2023_Blaschke_Stroke_tDCS_rsfMRI/scripts/AIDAmri-master_1.2/README.md

AIDAmri

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

Manual v1.1

Information about Version 1.1
Information about Version 1.0

ARA CREATOR

Matlab script to generate a custom version of the Allen Mouse Brain Atlas.

EXAMPLE FILES

Mouse MRI data, acquired with Bruker 9.4T - cryo coil setup: adult C57BL7/6 mouse, T2-weighted (anatomical scan), DTI (structural connectivty scan), rs-fMRI (functional connectivity scan).

CONTACT

Niklas Pallast and Markus Aswendt (contact: markus.aswendt@uk-koeln.de)

Need help? Chat with us and find answers to FAQs in the AIDA_Tools Gitter rooms:

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LICENSE GNU General Public License v3.0

REFERENCES

• AIDAmri
  • Pallast, N., et al. "Processing pipeline for Atlas-based Imaging Data Analysis (AIDA) of structural and functional mouse brain MRI" Frontiers in Neuroinformatics, 2019
• Brain Connectivity Toolbox
  • M. Rubinov and O. Sporns (2010). Complex Network Measures of Brain Connectivity: Uses and Interpretations. NeuroImage 52 (3), 1059–69.
• Allen Mouse Brain Reference Atlas
  • Wang et al. (2020). The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell 181 (4), 936-953.
• Niftyreg
  • Ourselin, et al. (2001). Reconstructing a 3D structure from serial histological sections. Image and Vision Computing, 19(1-2), 25–31.
  • Modat, et al. (2014). Global image registration using a symmetric block- matching approach. Journal of Medical Imaging, 1(2), 024003–024003.
  • Rueckert, et al.. (1999). Nonrigid registration using free-form deformations: Application to breast MR images. IEEE Transactions on Medical Imaging, 18(8), 712–721.
  • Modat, et al. (2010). Fast free-form deformation using graphics processing units. Computer Methods And Programs In Biomedicine,98(3), 278–284.
• FSL
  • M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
  • 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)