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Maniphest T27554

Handling of 2D and 2D+t sonographic (US) images
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Description

For a segmentation project with sonographic images we would like to create the ground truth using MITK. We have images from different vendors and in different formats, i.e. "normal" 2D stills and "movies" 2D+t.

I noticed the following while using the dicom data with MITK:

  • The Canon images (stills) cannot be read (see screenschot attached)
  • Philipps movies and Canon movies can be read without error. However, they are displayed a) turquoise and b) as a 3D volume (which sort of is correct)
  • Phillips stills can be read without error, but are also colored in turquoise (although the colormap is set to grayscale, changing the colormap does not have an impact). Adjusting the levelwindowing is not easy / hardly possible wrt finding optimal thresholds for segmentation
  • Multilabel segmentation is for neither vendor or format available (series does not show up in drop down for "Patient Image"

Attached are the various images and formats, hopefully named in a self-explanatory way.

US Testbilder.zip34 MBDownload

Tested using MITK v2018.04.2 for Mac (newest binary from the webpage)

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Event Timeline

kleesiek created this task.Jul 13 2020, 12:45 PM
kleesiek added a subscriber: floca.Jul 16 2020, 2:07 PM
nolden added a project: Restricted Project.Jul 16 2020, 2:08 PM

Added FS-E IT since this is coming from DKFZ radiology

floca removed kislinsk as the assignee of this task.Jul 19 2020, 2:39 PM

As this task containes multiple issues/tasks, I have splitt it in sub tasks. This meta task will be closed as the work will be done in the sub tasks.

floca mentioned this in T27568: US 2D image cannot be read: invalid tilt information.Jul 19 2020, 3:03 PM
floca mentioned this in T27569: US DICOM images are displayed turquoise and LUT cannot be changed.Jul 19 2020, 3:08 PM
floca mentioned this in T27570: US DICOM images are read as 3D volume.Jul 19 2020, 3:22 PM
floca mentioned this in T27571: Multilabel segmentation does not work with US DICOM images.Jul 19 2020, 3:26 PM
floca closed this task as Resolved.Jul 19 2020, 3:28 PM
floca claimed this task.

Spawned concrete tasks for each problem.

kislinsk closed subtask T27570: US DICOM images are read as 3D volume as Wontfix.Mar 10 2021, 9:02 AM
floca reopened subtask T27570: US DICOM images are read as 3D volume as Open.Mar 10 2021, 9:48 AM
floca closed subtask T27571: Multilabel segmentation does not work with US DICOM images as Invalid.Jul 27 2021, 9:59 AM
kislinsk closed subtask T27570: US DICOM images are read as 3D volume as Wontfix.Oct 14 2021, 11:39 AM
floca reopened subtask T27570: US DICOM images are read as 3D volume as Open.Oct 14 2021, 11:57 AM
kislinsk closed subtask T27570: US DICOM images are read as 3D volume as Wontfix.Apr 29 2022, 1:44 PM
floca reopened this task as Open.Apr 29 2022, 3:04 PM
floca reopened subtask T27570: US DICOM images are read as 3D volume as Open.
kislinsk triaged this task as Normal priority.May 5 2022, 9:41 AM
floca closed subtask T27569: US DICOM images are displayed turquoise and LUT cannot be changed as Wontfix.Feb 20 2023, 9:51 AM
floca changed the status of subtask T27569: US DICOM images are displayed turquoise and LUT cannot be changed from Wontfix to Resolved.
kislinsk closed subtask T27568: US 2D image cannot be read: invalid tilt information as Wontfix.May 17 2023, 2:59 PM
kislinsk closed subtask T27570: US DICOM images are read as 3D volume as Wontfix.
floca reopened subtask T27570: US DICOM images are read as 3D volume as Open.May 17 2023, 5:03 PM
floca reopened subtask T27568: US 2D image cannot be read: invalid tilt information as Open.May 17 2023, 5:07 PM
kislinsk closed subtask T27570: US DICOM images are read as 3D volume as Wontfix.Dec 5 2023, 10:45 AM
floca removed floca as the assignee of this task.Thu, Apr 18, 4:38 PM
MITK · MIC · IMSY · DKFZ