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Flywheel Core 18.4

July 2024

18.4.0

EARLY ACCESS

Enablement

Early access (BETA) features are disabled by default. To request enablement of an early access feature for your site, contact Flywheel Support.

(BETA) Duplicate Handling during Bulk Import

  • A new "Keep All" action is available to resolve file name conflicts in a way that preserves both the incoming and existing data by appending a suffix to the incoming file name (e.g., *_1.zip).
  • Minor styling updates to the "Review Conflicts" page for Bulk Imports.

(BETA) OHIF v3 Viewer

  • The OHIF v3 Viewer is available in BETA for read-only workflows.
  • Now supports most DICOM Ultrasound modality image formats and DICOM overlay files (RTStruct, SR, and SEG).

FEATURES

Flywheel Jupyter Notebooks General Release (Module)

Flywheel Notebooks provide an interactive compute option that allows researchers to easily apply Python data science tools within the Flywheel platform.

Flywheel integrates with the familiar JupyterLab/Notebooks to combine Python code, reports, and documentation in a single document.

The notebook servers are managed within Flywheel Projects and controlled via User permissions. The compute resources are configurable and managed by Flywheel.

Flywheel Notebooks have a wide array of applications, including the following:

  • Data and Image Curation
  • ML and AI Training and Inference
  • Analytics and Reporting
  • Automate Administrative Functions

Quickly access details of the data used for a gear run by clicking on links in the Jobs log to open the relevant page in a new window. Links include project, subject, session and acquisition. Input file links will go to the acquisition containing the file.

FIXES

(BETA) New Web Uploader

  • Fixed an issue with the new web uploader where uploading one bad file blocks all further uploads by the same user.
    • Files that were uploaded but failed to be imported into the Flywheel project would be included in future uploads initiated by the same user, resulting in the every future upload to report failures.
  • Fixed an issue with the new (BETA) web uploader where the bottom of the upload dialog would get cutoff after expanding the list of uploaded items.
  • Fixed an issue with the new (BETA) web uploader causing some files to get uploaded multiple times unnecessarily.
  • Revised the boundaries of the file drop-zone in the new (BETA) web uploader so that it is easier to hit.

(BETA) Bulk Import + New CLI

  • Fixed an issue with the "Review Conflicts" page for (BETA) Bulk Imports where the details pane for a particular conflict item would still be displayed after the conflict was resolved.
  • Fixed a minor issue with the "Conflicts Review" page for (BETA) Bulk Imports causing tooltips to not be displayed in certain scenarios.
  • Fixed an issue with the "Review Conflicts" page for Bulk Imports where the hint text for the Actions menu was cut short.
  • Minor styling updates to the "Review Conflicts" page for (BETA) Imports.
  • Fixed an issue with (BETA) Bulk Import where the counts of "impacted containers" did not include newly-created containers.
  • Reworded error messages for better clarity in the new CLI (fw-beta) when attempting to schedule an import for a project in which the user does not have access.

Bulk Export

  • Fixed an issue with Bulk Exports where if a new export was created by copying an older export, the copy action would not preserve all filter condition settings.

Data Management

  • When trying to use the SDK to add metadata to a file in an analysis container, nothing happens.

Ingest + Classic CLI

  • Fixed an issue where the Classic CLI (fw) stored the current API key in clear text in configuration file on user's local machine. The API key is used to authorize actions in Flywheel on the user's behalf.
  • Fixed an issue with fw ingest dicom when --copy-duplicates is enabled where the process would sometimes fail with an error saying, User already has permission on the project.
  • Fixed an issue where the Flywheel CLI would retry POST and DELETE requests when receiving an error response, resulting in duplicate cluster ingest jobs being created (but not started) in certain cases.

Jupyter Notebooks

  • Flywheel Notebooks - Removed the database validation limitation on displaying more than 16 CPU computes. Also removed database validation limitation on displaying more than 100GB RAM. There still exists a technical limitation of 100GB RAM for the kubernetes cluster definition.

Viewer

  • Fixed issue displaying TIF images in the default viewer.

18.4.1

FIXES

Ingest (All)

  • Fixed an issue with fw ingest where data would be uploaded even without being de-identified if an invalid de-ID profile was specified via the --deid-profile option, resulting in a potential PHI risk.
    • Now, an error will returned and the data will not be uploaded if the specified de-ID profile does not exist.
  • Fixed an issue with fw ingest where the entire Ingest job would fail if the source data included DICOMDIR files.
    • Now, the DICOMDIR files will be skipped and the Ingest job will proceed normally.
  • Fixed a rare issue with fw ingest when the --detect-duplicates and --copy-duplicates options are enabled where the sidecar project could not be created if another sidecar project already existed with the same name.
    • This issue is exceedingly rare since the sidecar project name is derived from the current timestamp of when the sidecar project is created, so it would only occur if multiple ingest jobs targeting the same project reached the same step at the same time (<1 second apart).
    • Now, when this condition occurs, a suffix will be added to the new sidecar project name so that it can be created successfully without conflict.

Ingest Cluster

  • Fixed an issue with fw ingest --cluster introduced in version 18.2.3 which prevented the cluster Ingest system from functioning if very old Ingest jobs launched on a version prior to 17.8 (which used an older database schema) had not completed before the system was updated to version 18.2.3.
    • The issue of old, stuck Ingest jobs was already identified and fixed in the 18.2.3 patch to prevent such cases from reoccurring in the future, and the 18.2.4 patch contains additional code fixes to handle the schema changes more gracefully.

18.4.2

FIXES

Reader Tasks

  • Resolved an issue where Reader workflow tasks do not give option to open task in OHIF v2 viewer
  • Resolved the "Problems saving" error message when user is saving ROI annotations in PNG data with non reader task environment.

SDK

  • Fix for a rare retrieval error in SDK when using get_session with a key.

18.4.3

FIXES

Gears & Compute

  • Resolved issue where gear upload errors were not ending the gear run or being reported as an error.

Validated Instances

  • Resolved issue where deleting projects from the Web UI was not possible for non-Validated Instance configurations.

18.4.4

FIXES

Gears & Compute

  • Fixed an issue where SDK Gears triggered from a Gear Rule configured to use a Role will fail with permission error when the SDK makes requests to the Flywheel API.