Dec 22 2022
Dec 19 2022
Dec 16 2022
Without a data sample we are not able to reproduce this issue. Can you upload one of these nrrd files? Please make sure that the data does not contain any personal information. You can also restrict access to uploaded files to certain users like me.
Dec 14 2022
Unfortunately, it is all nrrd files. I updated my nvidia drivers and it seems to have improved slightly in that it doesn't crash within moments of loading a base nrrd file, but after I create, save and remove a segmentation nrrd, MITK Workbench crashes when I try to reload (open) the segmentation nrrd.
Dec 13 2022
Thanks for reporting. We are not aware of any crash like this with valid nrrd files. Since ITK snap crashes as well it could be a strong indicator that the crash is happening in the ITK reader that we use as well. It could be probably related to a corrupt nrrd file, or, in case it is a huge file, it could be simply related to running out of memory. Anyway, without the data we are not able to reproduce this issue.
Nov 30 2022
Nov 25 2022
Nov 24 2022
Example data
Nov 23 2022
Which data has been used to provoke the problem.
Nov 9 2022
Unfortunately not solved. Same error.
Oct 25 2022
Oct 21 2022
I guess the second issue is not yet fixed and will be covered in T29369: [Segmentation Utilities] Handle / select different labels independently.
Oct 19 2022
We discussed this and we decided to remove the options from the preferences completely. That means, that
- the user cannot change the smoothing hint / value
- the user cannot change the decimation rate
- the checklists don't need to ask for changing these values
- the smoothing will use the default values (set inside QmitkCreatePolygonModelAction::Run)
- "smoothing hint" = true (will always use image spacing as hint)
- "smoothing value" = 1.0
- "decimation rate" = 0.5
- "closing ratio" was not used at all
- note that different default values are given in ShowSegmentationAsSurface::Initialize (and other functions of this class), but are overwritten / reset by the polygon action.
I think it actually is an issue or at least unexpected. The level window seems to have trouble with color images in general.
Oct 18 2022
I looked into this and can verify that there is no visible effect when changing the decimation rate. The property "Decimation rate" is correctly used inside ShowSegmentationAsSurface::ConvertBinaryImageToSurface as reductionRate. It is then used as an argument for ImageToSurfaceFilter::SetTargetReduction. The brief description of this parameter is:
Oct 17 2022
Oct 14 2022
Same for Windows 10, Ubuntu 20.04, and Ubuntu 22.04.
Oct 13 2022
On MacOS Monterey, the level window default values for the image are 83, 226.
As far as I can tell, this is the expected behavior. Any voxel that has a (greyscale) value above the level-window range is shown completely white. The colors only extend this to multiple channels, but the behavior is still the same. So with very low level-window, the colors are expected to stay visible very strongly
We need information of the minimal setup to reproduce the problem.
Needs more investigation, how and why the values are different. Naive assumption would be that they should be the same.
Verify if it is a code or a teaching problem
We should double-check if there's really a bug as there's a good chance that it was just misunderstood how it works. Everything that's not covered by the level window is supposed to be transparent. We should probably improve the checklist to be more clear.
Please double check, if there is realy an error with Jet Transparent (or with the checklist). And on which systems.
Oct 10 2022
Sep 28 2022
Thank you 🙏
Sep 27 2022
thank you for looking into that matter.
Our side or also the CTK part.
I looked into the dicombrowser plugin and found out that the directory on Windows is something like %APPDATA%/../Local/Temp/TmpDicomFolder.************. However I didn't see pop up any files after retrieve.
Sep 23 2022
I just tried to retrieve data from dicomserver.co.uk and I am able to query and kind of retrieve data. A repeated retrieve even tells me that existing files are overriden. At least that is what the console output tells me. But where are the retrieved images supposed to be stored? And shouldn't the retrieved images appear somewhere in the DICOM editor?
Sep 21 2022
To make our live a bit easier. I would say it is a data problem ;).