Uploading Dicom files

Using Labelbox Annotate
1

Hello,
I m new to labelbox, and i would like to use labelbox to annotate dicom files.
But when i try to upload the dicom files, I get the following error message: " File upload error - invalid file extension for file".
thank you for your help.

2

Hey @khaled.radhouane - thanks for reaching out!

This has caught me off-guard before also. Here’s the doc page on uploading DICOM files: Import DICOM data

Currently, Labelbox only suports uploading DICOM assets via delegated access or public-accessible URLs. You can’t upload the file directly, you have to reference it via a JSON file like this:

[
  {
    "row_data": "https://path/to/your/file.dcm",
    "global_key": "<unique global key>",
    "media_type": "DICOM"
  }
]

Hope this helps!
John

3

Appreciate your your help.
It won’t be easy for me then.
Thank you again.

4

Hello,

I’ve been trying for a while to annotate dicom file on Labelbox. I created a public bucket on Google Cloud Platform to store a multi frame dicom file. However when I add it to a dataset like this:

client = Client(api_key=LB_API_KEY)

dataset = client.create_dataset(name="test DICOM")

url = 'https://storage.googleapis.com/XXX/XXX/FILE.dcm'


assets = [{
        "row_data": url,
        "global_key": url,
        "media_type": "DICOM"
    }]

task = dataset.create_data_rows(assets)
task.wait_till_done()

When I try to annotate it, I get stuck on this loading screen.

image
image1911×982 15.3 KB

Any ideas?

5

Hey @ncotoni ,
I’m looking into it however given DICON can be quite large asset it can take time to load in the editor.

Many thanks,
PT

6

Hello @ptancre,

I don’t think that’s the problem, I let the editor load for 1 hour without anything happening…

Does labelbox accept a specific Dicom format? With a specific field?

Can you provide me with a 3D Dicom volume that would work on Labelbox so that I can compare it with mine?

7

Your file actually does work, the issue is those file needs to be hosted in your buckets to work on our editor (i.e. AWS, Azure or GCP) we currently don’t support DICOM from the Labelbox storage directly.

ref : Import DICOM data

The link provided should give you some pointers onto what we currently support, basically 3D, multi-frame.

Many thanks,
PT

8

Hi @ptancre,

My file is actualy hosted publicly in a bucket on Google Cloud Storage and it still doesn’t work.
I’ve just hosted your 3D multi-frame dicom ‘sample-dicom-2.dcm’ to check if Labelbox could load the editor, and unfortunately no, the problem remains unchanged.

9

I believe this has been communicated to you already (thanks to ECCV) but for GCP asset you need to use the URI instead of the URL:

assets = [
  {
    "row_data": "gs://lb_integration_gcp/myDicomData.dcm",
    "media_type": "DICOM"
  }
]

It’s only a limitation we have with GCP, doc ref : Google Cloud Storage

Many thanks,
PT

10

Actually, it should be working now, this is on us, the dicom editor was not enabled for you…
The previous message still stands if you use GCP, use the URI to import your files.

Many thanks,
PT

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