Mouse QC Manual (Structural)
This manual was created by Mila for use on Chloe's project. The scans were Manganese enhanced and acquired with an old (PV5) sequence- so your scan quality may look different from this! I'm definitely not an expert so suggestions are welcome!
Includes all of Colleen’s scans as well as the first batch of Chloe’s scans Location: data/chamal/projects/chloe/chloe-2017/combined_data/data/scan/E2_preprocessed/xxx
*replace xxx with either Chloe, Mila or Interrater
Scale from 0 to 1 with 4 levels ie: 0, 0.5, 0.75, 1
0: Unusable scans. Even if we are really desperate for more scans, we can’t include these.
0.5: Bad scans that we should only include if we are desperate.
0.75: Okay scans that are usable but still have minor problems.
1: Good scans, might have really minor imperfections.
- major hydrocephaly that takes up most of the brain is a 0
Ventricles that are bigger than normal are still acceptable and in that case the score should be based on the
presence of other artefacts
- motion can show up as ringing (concentric ripples in the scan), crumpling (as though the scan is a paper that was crumpled) or blurriness
- If the motion is localized to a few slices and is not in a region of importance then the scan may be given a score of 1
- If the motion is minor and localized to a few slices but is in a region of importance (ie hippocampus) then the score is 0.75
- If the motion is more widespread then the score is 0.5
- If the motion is really obvious, with large ringing or crumpling, or if it obscures the structure of an important region then the score is 0
- often shows up as a black region that obscures an area of the brain
- Outer edges of the brain are the most susceptible
- If there is only minor signal drop-off (dark gray region) in areas that are not important then the score is 1
- If there is a minor artefact in the cerebellum or cerebrum then the score is 0.75
- If there is a major artefact in the cerebellum then the score is 0.5
- If there is a major artefact in the cerebrum then the score is 0
- Black dots and lines: occasionally there are brains with black dots and lines throughout the brain. It is possible that these occur because the mouse is so still during the scan that we can see the blood vessels. Or they could indicate a mouse with vascular problems. Either way, they are small and hence won’t affect the registration much so these scans should receive a score of 1.
- Multiple light shadows: Sometimes there are scans with multiple shadows. These aren’t dark like artefacts and they don’t seem to be due to motion. These scans should receive a score of 0.75.
Here are examples of perfect scans for comparison.
