toekneesunshine
commented
7 years ago | status | deliverable | notes |
|---|---|---|
| 👍 | For Thursday: Update ndreg docker image, update registration part of Clarity pipeline. Results | @toekneesunshine @jonl1096 |
| 👍 | For class meeting (April 3): Diagram (following Science in the Cloud paper example) showing how our pipeline will use Batch/AWS. UPDATE after meeting Greg: make diagram much more detailed for individual function calls/throughput. Fix issues with MemoryError in registration step. We went ahead and fixed the MemoryError, (solved by saving a local copy of the brain and loading via SITK directly). We then bumped into an issue with our existing registration script, which was solved by the addition of "inImg.SetSpacing(np.array(inImg.GetSpacing())*1000)" after a bunch of trial-error. The script runs smoothly now until LDDMM, at which it just pauses - after copying and pasting Kwame's existing code, we realize his code also freezes at the LDDMM step. We're not sure what's going on here - will talk to Greg/Kwame about this (it's not memory, since checking "free -m" during the LDDMM step shows there's around 10 GB of available memory, and it's probably not ndreg/ndio, since we cloned and ran the latest version from the Github repos). | @toekneesunshine @jonl1096 |
| 👍 | For Thursday: Show Greg the Ailey brain with the proper hyperparameter set | @alee156 @lukezhu1 |
| 👍 | For class meeting (April 3): Run a small hyperparameter sweep on the optimal hyperparameter s275 2 3 4 5 6 | @alee156 @lukezhu1 |