Graphic User Interface (GUI) for the Braindancer Dynamic phantom. We acknowledge support for this package from the Center for Biotechnology, an Empire State Development Division of Science Technology and Innovation (NYSTAR) Center for Advanced Technology, and ALA Scientific Inc.
Installation Instructions
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Install Julia from https://julialang.org/downloads/
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Launch Julia
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Install Pluto by going into the package manager (type "]")
Pkg> add Pluto
type "delete" to get back to the Julia prompt
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Launch Pluto by
julia> import Pluto
julia> Pluto.run()
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Go to your default web browser to see the Pluto notebook
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Prepare analysis folder that should contain
epi.nii - phantom nifti file
acq_times.csv - acquisition times of the phantom scan
log.csv - log file from phantom scan
time_series.jl - fresh copy from BDGui.jl/local denoiser.jl - fresh copy from BDGui.jl/local noisenet.jl - fresh copy from BDGui.jl/local
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Launch time_series.jl in Pluto notebook
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Lerform time-series analysis and save results at the end
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Launch denoiser.jl notebook to train a neural network on the scanner noise and save the neural net parameters
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Launch noisenet.jl to clean human brain fMRIs using a mask