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@@ -1,3 +1,12 @@
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-# WT_Thrombin_4wks
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+# WT_Thrombin_4wks_T2w_DTI
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+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).
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-Longitudinal MRI of thromboembolic stroke model in C57BL/6 mice.
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+## Files:
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+* **File structure:** Study > MRI_proc/raw_data > Group > Time point > Subject ID.
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+ * Time point (Baseline, post stroke days 1, 14, and 28)
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+ * Group (Stroke and Sham)
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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), functional connectivity analysis (in the folder MRI_proc_data/_Evaluation generated with [AIDAconnect_v1.0](https://github.com/maswendt/AIDAconnect)).
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+
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+## Authors:
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+Frederique Wieters and Markus Aswendt
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