niftiwrapper IO about dcmstack HOT 8 CLOSED

@bpinsard, you might want to take a look at our fork of dcmstack at https://github.com/IBIC/dcmstack that has some support for Philips Enhanced DICOM. Hoping to get these changes incorporated into the main branch of dcmstack soon.

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I haven't seen this before. Could you send me the JSON? For example you could do "nitool dump myfile.nii.gz > myjson.txt".

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I had tried the guess-dim branch directly on the enhanced data but the same thing happens.
here are the lines I extracted that make json library crash at loading:

            "DimensionIndexSequence": [
                {
                    "DimensionOrganizationUID": "2.16.124.113543.6006.99.02479373120167955565", 
                    "DimensionIndexPointer": (0020, 9056), 
                    "FunctionalGroupPointer": (0020, 9111)
                }, 
                {
                    "DimensionOrganizationUID": "2.16.124.113543.6006.99.02479373120167955565", 
                    "DimensionIndexPointer": (0020, 9057), 
                    "FunctionalGroupPointer": (0020, 9111)
                }
            ], 

maybe these self referential dicom tags code are the problem?

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It looks like those tags are not being serialized correctly. What is the VR of those elements?

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the VR is AT

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Could you test the referenced branch, I think it should fix the issue. You will need to reconvert the files.

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it works, thanks, maybe these tags should be filtered out as they do refers to dicoms ?

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OK, merged it into master.

Currently, the default filtering is just intended to remove PHI. It should however be easy enough to filter any tag with a given VR if a user wants that.

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