ACID - an open-source, bids compatible software for brain and spinal cord dMRI: preprocessing, DTI/DKI, biophysical modelling
Björn Fricke1, Gergely David1,2, Jan Malte Oeschger1, Patrick Freund2, Lars Ruthotto3, Karsten Tabelow4, and Siawoosh Mohammadi1,5
1Department of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, 2Balgrist University Hospital, University of Zurich, Zürich, Switzerland, 3Department of Mathematics, Emory University, Atlanta, GA, United States, 4Weierstrass Institute for Applied Analysis and Stochastics, Berlin, Germany, 5Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
The ACID-Toolbox is an open-source toolbox for brain and spinal-cord diffusion data. It enables the preprocessing and creation of DTI/DKI, and biophysical parameter-maps in one single pipeline. Preprocessing covers correction for eddy-currents and motion-artefacts, susceptibility distortions and adaptive denoising. For model-fitting, the toolbox offers several algorithms to estimate the diffusion or the kurtosis tensors as well as estimation of biophysical parameters. ACID is integrated into the batch system of the Statistical-Parametric-Mapping (SPM12) software for the analysis of neuroimaging data and thus benefits from associated spatial and statistical processing modules. Additionally, ACID is BIDS compatible but also applicable to non-BIDS-conform data.
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