# WT_Thrombin_4wks_T2w_DTI
Longitudinal MRI including T2-weighted (T2w) and diffusion tensor imaging (DTI) WT mice with cortical stroke lesions induced by injection of thrombin and survival time of 4 weeks (4 wks).

## Files:
* **File structure:** Study > MRI_proc/raw_data > Group > Time point > Subject ID. 
    * Time point (Baseline, post stroke days 1, 14, and 28)
    * Group (Stroke and Sham)
* **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:
Frederique Wieters and Markus Aswendt