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Upload DICOMs via Web UI

Introduction

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.

This article explains how to use the DICOM uploader. This method works best for smaller datasets.

New Uploader in BETA

As of Flywheel 18.2, a new web-based DICOM uploader supporting very large datasets is now available in early access.

With the new uploader, there is no set limit on the size of each individual file or the total volume of data that can be uploaded using the new uploader. However, each individual file must complete uploading within 24 hours. For example, a 50 GB file could be uploaded depending upon the user's connection speed (subject to the 24-hour timeout).

After the files are uploaded, a new Project Import job is started to process and place the files into the Flywheel hierarchy. The processing and placement of the files can be monitored via the import job details.

The uploaded DICOM files will be placed into the Flywheel hierarchy based on the DICOM header information using system-defined mapping rules. Only DICOM files are supported in the new uploader at this time. However, additional file types are planned to be supported in a later release.

The new DICOM uploader is disabled by default (while in BETA). To enable this features on your site, contact Flywheel Support.

Once the new uploader is enabled for your site, it can be found by navigating to the "Imports" tab in the overflow menu of the "Project" page, selecting the "Import Data" button, and choosing the "Local Upload" option.

De-identification is not yet implemented in the new uploader and is planned for a later release. Do not use the new uploader at this time if you require Flywheel to de-identify your data before it is loaded into Flywheel.

Instruction Steps

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.

Tip: Drag and drop files or folders from your computerTo select a range of files or folders, click on a file in your browser, hold down the Shift key, and select the last file. All files (or folders) in between are selected and can be dragged and dropped to Flywheel.

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. Click Upload DICOM in the left menu.
    The DICOM Uploader appears.
    DICOMUploader-export.png
  3. Select a Project from the dropdown menu.
    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 click anywhere on the uploader to launch the file selector (NOTE: file selector works for files only, not folders).
    The uploader immediately begins parsing and organizing your Files into Sessions. Properly uploaded files are displayed and grouped by Acquisition. Non-DICOM files and other files not loaded correctly display an error message. .
  5. Review the upload summary information and make sure that labels are correct. If they are not correct, click Edit and update the fields.
    EditDICOMHeaders-UploadDICOM-export.png
  6. Enable de-identify data to remove the PatientID, PatientName, and PatientBirthDate headers from the DICOM file. This means that those fields are not imported when you upload the image. This also converts the Age to months.

Note: Your Project may require those fieldsSome Flywheel Projects use the PatientID, PatientName, or PatientBirthDate for their workflows. This method of de-id removes those fields altogether (instead of replacing the fields with something else). If the Project requires those fields, you should use a different method for  importing and de-identifying your images. See our Importing Overview article for more options. 7. Click Upload Data. If the Upload data button is disabled, your images are missing required metadata.
Flywheel displays an upload progress bar. 8. Navigate to the Project to review the images.

Invalid Characters

List of invalid characters that will result in blocked uploads via the CLI or DICOM uploader if they are included in a filename:

  • ~
  • :
  • *
  • ?
  • “
  • <
  • |
  • \
  • /
  • Tab
  • Line feed
  • Carriage Return
  • Vertical Tab
  • Form Feed