@kirezgik yes, you should report that the data generated by the system is not standard-compliant, please do that, but I don’t expect a quick fix.
Since it works in OsiriX, it must be possible to figure out how to make it work in Slicer, it’s just a matter of resources. I don’t have a lot of time to spend on this today.
Do you know if I can make your dataset public? We could share it with the ITK/GDCM developers, since the problem is outside of Slicer really (but Slicer should rightfully take the full blame for the dataset not loading!)
GDCM reader fails with the same error as in Slicer:
Exception thrown while reading the series
itk::ExceptionObject (0x7ff2538696d8)
Location: "virtual void itk::ImageBase<3>::ComputeIndexToPhysicalPointMatrices() [VImageDimension = 3]"
File: /Users/fedorov/local/builds/Slicer4-Release/ITKv4/Modules/Core/Common/include/itkImageBase.hxx
Line: 187
Description: itk::ERROR: Image(0x7ff253873c90): A spacing of 0 is not allowed: Spacing is [0.3125, 0.3125, 0]
DCMTK reader works just fine, and results in a volume with slice thickness 1.3, as expected.
I will follow up with the ITK folks, but this experience, once again, begs the question - why do we rely in ITK and Slicer on GDCM and not on DCMTK?
@kirezgik are you able to build Slicer from source, or you only use the downloaded binaries?
I have a modified version of code that works for your dataset, but other people have concerns about integrating that solution into the main application, so I need to work on another approach.
@kirezgik I feel sorry to ask you to build it, since it might be easier for me to implement this feature in the extension, than for you to build Slicer. I think it is too much trouble for you. I am not sure if I can get to it this week, but if not then next week for sure.
I am trying to built the slicer again, currently I am using slicer version 4.6.2 and Viusal studio 2013 desktop with update 5, Qt 4.8.7 and CMake 3.8.1
Do you think I need to try different version of slicer?
For the branch you mentioned below, how to put it in build slicer?
You will have to check out the branch I mentioned above from GitHub, and build Slicer from scratch. Looking at the instructions [1], your setup should work.
Do you have CMake running? Do you have any anti-virus software that may prevent extraction of executable files? Can you extract the files in your user directory or desktop?
We should hopefully have it in the application sometime soon. I will followup with @pieper later this week. I think fixing this problem of failing read of scalar volume in the Slicer application should be done no matter what.
@kirezgik the issue you identified should be fixed in today’s nightly of Slicer. At least I can say I am able to load the dataset you shared without problems.