AIDAmri

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

Information latest Version 2.0

Manual v2.0

Link

Important note: read this before you install AIDAmri for the first time

We fully moved to the containerized version of AIDAmri via Docker. All information can be found in the manual above. Please report issues and bugs directly in the issue section of this repository or at gitter (Link below in the contact section).

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).

ARA CREATOR

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

VERSION HISTORY

Information about Version 1.2 (Docker stable release)
Information about Version 1.1.1 (Docker pre-release)
Information about Version 1.1 (Stable)
Information about Version 1.0

CONTACT

If you encounter problems, report directly in

or

join our Open Office Hour - each Thursday 3:00 pm (UTC+2)

For all other inquiries: Markus Aswendt (markus.aswendt@uk-koeln.de)

LICENSE/CITATION

GNU General Public License v3.0

If you use our software or modify parts of it and use it in other ways, please cite:

Pallast N, Diedenhofen M, Blaschke S, Wieters F, Wiedermann D, Hoehn M, Fink GR, Aswendt M. Processing Pipeline for Atlas-Based Imaging Data Analysis of Structural and Functional Mouse Brain MRI (AIDAmri). Front Neuroinform. 2019 Jun 4;13:42.doi: 10.3389/fninf.2019.00042.

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REFERENCES

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• Allen Mouse Brain Reference Atlas
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• Niftyreg
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• FSL
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• DSIstudio
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