# C3a_PT_8wks_T2w_rsfMRI
Longitudinal MRI including T2-weighted (T2w) and resting-state functional MRI (rs-fMRI) of WT mice with cortical stroke lesions induced by photothrombosis (PT) monitored for 8 weeks (8 wks). The mice received either intranasal C3a (complement factor) or PBS treatment from day 7 to day 28 post stroke.

## Files:
* **File structure:** Study > proc/raw_data > Time point> Group > Subject ID. 
The physio folder contains the physiological monitoring raw data (breathing, anaesthesia gas, temperature, etc.). 
    * Time point (Baseline, post stroke days 7-56)
    * Group (Treatment_C3a/PBS)
* **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_v1.1](https://github.com/maswendt/AIDAmri) pipeline. Processing steps: define stroke masks, convert Bruker to NIfTI-1 data format, image re-orientation, bias-field correction, brain extraction, region-of-interest segmentation, registration with the [Allen Mouse Brain Atlas](https://www.nature.com/articles/nature05453)[ (CCFv3)](http://help.brain-map.org/display/mousebrain/Documentation), functional connectivity analysis (in the folder MRI_proc_data/_Evaluation generated with [AIDAconnect_v1.0](https://github.com/maswendt/AIDAconnect)). 

## Authors:
Markus Aswendt, Olivia Käsgen, Frederique Wieters, Michael Diedenhofen, Dirk Wiedermann