Skip to content

Flywheel Core 19.5

19.5.0

FEATURES

Bulk Import & Export

  • The "canceled" and "canceling" states for Bulk Import and Bulk Export have been renamed to "cancelled" and "cancelling" (1 l vs. 2 l's) to align with the similar Gear Job states.
Bulk Import
  • Filenames consisting of numeric digits only are now assumed to be DICOM with the default mapping rules.
Bulk Export
  • Styling and user experience refresh for the Bulk Export page in the Flywheel Core Web App.

CLI

Legacy (fw)
  • A new option, --ssl-verify no (or --ssl-verify false), is available in the legacy CLI for disabling TLS/SSL certification validation to assist with troubleshooting issues related to certificates issued by private authorities.
New/BETA (fw-beta)
  • The new (BETA) CLI is now available for use on Windows clients.
  • A new option, --ssl-verify no is available in the new (BETA) CLI for disabling TLS/SSL certification validation to assist with troubleshooting issues related to certificates issued by private authorities.
  • New options, --connect-timeout <SEC> and --read-timeout <SEC>, are available in the new (BETA) CLI for modifying the HTTP connect and read timeout settings to help avoid issues related to slow networks.

DICOM Connectors

  • Network security hardening for DICOM connectors, including:
    • Mutual TLS (mTLS) support is available for both encrypting and authentication connections with DICOM devices
    • HTTP/S ports are disabled by default

External Storages

  • Styling and user experience refresh for the External Storages page in the Flywheel Core Web App.
  • For External Storages using a File System source, UNIX-style file ownership rules can be configured via the Flywheel Core Web App. Previously, these settings could only be configured via the new (BETA) CLI.

Jupyter Workspace

  • Upgrade of Jupyter Workspace to JupyterLab version 4.2.5.

Smart Copy Exclude Empty Containers

Smart Copy now includes a new option to exclude empty containers (subjects, sessions, acquisitions) from the destination project. This includes containers that are empty after the application of Smart Copy include and exclude containers.

Smart Copy Dialog

Viewer

V2 viewer
  • The viewer can now be configured to include a link to the Flywheel session in the left-side navigation panel.
V3 viewer

  • Improvements and enhancements in 3D segmentations:

    • Segmentation files (DICOM SEG and DICOM RTSTRUCT) from analyses can now be loaded in the viewer.
    • Clicking on an annotation, measurement or ROI in the measurement panel while in 2D MPR mode now resets the orientation of the viewports and displays the slice associated with that annotation.
    • Users get a warning when they try and create more than 255 ROIs in one segmentation.
    • The active segmentation is now highlighted in the segmentation panel when multiple segmentations exist.
    • Permissions are now enforced for saving and downloading segmentations.

  • Improvements and enhancements in the TMTV mode:

    • Patient Information section is now available in the segmentation panel for quick verification and includes Patient Sex, Weight, Total Dose, Half-Life, Injection Time and Acquisition Time.
    • The Total Metabolic Tumor Volume (TMTV) is now displayed in the segmentation panel in milliliters (mL)
    • TMTV mode segmentation results can now be exported as a csv file.
    • A Reset View button is now available to reset zoom levels, slice position, pan and crosshair position.

  • UI/UX fixes/improvements:

    • Removed unnecessary tooltips throughout the viewer.
    • Annotations, measurements and ROIs are now grouped by image series in the measurement panel.
    • Added icons to identify the tool used for each annotation, measurement or ROI in the measurement panel.
    • Added Flywheel logo and branding on loading page in viewer and browser tab title.
    • Other minor UI/UX improvements

  • Other improvements:

    • DICOM SR report name is pre-populated in save pop-up window when saving an existing DICOM SR report.

FIXES

  • Resolves issue where Search does not return correct results
  • Update Search Web UI to use more efficient bulk delete API

Bulk Import & Export

  • Fixed an issue with system auto-scaling for Bulk Import and Bulk Export causing the system to use less resources than it has available, which resulted in slower overall import/export speed than anticipated.

Bulk Import

  • Fixed an issue where Bulk Import would fail with a timeout error when preparing to export a very large project.
  • Fixed an issue with Bulk Import from object (cloud) storage where the import would skip all files located under a prefix that contained special characters (e.g., s3://data-for-import/20241201-ABCD +EF/Studies) due to improper handling of the special characters.

Bulk Export

  • Fixed an issue where Bulk Exports would fail with an error saying AttributeError: 'AttrDict' object has no attribute 'dst_path' when exporting multiple containers located at the exact same Flywheel hierarchy path (i.e., duplicate container labels).
    • With this fix, a numerical suffix will be appended to avoid the conflict when writing to the export destination (e.g. sub/sess/acq and sub/sess/acq_1).
  • Fixed an issue with Bulk Export when launched via the Flywheel Core Web app where the "Container Template" selection criteria values containing spaces would be wrapped with quotes in an incorrect way, causing the incorrect data to be selected for export.

CLI (Legacy)

  • Fixed an issue with the legacy CLI where object sizes were calculated in Gibibytes (GiB) but displayed with units of Gigabytes (GB).
    • With this fix, object sizes are both calculated and displayed using only Gigabytes (GB); Gibibytes (GiB) are not used at all.
Ingest (Legacy)
  • Fixed an issue with legacy Ingest (fw ingest) where an ingest job would get stuck in the Resolving state due to running out of memory.
  • A new duplicate code and related error message has been added to legacy Ingest duplicate detection (fw ingest ... --detect-duplicates) for better clarity.
    • The new code, DD12, addresses a scenario in which an object is skipped because there was another duplicate detection (different DD code) detect in its parent container even if the object itself had no duplicates detected.
    • In this case, the duplicate detection in the parent container needs to be located and resolved.
    • This scenario was previously reported with "UNKNOWN" instead of a DD## code and with an error message saying, Skipped due to erroneous parent container.
    • Now, this scenario will be reported as a DD12 code with an error message saying, Parent container was marked erroneous because of a DD error in another item.
  • Fixed an issue with legacy Ingest (fw ingest) where the behavior for specifying --include and --exclude flags was inconsistent.
    • With this fix, when multiple include or exclude filters are to be specified, they must be specified by repeating the entire option (name and value). Specifying one option with multiple values is no longer allowed.
    • For example, ... --include "*.dcm" --include "*.MRDC.*" is correct while --include "*.dcm" "*.MRDC.*" is incorrect.
    • This behavior applies to the --include, --exclude, --include-dirs, and --exclude-dirs options consistently.
Sync (Legacy)
  • Fixed an issue with fw sync that prevented syncing with AWS S3 storages due to an error saying 'S3File' object has no attribute 'filepath'.

Gears & Compute

  • Resolved an issue with the compute container environment (Env Variables handling and executable file status) caused by maintenance upgrades to the compute platform. This was causing certain gears to fail depending on their use of the container environment.
  • Resolved issue where custom gears were failing on Azure sites due to an issue with docker image registry.

Jupyter Workspace

  • Resolved issue with JupyterLab Read permissions appearing to be editable when making custom roles, and throwing an error on Save. It now is permanently enabled, matching other read permissions in Flywheel.

Viewer

V2 Viewer
  • Fixed an issue with the force parameter of the IO-proxy indexing endpoint, allowing files to be re-indexed even when they appear to be already properly indexed.
V3 Viewer

  • 3D segmentations:

    • Fixed an issue where clicking on a ROI would not jump to the slice associated with that ROI.
    • Users can no longer save a segmentation that does not have any ROI.
    • Fixed an issue where segmentation files could not be loaded after switching back and forth between a 2D MPR viewport and common layout 2D viewport.
    • Fixed an issue where the names of DICOM SEG files saved from the viewer included the SeriesInstanceUID instead of the StudyInstanceUID.
    • Fixed an issue where a segmentation file could not be re-loaded after closing it.
    • Other minor bug fixes

  • TMTV mode:

    • The rectangle region drawn with the rectangle ROI threshold tool can now be deleted through the right-click context menu.
    • The rectangle ROI threshold tool is now only enabled when a ROI is created and active.

Reader tasks

  • Fixed an issue where a task due date would default to Dec 31st, 1969 if left empty.

19.5.1

FIXES

Bulk Import & Export

  • Fixed an issue where Bulk Import and Export jobs would not appear to transition to the "failed" state in the case of a timeout error.
Bulk Import
  • Fixed an issue with Bulk Import using the browser-based local file upload where certain DICOM files could not be uploaded when a de-ID profile was applied even though no de-ID-related errors were present.
Bulk Export
  • Fixed an issue with Bulk Exports where the schedule details for a scheduled export job could not be viewed.
  • Fixed an issue with Bulk Export where many of the filter options (e.g., <, >, etc.) were missing and not available for use in the selection criteria for selecting which data to export.

Gears and Compute

  • Resolves issues of gears not running and gear installs failing for Azure sites due to an issue with the docker image registry.

19.5.2

FIXES

Bulk Import

  • Fixed an issue with de-identification before uploading local files via a web browser where the de-ID process would fail if the associated de-ID profile had the recurse-sequence option enabled.

CLI (Legacy)

  • Fixed an issue with fw export bids in the legacy CLI where the export would fail with an error saying, There was en error: (403) Reason: User does not have privilege is_admin.

Reader tasks

  • Fixed an issue where the file container filter would return all versions of files instead of the latest version only in the task creation menu.

Site Wide Project Catalog

  • Fixed an issue in the Site Wide Project Catalog where some filters (Project Site Catalog Age, File Type, Modality, and Measurement) would not return the expected projects.

Viewer

  • Fixed an issue where the V3 viewer would stop working when trying to load a session with a large volume of image data.

19.5.3

FIXES

Gears and Compute

  • Resolves an issue when uploading large (>5GB) files to an AWS-hosted site for customers using the self-service HPC Client.

19.5.4

FIXES

  • Resolved a build issue which prevented Flywheel Operations staff from being able to deploy 19.5.3.