Writing DICOM Spacing Between Slices

Beginner Questions
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1

Hello,

I’m trying to write a DICOM series after some image processing, and to do that I’m following the code in the example.

Since I upsampled the volume, the spacing between slices has changed and I added it to the tags to be modified, here is an extract of the code (after having loaded a sitk image, img, and its metadata, reader):

# Initialize writer object
writer = sitk.ImageFileWriter()
    
# Use the study/series/frame of reference information given in the meta-data
# dictionary and not the automatically generated information from the file IO
writer.KeepOriginalImageUIDOn()
    
# Copy all the DICOM tags from the first slice
tags_to_copy = reader.GetMetaDataKeys( 0 )
    
# Get spacing between slices (DICOM tag "0018|0088")
spacing = img.GetSpacing()[2]
    
# Create list of tuples (tag, values), and add the ones to modify
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
                         ]
    
# Save DICOM slices                
for i in range( img.GetDepth() ):
        image_slice = img[:, :, i]
        
        # Tags shared by the series.
        for tag, value in series_tag_values:
            image_slice.SetMetaData(tag, unidecode.unidecode(value))
            
        # Slice specific tags.
        #   Instance Creation Date
        image_slice.SetMetaData("0008|0012", time.strftime("%Y%m%d"))
        #   Instance Creation Time
        image_slice.SetMetaData("0008|0013", time.strftime("%H%M%S"))
        #   Instance Number
        image_slice.SetMetaData("0020|0013", str(i))
        #   Image Position (Patient)
        image_slice.SetMetaData("0020|0032", '\\'.join(
            map(str, volume.TransformIndexToPhysicalPoint((0, 0, i)))))
        # In-Stack Position Number
        image_slice.SetMetaData("0020|9057", str(i))
        
        # Write to the output directory and add the extension dcm, to force writing
        # in DICOM format.
        writer.SetFileName( os.path.join( saving_directory, "IM-" + str(i).zfill(4) + '.dcm') )
        writer.Execute(image_slice)

The problem is, if I print the SpacingBetweenSlices metadata juste before the writer execution,
by image_slice.GetMetaData("0018|0088"), I get the correct spacing, but once the whole volume is written the spacing between slices tag is always changed to 1.

Do you have any clue of what I could be doing wrong?
Thanks!

2

Only the “Image Position Patient” and “Image Orientation Patient” tags are taken into account when a volume is reconstructed from slices. See this classic for details.

Since (0018,0088) “Spacing Between Slices” tag is generally not used and it is a type 3 (optional) DICOM field, I would recommend to just not include it in the output image.

3

Thanks for your reply, but since I have a full volume of images and not just one slice, in my case having the right Spacing Between Slices is key to know the full physical dimensions of my volume (Image Position Patient and Orientation are not sufficient to evaluate the full volume dimensions).
I’m aware that it is different from the slice thickness tag, and I know how to deal with it, but I would really like to put the correct Spacing Between Slices tag in my DICOM series.

Do you think then that it is not possible with the SimpleITK writer?

4

Value of “spacing between slices” tag does not affect the physical dimensions of your volume and it does not add anything to the spacing implicitly stored by using “image position patient” tags.

5

The problem is, that even if I leave the tag empty, i.e. if I change the code I put on the top with this line:

# Create list of tuples (tag, values), and add the ones to modify
series_tag_values = [
                            (k, reader.GetMetaData(0, k))
                            for k in tags_to_copy
                            if reader.HasMetaDataKey(0, k)] + \
                        [   # Tags to modify #
                            ("0018|0088", "",    # Spacing Between Slices
                         ]

the tag value is changed to 1 when the DICOM image is written, so I suspect a bug in the library.
Does anyone have an explication, or shall I open an issue on github?

Thanks a lot!

6

for reference this seems to have been reported in Writing DICOM Spacing Between Slices tag (0018,0088) correctly · Issue #2891 · InsightSoftwareConsortium/ITK · GitHub