Week 6

This week I worked on analyzing the MR images of rat tendon we were able to take last week. A unique challenge with these images was segmentation using ITK-SNAP. Whereas the scans of horse and pig tendon had taken UTE slices in the sagittal direction, we had to take slices in the axial direction for the rats, as this was the only direction in which multiple slices of the tendon could be taken in such a small animal. This made the cross sectional area of the tendon much smaller and difficult to differentiate in the image. In order to improve segmentation accuracy, I attempted to use a different pulse sequence with higher resolution to guide segmentation of the lower resolution UTE images. This required me to use an algorithm to "reslice" the higher resolution images to match the UTE images. Next week I hope to use these images to segment and finally quantify T2* values in the rat tendon.

In addition, on Monday I had the opportunity to see multiple knee surgeries including a total knee replacement and a patellar realignment. These were particularly interesting to me given that much of my research so far has concerned the knee and patellar tendon.  

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