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InsightSoftwareConsortium / ITK

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
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Writing DICOM Spacing Between Slices tag (0018,0088) correctly #2891

Open wwaleww opened 3 years ago

wwaleww commented 3 years ago

Description

Following this discussion, I noticed that the DICOM tag (0018,0088) - Spacing Between Slices - is not written correctly when writing an ITK image using the DICOM writing example from SimpleITK.

Expected behavior

I would expect that, just by modifying the example by adding the (0018,0088) tag in those to be modified (series_tag_values), would write an appropriate spacing value in the DICOM metadata. The modification would change as follows the concerned part of the example code:

series_tag_values = [
                            (k, reader.GetMetaData(0, k))
                            for k in tags_to_copy
                            if reader.HasMetaDataKey(0, k)] + \
                        [   # Tags to modify #
                            ("0018|0088", str(spacing)),    # Spacing Between Slices
                         ]

Actual behavior

What actually happens is that the tag is always written to 1 (even if I leave it empty) - which does not correspond to the reality of the Spacing Between Slices of my image, leading to extreme confusion in the metadata header, that could potentially be read and used by any kind of user (radiologist or not an ITK person).

Additional Information

More details on the discussion of this topic could be found in this issue.

I would be very grateful if this feature could be added in the DICOM writing procedure!

issakomi commented 2 years ago

Occasionally i have run into the same problem and have remembered this issue. I have imported enhanced MR (multi-frame) file into Slicer (4.13.0-2021-12-06-linux-amd64) DICOM database and exported (to check other things) immediately (right click at series in Data module, Export DICOM). Slicer export is classic MR series. There are so far no other problems with export (except German word Brüder was messed or maybe Specific Character Set attribute is missing). spacing

Spacing Between Slices in MR Image Storage SOP class is Type 3 and usually unused. I don't use this workflow and shall not look closer, sorry, just FYI. IMHO, the problem might be somewhere in gdcmImageHelper.cxx.

Edit: there are other minor issues with the export, not related to the actual issue, specially VR DS is too long for window center/width. I have informed Slicer team about it.

Error - Value invalid for this VR - (0x0028,0x1050) DS Window Center  DS [1] = <927.8947011975163> - Length invalid for this VR = 17, expected <= 16
Error - Value invalid for this VR - (0x0028,0x1051) DS Window Width  DS [1] = <1855.7894023950325> - Length invalid for this VR = 18, expected <= 16
Error - Dicom dataset contains invalid data values for Value Representations