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Flywheel Core 22.3

22.3.0

FEATURES

Tasks Manager

Verification Workflow

Trial Coordinators using Tasks Manager can now clone a completed Read task and carry the original form responses forward as pre-filled values. This supports a verification workflow, in which a designated verifier independently reviews, edits, and submits the form, taking ownership of any fields they change. The audit trail records exactly which fields were modified, so each participant's contribution remains clearly identifiable for compliance purposes. Cloning is available for standalone Read tasks; adjudication tasks and their associated Reader Tasks are out of scope.

Adjudication Workflow

Adjudicators can draw measurements while reviewing an adjudication task in the Viewer but are now warned that those measurements will not be saved with their task, unless they specifically chose to perform their own read.

The adjudication comparison form now hides conditional-visibility questions that neither reader answered, showing only the questions relevant to the readers' responses.

Viewers

V3 Viewer
3D Segmentations

The Viewer now includes a Freehand tool for creating segmentation regions of interest (ROI). This offers an alternative to the brush tool that requires painting an entire region, and allows more precise delineation, particularly along edges.

ETDRS Grid for Ophthalmology

Users viewing Color Fundus and Fluorescein Angiography (FA) images (or any DICOM image with the OP modality) can now overlay the standard ETDRS (Early Treatment Diabetic Retinopathy Study) grid to support qualitative and quantitative assessment of retinal lesions.

The grid consists of 9 standard subfields, with the outer, middle, and inner circles' diameters measuring 7.2 mm, 3.6 mm, and 1.2 mm respectively. The grid also includes the foveal avascular zone (FAZ) reference circle with a diameter of 720 microns.

Users can move and rotate the grid to ensure it is centered on the fovea and aligned with the optic nerve head for accurate assessments.

Users can save the position of the grid, allowing a grader reviewing another grader's assessment to see exactly how the grid was positioned.

Note

The diameters for the grid's circles and the visibility of the FAZ reference circle will be configurable in a future release.

UI/UX Improvements in the Measurements Panel

The measurements panel has been refined to reduce visual clutter. Hover pop-overs no longer appear over labels or over annotation, length, bi-directional, angle, and freehand measurements. Pop-overs only remain for area measurements, but now appear after a longer hover delay.

Data Transfer

Pre-zipped DICOM Import

Flywheel now applies its full DICOM processing to pre-zipped DICOM data, so archives that were previously treated as opaque files receive the same handling as loose DICOM files.

  • The browser-based upload interface now de-identifies pre-zipped DICOM files (.dcm.zip or .dicom.zip) and uploads them as a tar archive. Previously, pre-zipped DICOM files uploaded through the browser skipped de-identification, header processing, and metadata extraction.

  • The command-line interface (CLI) local import feature now supports pre-zipped DICOM files. When a user imports a ZIP archive containing DICOM files, the CLI extracts the DICOM files, removes protected health information, and packages the de-identified files into a tar archive before uploading them. This removes the need to manually unzip pre-zipped DICOM data before import.

  • Flywheel now correctly sets the zip_member_count field for pre-zipped uploads to reflect the number of files contained in the archive. Previously, this count was set only for archives that Flywheel created during import.

External Storage

Administrators can now configure external Azure storage connections using client credentials (client_id, client_secret, and tenant_id) as an alternative to access keys. This credential-based authentication method aligns with recommended Azure security practices and gives administrators an additional option for connecting Flywheel to Azure storage.

Rule Sets

Import and export rule sets now support label templates. Users can define labels that automatically incorporate details such as the job type, origin type, origin ID, and creation date, including custom date formatting. This makes it easier to generate consistent, descriptive labels for imported and exported data without manually specifying them each time.

Uploads

Uploads now retry individual chunks that fail to transfer, rather than restarting the entire file upload. This reduces the need to re-upload large files after a temporary network interruption.

Import and export operations in the CLI now treat skipped-file reporting as optional. Previously, every skipped file was automatically included in the report output. Users can now include this detail explicitly using the new --report-skip command-line argument, reducing report noise by default while still allowing users to view skipped-file details when needed.

Command-Line Interface

The CLI now provides clearer, separate options for managing the root certificates it trusts when connecting to Flywheel. Previously, a single ssl-verify option combined several behaviors, making it difficult to tell whether a custom certificate authority (CA) bundle would replace or add to the CLI's default set of trusted certificates. The CLI now distinguishes between adding certificates to the default trust store and replacing it entirely, so users in environments that rely on a corporate proxy or a private certificate authority can configure trusted certificates predictably.

Data Management

Flywheel now supports adjustable time limits for file downloads. Customers can request a longer limit when the default interferes with downloading large files (typically 500 GB or more).

Usage Reporting

Flywheel enhanced Usage Reporting to give administrators a clearer view of resource consumption across their organization. The redesigned experience separates an at-a-glance dashboard from a detailed, exportable report:

  • Interactive dashboard — displays file count, content size, and gear run time trends over time, with breakdowns by group.
  • Detailed report view — lets administrators group results by project, group, or month, filter by date range and group or project, and save filter selections for reuse.
  • Expanded metrics — reports now include an end-of-range value for files, content size, jobs, gear run time, and sessions, in addition to the change over each selected period.
  • Flexible export — administrators can export the report as a comma-separated values (CSV) file, choosing between a standard set of columns or the full set of available data columns.

Usage Report dashboard

For details on the dashboard, report grouping and filtering, and CSV export, see the Usage Report documentation.

FIXES

Viewers

V2 Viewer
  • Fixed an issue where a NIfTI segmentation mask generated from an analysis failed to display over its corresponding NIfTI image when that image was loaded from an analysis container rather than an acquisition.
V3 Viewer

  • Fixed an issue where scroll position did not stay synchronized between datasets when one or more series lacked a valid FrameOfReferenceUID or had mismatched FrameOfReferenceUID values. Scrolling now stays synchronized when datasets share the same ImagePatientPosition and ImageOrientationPatient values.

  • Fixed an issue where opening a file-level task for a file that had been deleted displayed a blank screen. Users now see appropriate information when the file no longer exists.

  • Fixed an issue where selecting a measurement set in the measurement panel caused the viewport to jump to a different slice unexpectedly.

Adjudication Tasks

  • Fixed an issue in Adjudication where users could still proceed with their task even when some datasets could not be loaded, for example due to file corruption or invalid file types. Users now get a full-page error and are prevented from completing the task.

  • Fixed an issue where hovering over or selecting a reader in the adjudication comparison table caused measurements from another reader to remain highlighted in the viewport at the same time. Only the measurements belonging to the selected reader are now highlighted.

  • Fixed an issue where clicking a reader's column or avatar did not correctly activate that reader's measurement set, and hover states did not consistently highlight the corresponding measurements across viewports.

BrainBrowser
Montage Viewer

Tasks Manager

  • Fixed an issue where adjudicators could see the names of the readers who completed the associated reading tasks on the adjudication task card, breaking the blinding required for the adjudication workflow.

  • Fixed an issue where users could not update the status of tasks associated with deleted projects, which returned the error Unable to load notification. Tasks orphaned by container deletion are now automatically cancelled, and the task displays an alert indicating why.

  • Fixed an issue where the Create Protocol button did not appear for site administrators who lacked specific write permissions for the group. The button now appears correctly for site administrators.

  • Fixed an issue where viewer configuration settings in the protocol editor — including file browser options, toolbar display, and label behavior — failed validation due to a mismatch with the expected format. Viewer configuration settings now validate correctly within protocols.

  • Fixed an issue where users could bypass restrictions on unavailable protocol types by typing directly into the type field of the create protocol dialog. Only supported protocol types can now be selected.

  • Fixed an issue where the e-signature badge in tasks required a click to reveal signature details. The badge now shows details on hover.

  • Fixed an issue where the adjudication trigger fields were not highlighted with distinguishing colors in the comparison form when a newly created adjudication task was launched. The trigger fields are now clearly highlighted.

  • Fixed an issue where submitting a task could fail during form validation when the form used the some operator, returning the error Unrecognized operation some. Forms that use the some operator now validate and submit consistently.

Legacy Tasks

  • Fixed an issue in Legacy Tasks where annotations created before version 22.0 failed to render when a previously completed or in-progress reader task was reopened in version 22.0 or later.

Gears and Compute

  • Fixed an issue where the FW_XFER_STORAGE_CREDS environment variable did not appear when listing environment variables in a JupyterLab workspace configured for external storage, which could prevent the workspace from connecting to its configured external storage.

  • Fixed an issue where graphics processing unit (GPU) jobs could fail with an InsufficientInstanceCapacity error when the requested Amazon Web Services (AWS) availability zone temporarily lacked capacity. Flywheel now retries the request in other configured availability zones before falling back to an alternate instance type.

  • Fixed an issue in the Gears Manage Access dialog where the project and user dropdown lists remained open after adding a project. The dropdown lists now close as expected.

  • Fixed an issue in the Gears Manage Access dialog where removing a project from the access list prevented it from being re-selected in the project dropdown.

  • Fixed an issue in the Gears Manage Access dialog where searching for a user by email address returned no results even when a matching user existed.

  • Fixed an issue where the Gear Rules page crashed and generated over 1,000 console errors when reloaded while certain browser extensions that modify page content were enabled.

  • Fixed an issue where uploading large gears could exhaust server memory and cause the upload to fail. Large gear uploads no longer strain backend resources.

Data Management

  • Fixed an issue where a session weight of 0 did not display in the user interface. A weight value of 0 now renders correctly.

  • Fixed an issue where tooltips in the search results table were inconsistent across tabs. Tooltips now display consistently across all tabs in search results.

  • Fixed an issue where clicking the active Sessions or Subjects tab within a project deselected the current session or subject. Clicking the active tab no longer clears the selection.

  • Fixed an issue in Session Templates where the Save button remained disabled when the Session Label field was left empty, even though the field is optional. An empty Session Label matches any or all sessions in a project, and the Save button now enables correctly in this case.

Data Transfer

  • Fixed a configuration issue that prevented DICOM Router from starting in some Flywheel-hosted environments.

  • Fixed a networking configuration issue that could prevent data transfer operations from completing on some Flywheel-hosted AWS deployments.

  • Fixed an issue where de-identification failed during import if a DICOM date (DA) field contained multiple values, producing an error such as Unable to parse date field with format %Y%m%d.

  • Fixed an issue where a site's default classification rule set could unexpectedly revert to a mixed configuration after an upgrade instead of remaining as configured.

  • Fixed an issue where data exports that included files with no content (0 bytes) could stall or fail to complete. The export process now skips these empty files, reports them with the reason zero-byte file, and finishes successfully.

  • Fixed an issue where the fw ingest command failed with a not enough permissions error for users who had full upload permissions, on sites running version 22.0 or later.

  • Fixed an issue where the CLI crashed with a UnicodeDecodeError when monitoring import progress for data containing accented or other multi-byte characters in labels.

  • Fixed an issue where users without the site-admin role received a confusing, technical error message when creating or updating storage locations using the CLI. The CLI now checks permissions before running admin storage commands and displays the message admin commands require site-admin role, while the storage list and storage get commands no longer require site-admin access.

  • Fixed an issue when resolving import conflicts using the "Keep all" action, where the "Resolve conflict" button remained disabled on the next page of conflicts. The button now enables automatically when the next page loads.

  • Fixed an issue where clicking a conflict indicator on the imports page navigated to the import details page instead of the conflicts page.

  • Fixed an issue where an ad hoc filter during export failed to return valid matching options in the suggestion list after a value was typed, preventing users from selecting a filter value.

  • Fixed an issue where configuration dialogs — including those for storage providers, connectors, and rule sets — closed when a user clicked outside the dialog, causing accidental loss of in-progress data. These dialogs no longer close on an outside click.

  • Fixed an issue where text box fields could not have their disabled state changed and remained disabled regardless of the intended setting.

  • Fixed an issue on the Imports and Exports pages where the displayed item range did not update when moving between pages of results, always showing 1-25 even though the correct page of data loaded. The displayed range now reflects the selected page.

  • Fixed inconsistent padding in the Rule Set Group table, improving visual consistency in the Gear Rules interface.

22.3.1

FIXES

Viewers

V2 Viewer

  • Fixed an issue where the required.specific setting in a reader task protocol's bSlices configuration did not prevent task submission when the designated fields were left unanswered on their specified slices.

  • Fixed an issue where including a text field in a reader task protocol's bSlices.required.all or bSlices.required.any configuration caused task submission to fail silently with no error message.

V3 Viewer
  • Fixed an issue where entering 0 in an integer or float form field prevented readers from submitting the form, returning a Something went wrong message.

Tasks Manager

  • Fixed an issue where the Task Details fields of an adjudication task remained editable for a user assigned to one of its linked Reader tasks. Attempting to change a field returned the error Failed to update task fields. Please try again. The Priority, Due Date, Task Description, Task Tags, and Status fields are now disabled in this case.

Gears and Compute

  • Fixed an issue where gear jobs that require a graphics processing unit (GPU) failed to start on newly provisioned compute nodes, returning the error stat nvidia.com/gpu=all no such file or directory. Compute nodes now use a container runtime version that supports GPU device passthrough.

  • Fixed a configuration issue that prevented the gear image registry from starting on Flywheel-hosted Microsoft Azure deployments that authenticate to storage with a shared access key rather than workload identity.

Data Management

  • Fixed the following issues on sites configured with multiple storage providers:

    • The Bookmarks, Help, and user dropdown menus in the top navigation bar did not open.
    • The Create Group button on the Admin Groups page did not respond, preventing administrators from creating new groups.
    • Projects did not appear under their groups on the Groups tab. Affected groups displayed either no projects at all or only storage details.

Data Transfer

  • Fixed an issue on Microsoft Azure sites where Flywheel sometimes used incorrect credentials when connecting to a storage location, causing imports and exports that used that location to fail. Flywheel now selects the correct credentials for each storage location.
Guided Case Uploader
  • Fixed an issue where uploads of large DICOM datasets, including datasets of 3 GB and larger, failed. In these cases, only two parallel upload threads started.
DICOM Router
  • Fixed an issue that prevented the DICOM Router from starting on newly deployed Flywheel sites, leaving DICOM transfers unavailable there.

22.3.2

FIXES

Data Management

  • Fixed an issue causing Project Smart Copy operations to fail on sites using customer privately signed certificates.

  • Fixed an issue on sites configured with a single storage provider where the Create New Project button was missing from the Groups tab. Long group names that overflowed their container are now also truncated correctly.

Data Transfer

Bulk Export
  • Fixed an issue where Bulk Export failed with a Transport Layer Security (TLS) certificate verification error, SSL: CERTIFICATE_VERIFY_FAILED, on sites that use a private certificate authority.
Case Uploader

  • Fixed an issue where uploads failed with a 422 Blob not found on storage error, preventing users from completing an upload.

  • Fixed an issue where uploads of DICOM files larger than 10 MB failed with a 400 Bad Request error. Affected files were sent as a single upload request instead of being split into smaller parts. This fix also resolves related issues where canceling an upload did not stop the transfer already in progress, and where restarting an upload after canceling resumed a stale, already-deleted session instead of starting a new one.

  • Fixed an issue where the progress bar did not display the percentage complete during an upload, leaving users unable to track progress until the upload finished.

  • Fixed an issue where canceling an upload during the upload phase displayed unnecessary error pop-ups.

  • Fixed an issue where the file size column in the Prepared Files list overlapped adjacent content and became unreadable when file names were long.

Legacy CLI (fw)

  • Fixed an issue where the Legacy CLI (fw) failed TLS verification against sites that use a private certificate authority, preventing login and import operations. The --ca-cert and --ssl-verify options had no effect on affected sites.

  • Fixed an issue where the fw gear install, fw gear update, and fw gear upload commands failed with a CERTIFICATE_VERIFY_FAILED error when connecting to the gear exchange service, even when the CLI was configured to skip TLS certificate verification. These commands now use the CLI's configured TLS certificate settings.

Viewers

V3 Viewer
  • Fixed an issue where DICOM Segmentation (SEG) files containing many regions of interest took several minutes to open. The viewer generated a separate frame for each region of interest on each slice where it appeared, so a segmentation with 100 regions across 250 slices produced tens of thousands of frames, each carrying its own metadata. The viewer now transmits the metadata it requires without generating a frame for every region on every slice.