How to Upload a Case

This guide walks through the process of uploading imaging data for a single case using the Case Uploader.

Prerequisites

Before you begin, confirm that a Trial Coordinator or Project Administrator has:

• Configured Session Templates for your project with the expected session and acquisition labels. If the options you need are missing from any drop-down menu, contact your Trial Coordinator.
• Granted you upload permissions on the target project.
• (Recommended) Configured a de-identification profile for your project. If no profile is configured, the Case Uploader displays a PHI Risk warning before you select files.

Step 1: Select Group and Project

The Case Uploader displays two drop-down menus: Group and Project. You must select a value for each before you can proceed.

The two menus filter each other, so you can start with either:

• Selecting a Group first filters the Project menu to show only projects within that group.
• Selecting a Project first filters the Group menu to show only groups that contain a project with that label.

Step 2: Select the Upload Destination

After selecting a Group and Project, choose where in the Flywheel hierarchy to place the upload. There are three fields: Subject, Session, and Acquisition.

Subject

The Subject field is a searchable combo box. It lists all existing subjects in the project, and you can type to filter the list. If you type a label that does not already exist, the Case Uploader offers the option to create a new subject with that label.

Session and Acquisition

You must select a Session before you can select an Acquisition.

Both fields are searchable drop-down menus populated from the project's Session Templates. You can only select session and acquisition labels that are defined in the project's Session Templates. If a label you need does not appear, contact your Trial Coordinator to have it added.

Step 3: Select Files to Upload

Drag and drop files or a folder onto the upload area, or click to browse your local file system. The Case Uploader uploads data to one Acquisition container at a time.

PHI Risk Warning

If no de-identification profile is configured for the current project, group, or site, the Case Uploader displays a PHI Risk warning banner. This banner appears before you select files and indicates that DICOM files will be uploaded with their original headers intact.

Whether uploading unmodified DICOM headers is acceptable depends on your site's configuration and your study's compliance requirements. If you are unsure, contact your Trial Coordinator or Project Administrator before proceeding.

Non-DICOM File Handling

Non-DICOM files are accepted as-is without modification. Flywheel performs only a malware scan on these files before importing them.

DICOM De-Identification

If a de-identification profile is configured, the Case Uploader de-identifies all DICOM files locally — before the files leave your computer. DICOM files that fail de-identification are blocked from upload.

See De-Identification Overview for more information.

DICOM File Grouping and Packaging

When you select loose DICOM files, the Case Uploader reads the header in each file and groups them by their SeriesInstanceUID value. Each group is then compressed into a single ZIP archive for upload.

The upload preview shows both DICOM ZIP archives and non-DICOM files in the same list. Expand any DICOM ZIP archive to see the individual files it contains. Hovering over a loose file within a DICOM ZIP archive displays the original filename from your local computer.

ZIP archives and their contained files are named using Flywheel's default Bulk Import file naming rules. See Bulk Import Default Behavior for details.

DICOM Consistency Check

Because the Case Uploader targets a single Acquisition container per upload, it checks the selected DICOM files for common signs of a data selection error. A warning banner appears if any of the following conditions are detected:

• The selected files include more than one unique PatientID (suggesting files from different patients were selected)
• The selected files include more than one unique StudyInstanceUID (suggesting files from different imaging sessions or time points were selected)
• The selected files include more than one unique SeriesInstanceUID (suggesting files from different series or modalities were selected)

These are best-effort checks intended to help you catch mistakes before submitting. There are valid scenarios where these conditions occur by design — you are not required to resolve them.

If the warning appears, you can select Review to open a side-by-side comparison table. Each column in the table represents a single DICOM file group. Each row represents a DICOM header value. The headers that triggered the warning are highlighted. Only the most relevant headers are shown, such as patient identifiers, dates, scanner details, and UIDs.

From the comparison table, you can remove one or more DICOM file groups before proceeding. Removal is optional.

Step 4: Upload

After reviewing your file selection, start the upload. The Case Uploader displays a progress view showing the transfer of data from your computer to Flywheel.

Completion

When the upload finishes, a status banner is displayed. The banner includes a link to the Bulk Import job so you or your Trial Coordinator can verify that the data was processed and imported successfully.

You are also presented with the option to start a new upload for another case.

Troubleshooting

No projects or groups appear

Problem: No options appear in the Group or Project menus, or authentication fails.

Solution: Sign out and sign back in. If the problem persists, contact your Flywheel Administrator to verify your project permissions.

An expected session or acquisition label is missing

Problem: The Session or Acquisition drop-down does not include the value you need.

Possible cause: The label has not been configured in the project's Session Templates.

Solution: Contact your Trial Coordinator to verify the Session Templates are configured with the expected labels.

DICOM header values in the comparison table are unexpected

Problem: The PatientID, StudyInstanceUID, or SeriesDescription values shown in the comparison table do not match what you expect.

Possible causes:

• You selected the wrong files.
• The source imaging system encoded metadata incorrectly.
• The files are from a different study or patient.

Solutions:

1. Cancel the upload and re-select the correct files.
2. Verify the source system configuration with your imaging technician.
3. Contact your Trial Coordinator if you believe the files are correct but the metadata is unexpected.

DICOM files are not grouping as expected

Problem: DICOM files that belong to the same series are being separated into different groups.

Possible cause: Inconsistent SeriesInstanceUID values across files in the same series.

Solution: Review the source DICOM files to confirm they were exported correctly from the imaging system. Contact your imaging technician if the inconsistency persists.

DICOM de-identification fails

Problem: One or more DICOM files are blocked from upload due to a de-identification failure.

Solution: Contact your Trial Coordinator or Project Administrator. The de-identification profile may need to be updated to handle the DICOM headers in your files.