Please note that the
exportfunction 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.
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:
│ ├── study01
│ │ └── series1.nii
│ └── study02
│ ├── series1.nii
│ └── series2.nii
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.
You can also find all of these steps, as well as pre-configured CLI commands, inside the "Export Labels" section of your Project Settings
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 -hto see a full list of export-related commands inside of the Terminal.
To export the latest state of all annotations for all Tasks (including those in Label and Review stages) run the following command.
$ redbrick export
For exporting only those annotations associated with Tasks in the Ground Truth Stage.
$ redbrick export groundtruth
For clearing your local Redbrick cache and forcing a fresh download of all annotation files within a Project.
$ redbrick export --clear-cache
For downloading your Project's image and/or volume files along with any created annotations.
$ redbrick export --with-images
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-images --dicom-to-nifti
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
Generating an audit trail can be useful material for regulators interested in your quality control processes and for managing your internal QA processes.
$ 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
eventsarray contains all key events/actions performed on the task, with
eventsbeing the first event.