DoD for 11/26 - Githubissues

wrgr commented 8 years ago

[x] pipeline code that generates multiscale graphs
[x] clear instructions
[x] R reliability code (script)
[x] timing of running pipeline somewhere
[x] reliability matrices & adjacency matrices for 2 atlases for 2 datasets
[ ] A qualitative assessment detailing pipeline performance (length ~1 paragraph containing observations and/or recommendations about how to process 10^4 subjects)

wrgr commented 8 years ago

I added an m2g section at the bottom of tutorials. Let's populate that. I did a first draft.

Things that need fixing:

[x] Scrub of the tutorials.md info
[x] On the sidebar, cloud services should be services. Clusters are not clouds.
[x] The validation page is a good start, but we should explicitly have a page that says against a tagged version of m2g, we ran the following 3 datasets and 3 atlases, and this is what happened. There should be a paragraph for each dataset and atlases, with reliability scores and pictures highlighted, along with a direct link (see below)
[x] In the link you give to the raw data, looks like there are random desikan results in the top level.
[x] Why are we providing graphs on data/public if we have MROCP? This is confusing. If there's a reason, let's explain it. Are these "nightly runs"? That's ok.
[x] Provide a brief explanation of the raw data suitable for someone just arriving. What is there? How can they read the files? How can they learn more?

[x] The validation page should have a preamble explaining how we validate the pipeline and an explicit link to the reliability function with instructions (linked to the sphinx doc for that function)
[x] Tag the current release
[x] Explicitly state that we validated capability by running a large data set (SWU) and two TRT datasets. For each of the three data sets, provide:
- [x] Runtime
- [x] Validation (the actual score and relevant debug info like how many subjects were available to compare) - for the TRT
- [x] Location of graphs and more detailed results
- [x] A summary saying whether that dataset did well or poorly and why (this is obvious to us, but not to new readers)
[x] Add a paragraph or two summarizing expected behavior of pipeline (where is the bulk of the work? Fiber tracking and graph gen...How long per subject (6 hours)...a link to the data format/spec that people need to meet. Any known issues that a new user might face and how to fix, like setting up paths, getting an account, etc.
[x] An overall statement stating that this concludes our validation of m2g.

[x] You should give people a clear pointer to where to go in tutorials
[x] If ec2 still doesn't work when we sell this off, let's make a git issue stating such and be clear
[x] Where does someone get a bc1 account?
[x] Where does someone get LONI v6.0.1? It's not available from LONI
[x] I would suggest sample scp and chmod commands
[x] where does one find the m2g workflow? In the sidebar? On disk?
[x] which variables should people change? Is there a link where they can know what each one does?
[x] link to the output format spec and description for each output file

[x] General links to ec2, and to AWS help. Nothing too involved.
[x] What choices should someone make for computer size, storage, and security?
[x] Link to the AMI page with details (or add the relevant ones here and link to building an AMI)
[x] Add recommendation for screenshare on a mac - built in and easy
[x] Link to mounting a harddrive - I have a good way to do this if you don't
[x] Example of moving data
[x] Again, explain or link to the variables
[x] Again, explain or link to the data derivatives people will find after the pipeline runs.

We can do a sample walkthrough of this tomorrow in our meeting; ideally doing everything except the data that are still running.

wrgr commented 8 years ago

[x] Clarify that client version is compatible, not 6.0.1
[x] Clarify which version is needed. If it's not on LONI's website currently, adjust documentation to say so.
[x] Add pointer to sample dataset e.g. kki42 and explain that people can skip the transfer step
[x] Remove link to LONI website if they don't have older versions.
[x] add the word 'client' to computer near the top of bc1 instructions

gkiar commented 8 years ago

(ignore the close, was a misclick) :)

wrgr commented 8 years ago

Closed per pull request and completion of this and other related git issues. Job well done team.

neurodata / ndgrutedb