Meeting 09 06 2018

The document for the following day can be found HERE

Current Itinerary

1. Make a copy of the demo repository in the _dev repository.
2. Write up your plan of work on the wiki in the _dev repository.
3. Adapt the configuration so that it works with the official data bucket.
   • Use Yaml files to encode the file trees for simplicity.
4. Run Each script on each old brain using AWS/EC2 and compare the result to the old result.
5. Document how to run the script.

Some things to remember (for Alex). The code will change in the near future!! Yuncong plans to merge this with the repo under review himself and will undoubtedly make tweaks to parts of the code. I will likely need to override any changes I make now once he finished doing that. Additionally, keep an eye on all his documentation files and port over any changes AFTER he merges with the main repo.

Update, the workstation is out of space to run any sort of demo... Yuncong has asked me not to remove any files in his directory so I do not have enough space to work. I'll have to delete some progress on the old brain and use an external hard drive..

General Information

5 major steps in the pipeline.

• Preprocessing
• Detection
• Registration
• Visualization
• Building Atlas

Available demos can be found at the DemoComplete.md document. Just for clarification demos are 90% of what the scripts will be, just hard coded to refer to specific examples.

There are currently 3:

• The preprocessing demo [incomplete]
• The computing patch features demo
• The generating probability volumes demo

Plus the 1 submitted to the journal, 4 total:

• The registration demo

I need to find exactly where in the pipeline the last two begin and end at.

Plan of Work

Run through the patch feature demo. Annotate it, make a write up in here.

Run through the generate probability volume demo. Annotate it, make a write up in here.