Exporting Annotations

Overview

The RedBrick CLI allows you to easily export your Project's annotations within a local project directory.

Please note that the export function only fetches newly created annotations when run. It will not generate an annotation file for a Task if no annotation work has been completed and saved on said Task.

For example, if you upload 100 images to your Project, annotate 80 of them and initiate an export using the CLI, the CLI will export annotations for 80 Tasks.

If your team annotates 5 additional Tasks the next day and initiates an export, the CLI will only export annotations for the 5 newly annotated Tasks, bringing the total number of annotation files in your local directory to 85.

By default, all segmentation files are exported in NIfTI-1 format. Please see our Format Reference for more information on exported annotations and alternative formats (such as PNG or RT Struct).

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Export Folder Structure

RedBrick AI exports annotations in a JSON structure, accompanied by NIfTI-1 masks for segmentations. All data will be exported within a folder named after your project_id, with the following structure:

project_id/
├── segmentations
│   ├── study01
│   │   └── series1.nii
│   └── study02
│       ├── series1.nii
│       └── series2.nii
└── tasks.json

Segmentations Subdirectory

The segmentation directory will contain a single sub-directory for each task in your export. The sub-directories will be named after the task name. A single task (depending on whether it was single series or multi-series) can have one or more segmentations.

The individual segmentation files will be in NIfTI-1 format and be named after the user-defined series name. If no series name is provided on upload, RedBrick will assign a unique name. Corresponding meta-data ex. category names will be provided in tasks.json.

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Export Annotations to a Local Directory using the CLI

You can also find all of these steps, as well as pre-configured CLI commands, inside the "Export Labels" section of your Project Settings

To export your data, first ensure that your credentials file has been properly configured and you have created a local project directory.

Next, navigate to the newly created Project directory.

$ cd my-project

Once inside your local project directory, you can initiate several types of exports. Please see some common examples below or use redbrick export -h to see a full list of export-related commands inside of the Terminal.

Export Annotations for All Tasks

To export the latest state of all annotations for all Tasks (including those in Label and Review stages) run the following command.

$ redbrick export

Export Ground Truth Tasks Only

For exporting only those annotations associated with Tasks in the Ground Truth Stage.

$ redbrick export groundtruth

Export Tasks and Clear Cache

For clearing your local Redbrick cache and forcing a fresh download of all annotation files within a Project.

$ redbrick export --clear-cache

Export Tasks with Images

For downloading your Project's image and/or volume files along with any created annotations.

$ redbrick export --with-files

DICOM to NIfTI Conversion

If you initially uploaded DICOM images/volumes to RedBrick and would like to convert them to NIfTI upon export (ensuring that both your annotation files and images/volumes are in the same format), use the following command.

$ redbrick export --with-files --dicom-to-nifti

Export Tasks from a Specific Stage

If you want to export tasks that are queued in a specific stage, for example, exporting all tasks queued in Review_2, you can do so in the following way:

$ redbrick export --stage Review_2

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Export an Audit Trail

Generating an audit trail can be useful material for regulators interested in your quality control processes and for managing your internal QA processes.

You can create such a report by running the following command within your local project directory.

$ redbrick report

The exported JSON object will contain data similar to what is shown below. Each entry will represent a single task (uniquely identified by taskId). The events array contains all key events/actions performed on the task, with events[0] being the first event.

[
  {
    "taskId": "...",
    "currentStageName": "Label",
    "events": [
      {
        "eventType": "TASK_CREATED",
        "createdAt": "...",
        "isGroundTruth": false,
        "createdBy": "..."
      },
      {
        "eventType": "TASK_ASSIGNED",
        "createdAt": "...",
        "assignee": "...",
        "stage": "Label"
      }
    ]
  }
]