Segmentations oblique to the acquisition plane of the source data are not yet supported

[Jun Xian]

Hello,

I was trying to run MONAILabel inference on a dicom scan, the inference runs smoothly without errors, but the output segmentation was not displayed on the viewer. In the console log, this error appeared.

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Initially i thought this would be a simple fix by changing the ImageOrientationPatient, rounding it to 1 and 0’s. But that doesn’t seem to work.

I have also opened an issue on monailabel’s repo: https://github.com/Project-MONAI/MONAILabel/issues/1336#issuecomment-1622914349

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[Mo Alsad]

Hi Jun,

Do the ImageOrientationPatient values are the same for all the frames in the DICOM dataset?

Kind regards,

Mo

[Jun Xian]

Hello Mo,

ImageOrientationPatient stays constant throughout the entire scan

ImagePositionPatient values are not the same

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Example:
First slice

Next slice

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Next slice

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[Mo Alsad]

I need to look into this further. Would you please be able to share the DICOM files?

[Jun Xian]

Can you give me your email please so I could send it to you?

[Jun Xian]

Anyway i have attached the dicom file in this zip folder here.

The segmentation output in nifti format here
The segmentation output in dcm format converted through 3D Slicer here

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This is CQ296 from CQ500 dataset, nifti converted to dicom files through 3D Slicer here

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[Jun Xian]

The segmentation output displays fine on https://v3-demo.ohif.org/local

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[Mo Alsad]

Thanks Jun, I will try to reproduce the issue and fix it. Will get back to you shortly.

[Jun Xian Tan]

Hello Mo, were you able to reproduce this error? I have been editing different tags and their values and I cant seem to find a workaround.

[Jun Xian]

I was modifying some dicom tags, trying to make it work, these are the dicom tags which i have edited on my end:

# Calculate the direction cosines for the image orientation
direction_cosines = reference_file.ImageOrientationPatient
row_cosine = [float(direction_cosines[0]), float(direction_cosines[1]), float(direction_cosines[2])]
column_cosine = [float(direction_cosines[3]), float(direction_cosines[4]), float(direction_cosines[5])]

for i, ds in enumerate(dicom_files):
    # Calculate the new ImagePositionPatient values using the slice number and direction cosines
    new_position = [(i + 1) * row_cosine[j] + ds.ImagePositionPatient[j] * column_cosine[j] for j in range(3)]
    # Update the ImagePositionPatient values for the current DICOM file
    ds.ImagePositionPatient = new_position
    # To ensure order of slices 
    ds.ImagePositionPatient[2] = ds.InstanceNumber

    ds.ImageOrientationPatient = [1,0,0,0,1,0]
    ds.ImageType = ['ORIGINAL', 'PRIMARY', 'AXIAL']
    ds.PatientOrientation = ['L', 'P']

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I haven’t tested it out on more scans yet, would anyone be able to confirm that this is one of the way to solve the oblique issue?

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[Jun Xian Tan]

So i figured the main issue was just the dicom metadata being corrupted / bad so some kind of editing was required. We can close this issue