Ive got some MRI volumetric data I am trying to do some image analysis on. Ive got an issue right now where the first and last 2-4 slices of the data are cropped circularly. Here is an example of what the slice should look like. The black background and the MRI image.
Here are examples of how the slice is getting corrupted at the start and end of the block.
How would you detect for this circular cropping effect. Ive tried looking at the average intensity of the voxels in each slice but theres no generally identifiable pattern in the data which allows me to identify the corrupt slices.