# 2021_Aswendt_GFAP_PT_4wks

Longitudinal MRI (T2-weighted and rs-fMRI) of GFAP-/-/Vim-/- and WT mice; 6 time points over 4 weeks post photothrombotic stroke.

## Files:
* MRI_raw_data - contains all raw data in Bruker 2dseq format and the original Bruker folder structure
* MRI_proc_data - contains all data processed with the [AIDAmri](https://www.frontiersin.org/articles/10.3389/fninf.2019.00042/full) pipeline. Processing steps: 1) convert Bruker to NIfTI-1 data format, 2) image re-orientation, bias-field correction, brain extraction, 3) region-of-interest segmentation (i.e. stroke masks), 4) registration with the [Allen Mouse Brain Atlas](https://www.nature.com/articles/nature05453)[ (CCFv3)](http://help.brain-map.org/display/mousebrain/Documentation), and 5) functional connectivity analysis using [AIDAconnect](https://github.com/aswendtlab/AIDAconnect). 

## Authors:
Markus Aswendt, Olivia Käsgen, Frederique Wieters, Felix Schmitt, Niklas Pallast

## Publication:

Aswendt et al. Prog Neurobiol 2022 https://doi.org/10.1016/j.pneurobio.2021.102199