Upload DICOMs via the Flywheel Core Web App (DEPRECATED)

One of the fastest ways to get your existing imaging data into Flywheel is to use the DICOM Uploader. The DICOM uploader allows you to drag and drop your images to a Project in Flywheel.

The DICOM uploader allows raw, uncompressed DICOM data to be added to projects. Flywheel reads the DICOM header information to fill out the appropriate metadata fields.

Limitations

Small Data Sizes

This method works best for smaller datasets. For optimal performance, limit uploads to 10,000 DICOM files or 200 MB per upload.

If larger data sets are needed, consider using either Bulk Ingest (if de-ID is required) or Bulk Import (if de-ID is not required).

Supported File Types

The uploader only supports the following filetypes and does NOT support folders or zipped files.

• .dcm, .dcm.gz
• .dicom, .dicom.gz
• .ima, .ima.gz

Image Requirements

Your DICOM images must meet the following requirements to use the web uploader:

• Your images are the DICOM filetype. To upload other image types, see our Importing Overview article.
• DICOMs are not compressed into a zip file.
• The total upload size is less than 10,000 DICOM files or 200 MB.
  • This is due to various browser limitations.
• See below for a list of invalid characters for filenames.

Next Steps

After you have verified that your data meets the above requirements, upload your files:

1. Sign in to Flywheel as a user with permissions to upload files to a Project.

2. Select Upload DICOM in the left menu.

   

3. Select a Project from the dropdown menu.

   1. Only Projects you have permission to upload files to are included in this list.

4. Drag and drop the files or folders you are uploading or select anywhere on the uploader to launch the file selector.

   1. The file selector works for files only, not folders.

   Selecting Multiple Files at Once

   To select a range of files or folders, first select one file, then hold down the Shift key and select the last file. All files (or folders) in-between the first- and last-selected file are selected and can be dragged and dropped to Flywheel.

5. The uploader immediately begins parsing and organizing your Files into Sessions.

   1. Properly uploaded files are displayed and grouped by Acquisition.
   2. Non-DICOM files and other files not loaded correctly display an error message.

6. Review the upload summary information and make sure that labels are correct. If they are not correct, select Edit and update the fields.

   

   

7. Enable the De-identify Data option to remove the PatientID, PatientName, and PatientBirthDate headers from the DICOM file.

   1. This means that those fields are not imported when you upload the image.
   2. This also converts the Age to months.

   Required Fields

   Some Flywheel Projects use the PatientID, PatientName, or PatientBirthDate for various workflows, and this method of de-id removes those fields altogether (instead of replacing the fields with something else).

   If the destination Project requires those fields, you should use a different method for importing and de-identifying your images.

   See our De-ID Overview article for more options.

8. Select Upload Data.

   1. If the Upload data button is disabled, your images are missing required metadata.
9. Flywheel displays an upload progress bar.
10. Once the upload is complete, navigate to the Project to review the uploaded images.

Learn more about using the image requirements for using the DICOM uploader.

Invalid Characters for File Names

Certain characters are not allowed to be used in file names. Refer to Illegal Characters for more details.