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@@ -1,12 +1,15 @@
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# C3a_PT_8wks_T2w_DTI
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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.
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## Files:
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-* **File structure:** Study > proc/raw_data > Time point> Group > Subject ID.
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+### **inputs**
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+* **MRI_raw_data:** - contains all raw data in Bruker 2dseq format and the original Bruker folder structure
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+* Study > proc/raw_data > Time point> Group > Subject ID.
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The physio folder contains the physiological monitoring raw data (breathing, anaesthesia gas, temperature, etc.).
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* Time point (Baseline, post stroke days 7-56)
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* Group (Treatment_C3a/PBS)
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-* **MRI_raw_data:** - contains all raw data in Bruker 2dseq format and the original Bruker folder structure
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* **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), structural connectivity analysis.
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+
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+### **code**
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* **AIDAmri_DTIdata_extract** - contains adapted Python scripts from the [AIDAmri_v1.1](https://github.com/maswendt/AIDAmri) pipeline to extract diffusion measures (FA, RD, MD, AD) from the DTI data.
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## Authors:
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