Document pipeline

[jcohenadad]

After working on #1 I noticed that the running of the pipeline should be documented, including how to do the QC. Few things I've noted:

• Detail how to launch the pipeline
• Detail how to run the QC, what to watch out for
• QC: If the vertebral labeling failed, instruct to manually create labels 1, 2 and 3 and put them under the derivatives with the appropriate file name

To be continued...

[jqmcginnis]

Thanks @jcohenadad for addressing this in an issue.

Before writing a more elaborate Readme.md, and detailling the instructions to run the pipelines,
I was thinking about adding the current status quo of our bidsification and stitching scripts to the repository #4.

Not sure if this is the right way to do it because it will make the repo a bit more bloated as well, but then again I think it would be nice to have everything documented and easily accessible for everyone involved.

#4 currently implements the following structure, do you feel it is a good representation of the different functionalities or should we organize it differently.

├── LICENSE
├── README.md
└── source
    ├── bids_tools
    │   ├── bids_templates.py
    │   ├── create_bids_db.py
    │   └── parse_database.py
    ├── pipeline
    │   └── brain
    │       └── process_brain_data_t1.sh
    └── stitching
        └── stitching.py

Moreover, who will be mainly working on this repository from your side, who should I tag in the PRs?

[sandrinebedard]

@jqmcginnis Here is an example of a README that is similar to what you need: https://github.com/sct-pipeline/ukbiobank-spinalcord-csa#readme

[jcohenadad]

Moreover, who will be mainly working on this repository from your side, who should I tag in the PRs?

You can tag me and hopefully @sandrinebedard @naga-karthik @kiristern will also chip in

[jqmcginnis]

@jcohenadad @sandrinebedard thank you for your comments and for providing the example. I'll work on this and keep you updated on it!