AIDAconnect

Atlas-based Imaging Data Analysis Pipeline (AIDA) for structural and functional MRI of the mouse brain

AIDAconnect is a comprehensive collection of MATLAB scripts for mouse brain MRI data analysis and connectivity analysis using graph theory. A detailed guide for the installation process and the usage of AIDAconnect is written in the manual.

Information about Version 1.0
Information about Version 1.1
Information about Version 2.0

INSTALLATION

=> MANUAL

EXAMPLE FILES

Download here (you probably have to clone the dataset from the gin repo. The files are annexed files, also use the raw_data folder as the test data).
Mouse MRI data, acquired with Bruker 9.4T - cryo coil setup: adult C57BL7/6 mouse, T2-weighted (anatomical scan), DTI (structural connectivity scan), rs-fMRI (functional connectivity scan).

The given tools from AIDAconnect are provided for anatomical T2-weighted MRI (T2w), diffusion tensor imaging (DTI) and resting-state functional MRI (rs-fMRI) data and are currently designed for creating weighted-undirected graphs only.

CONTACT

Leon Scharwächter and Markus Aswendt (contact: [email protected])

CONTACT

Chat with us

or

join our Open Office Hour - each Thursday 4:30 pm (UTC+2)

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LICENSE GNU General Public License v3.0

REFERENCES

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  • Pallast, N., et al. "Processing pipeline for Atlas-based Imaging Data Analysis (AIDA) of structural and functional mouse brain MRI" Frontiers in Neuroinformatics, 2019
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• Allen Mouse Brain Reference Atlas
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• FSL
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  • S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004
  • M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012
• DSIstudio
  • Yeh, Fang-Cheng, et al. Deterministic diffusion fiber tracking improved by quantitative anisotropy. (2013): e80713. PLoS ONE 8(11)