WT_Thrombin_4wks_T2w_DTI/README.md

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 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), functional connectivity analysis (in the folder MRI_proc_data/_Evaluation generated with AIDAconnect_v1.0).

Authors:

Frederique Wieters and Markus Aswendt