plotting results, **run figures_simulation.m**.
    - All code provided

- Location of specific Figure generation code:
    - Figure 1: no code - manually made.
    - Figure 2: figures_invivo.m
    - Figure 3: figures_simulation.m
    - Figure 4: figures_invivo.m
    - Figure 5: figures_invivo.m
    - Figure 6: figures_invivo.m
    - Figure 7: figures_invivo.m
    - Figure 8: figures_invivo.m
    - Figure 9: figures_simulation.m
    - Figure 10: figures_invivo.m
    - Supporting Information Figure S1: figures_simulation.m
    - Supporting Information Figure S2: figures_invivo.m
    - Supporting Information Figure S3: figures_invivo.m
    - Supporting Information Figure S4: figures_invivo.m
    - Supporting Information Figure S5: figures_invivo.m
    - Supporting Information Figure S6: figures_invivo.m
    - Supporting Information Figure S7: figures_invivo.m
    - Supporting Information Figure S8: figures_invivo.m
    - Supporting Information Figure S9: figures_invivo.m
    - Supporting Information Figure S10: figures_simulation.m