[1.2]: http://i.imgur.com/wWzX9uB.png [1]: http://www.twitter.com/AswendtMarkus

AIDAmri

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

[Manual v1.1](https://github.com/maswendt/AIDA/blob/master/manual.pdf)

[Information about Version 1.1](https://github.com/maswendt/AIDAmri/releases/tag/v1.1)
[Information about Version 1.0](https://github.com/maswendt/AIDAmri/releases/tag/v1.0)

ARA CREATOR

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

EXAMPLE FILES

](https://doid.gin.g-node.org/70e11fe472242e2d4f96c53ac9b0a556/) 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

](https://neurologie.uk-koeln.de/forschung/ag-neuroimaging-neuroengineering/) Niklas Pallast and Markus Aswendt (contact: markus.aswendt@uk-koeln.de)[![alt text][1.2]][1] Need help? Chat with us and find answers to FAQs in the AIDA_Tools Gitter rooms: [![Gitter](https://badges.gitter.im/AIDA_tools/community.svg)](https://gitter.im/AIDA_tools/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) ___ 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](https://www.frontiersin.org/articles/10.3389/fninf.2019.00042/full) + Brain Connectivity Toolbox + [M. Rubinov and O. Sporns (2010). Complex Network Measures of Brain Connectivity: Uses and Interpretations. NeuroImage 52 (3), 1059–69.](https://www.sciencedirect.com/science/article/abs/pii/S105381190901074X) + 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.](https://pubmed.ncbi.nlm.nih.gov/32386544/) + Niftyreg + [Ourselin, et al. (2001). Reconstructing a 3D structure from serial histological sections. Image and Vision Computing, 19(1-2), 25–31.](https://www.sciencedirect.com/science/article/pii/S0262885600000524) + [Modat, et al. (2014). Global image registration using a symmetric block- matching approach. Journal of Medical Imaging, 1(2), 024003–024003.](https://www.ncbi.nlm.nih.gov/pubmed/26158035) + [Rueckert, et al.. (1999). Nonrigid registration using free-form deformations: Application to breast MR images. IEEE Transactions on Medical Imaging, 18(8), 712–721.](https://ieeexplore.ieee.org/document/796284) + [Modat, et al. (2010). Fast free-form deformation using graphics processing units. Computer Methods And Programs In Biomedicine,98(3), 278–284.](https://www.ncbi.nlm.nih.gov/pubmed/19818524) + 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](https://www.ncbi.nlm.nih.gov/pubmed/19059349) + [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](https://www.sciencedirect.com/science/article/pii/S1053811904003933?via%3Dihub) + [M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012](https://www.sciencedirect.com/science/article/pii/S1053811911010603?via%3Dihub) + DSIstudio + [Yeh, Fang-Cheng, et al. Deterministic diffusion fiber tracking improved by quantitative anisotropy. (2013): e80713. PLoS ONE 8(11)](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080713)