Prevent slicer overwritting nrrd header.

Support
1

Hello,

I am trying to store some custom metadata in the nrrd header of my segmentation files. For example, the id of the annotator which segmented the file. The intended workflow is to:

  1. Load a nrrd segmentation file with custom header metadata into Slicer.
  2. Edit some segments.
  3. Save/Export the new segmentation file while keeping the custom metadata.

However, when I load a segmentation file into Slicer and export it again Slicer removes all metadata fields it does not recognise.

Is there a way of keeping the custom metadata while passing through Slicer?

Thanks for your help,

2

This would make sense. Instead of just passing through the data, it would be better to make the additional metadata available for reading/writing within Slicer. We already have this feature for each segment: for each segment you can store “tags” - a list of custom key/value pairs. Would it be OK if we added a single “Segmentation_tags” NRRD custom metadata field? The alternative would be to expose each unknown NRRD custom metadata field in a segmentation tag.

3

Thanks for your answer,

I noticed that even when passing metadata using the segment tags (e.g. Segment0_Tags), the metadata still gets overwritten by Slicer.

4

Segment tags are read from and written to the .seg.nrrd file. If you find that a tag is not preserved then maybe you did not use the correct format.

5

Maybe I misunderstood, this is my part of my header before going through slicer as printed by pynrrd using nrrd.read_header():

OrderedDict([...
             ('Segment0_ID', 'c05184dc-408d-428e-a95a-ec1a22e56127'),
             ('Segment0_Name', 'left-lung'),
             ('Segment0_Layer', '0'),
             ('Segment0_LabelValue', '1'),
             ('Segment0_Tags', 'AnnotatorID|asdf|'),
             ('Segment0_Color',
              '0.06274509803921569 0.9098039215686274 0.7098039215686275'),
             ...

However, after going through slicer Segment0_Tags gets overwritten to

OrderedDict([...
             ('Segment0_Color', '0.0627451 0.909804 0.709804'),
             ('Segment0_ColorAutoGenerated', '1'),
             ('Segment0_Extent', '0 98 0 67 0 27'),
             ('Segment0_ID', 'c05184dc-408d-428e-a95a-ec1a22e56127'),
             ('Segment0_LabelValue', '1'),
             ('Segment0_Layer', '0'),
             ('Segment0_Name', 'left-lung'),
             ('Segment0_NameAutoGenerated', '1'),
             ('Segment0_Tags',
              'TerminologyEntry:Segmentation category and type - 3D Slicer General Anatomy list~SCT^85756007^Tissue~SCT^85756007^Tissue~^^~Anatomic codes - DICOM master list~^^~^^|'),

What is the correct format for Segment0_Tags that ensures that custom tags will be preserved?

Thanks in advance,

6

The specification is available here:

https://slicer.readthedocs.io/en/latest/developer_guide/modules/segmentations.html#segment-custom-fields

In your example the field was discarded because you haven’t specified any key:value pairs.

1 Like
7

Thank you for clarifying, that solved the issue.
For future reference, as long as you add tags as key:value| slicer will not discard them.