Skip to content

Improve explanation of datalist format #2015

@DanielNobbe

Description

@DanielNobbe

Is your feature request related to a problem? Please describe.
The starting point for running Auto3DSeg on custom data is to use the tutorials here, but the explanation on building custom Decathlon-style datalist files is lacking.

Describe the solution you'd like
There should be a clear explanation on how to build a custom datalist, right in one of the autorunner notebooks or in the README.
I'm happy to add this.

Describe alternatives you've considered

  1. An extra notebook could be added that has instructions on running the autorunner on a custom dataset, including steps to create the datalist. -- This will be highly dataset-specific, though, and with information on the datalist format available, most users should be able to write a simple script to create a datalist.
  2. The run_with_minimal_input file shows a datalist, but does not completely describe it.

Additional context
See also my issue in MONAI.

There is a notebook titled msd_datalist_generator.ipynb. This notebook can generate a datalist file from an existing Decathlon Datalist. This works, but offers little explanation and depends on the directory structure of the existing Decathlon dataset, which already comes with a datalist.json file. The code there is also quite trivial to implement given a good explanation of the format.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions