C3a_PT_8wks_T2w_DTI/README.md

C3a_PT_8wks_T2w_DTI

Longitudinal MRI including T2-weighted (T2w) and Diffusion Tensor Imaging (DTI) 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 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 (CCFv3), structural connectivity analysis.
• AIDAmri_DTIdata_extract - contains adapted Python scripts from the AIDAmri_v1.1 pipeline to extract diffusion measures (FA, RD, MD, AD) from the DTI data.

Authors:

Markus Aswendt, Olivia Käsgen, Frederique Wieters, Michael Diedenhofen, Dirk Wiedermann