WT_PT_4wks_T2w_DTI/README.md

WT_PT_4wks_T2w_DTI

Longitudinal (4 wks) T2-weighted MRI and Diffusion Tensor Imaging (DTI) of WT mice with cortical stroke (photothrombosis model)

Files:

• File structure: Study > proc/raw_data > Time point> Group > Subject ID.
  • Time point (Baseline, post stroke days 1-28)
  • Group (Stroke/Sham)
• Groups:
  • Stroke: SP_T1_1_1, SP_T1_1_2, SP_T1_1_3, SP_T1_2_1, SP_T1_4_1, SP_T1_4_2, SP_T1_4_3, SP_T1_6_1, SP_T1_7_1, SP_T1_11_1, SP_T1_11_2, SP_T1_13_1, SP_T1_23_1, SP_T1_23_2
  • Sham: SP_T1_2_2, SP_T1_2_3, SP_T1_11_3, SP_T1_11_4, SP_T1_12_2, SP_T1_13_4, SP_T1_22_1, SP_T1_22_3
• raw_data: - contains all raw data in Bruker 2dseq format and the original Bruker folder structure
• 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 (in the folder MRI_proc_data/_Evaluation generated with AIDAconnect_v1.0).

Authors:

Niklas Pallast, Marieke Nill, Frederique Wieters, Dirk Wiedermann, and Markus Aswendt.