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

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.
  • Your DICOMs are not compressed into a zip file. The DICOM uploader also does not accept folders. You must upload single files.

Instruction Steps

Selecting Multiple Files From Your Computer To select a range of files, click on a file in your browser, hold down the Shift key, and select the last file. All files in between are selected and can be uploaded to Flywheel.

  • The total upload size is less than 10,000 DICOM files or 200 MB.

This is due to browser limitations.

  • See below for a list of invalid characters for filenames.

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 you are uploading or click anywhere on the uploader to launch the file selector.

*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.

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

editupdatefields.png

  1. 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 fields. Some 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.

  1. Click Upload Data. If the Upload data button is disabled, your images are missing required metadata.

Flywheel displays an upload progress bar.

  1. 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