Cannot open custom highdicom derived SC DICOM in ITK-Snap

[tomaroberts]

Hi – I'm not super familiar with highdicom; this seems like a fairly straightforward problem but I've not managed to find solution to my issue in the docs or existing Issues, so apologies if I've missed it.

I'm basically trying to write a 3D singleframe .dcm dataset following the second code block in the tutorial here. I have no segmentation overlay, so I've removed those parts.

My adapted code snippet is below:

import highdicom as hd
import nibabel as nib
import numpy as np
import os

input_nii_path = r'/path/to/niifile.nii/gz.nii.gz'
output_dcm_path = r'/path/to/output_dcm_folder'
os.mkdir(output_dcm_path)

nii = nib.load(input_nii_path)

# get pixel data from NIfTI
nii_img = nii.get_fdata()
nii_img = nii_img.astype("uint16")  # match DICOM datatype

pixel_spacing = [1.0, 1.0]
sz = nii_img.shape[2]
print(f'nii_img sz: {sz}')

series_instance_uid = hd.UID()
study_instance_uid = hd.UID()

patient_orientation=['L', 'P']

for iz in range(sz):
    this_slice = nii_img[:, :, iz]

    pixel_array = this_slice

    # Create the secondary capture image
    sc_image = hd.sc.SCImage(
        pixel_array=pixel_array.astype(np.uint16),  #originally uint8 in tutorial
        photometric_interpretation=hd.PhotometricInterpretationValues.MONOCHROME2,
        bits_allocated=16,  # originally 8 in tutorial
        coordinate_system=hd.CoordinateSystemNames.PATIENT,
        study_instance_uid=study_instance_uid,
        series_instance_uid=series_instance_uid,
        sop_instance_uid=hd.UID(),
        series_number=100,
        instance_number=iz + 1,
        manufacturer='Manufacturer',
        pixel_spacing=pixel_spacing,
        patient_orientation=patient_orientation,
    )

    sc_image.save_as(os.path.join(output_dcm_path, 'sc_output_' + str(iz) + '.dcm'))

When I try to open this in ITK-Snap, it errors with the following:

My input NIFTI dataset is derived from MRI data, hence MONOCHROME2 and BitsAllocation = 16. When I opened the DICOMs in MITKWorkbench, it also failed and indicated an orientation problem, so I tried manually adding ImageOrientationPatient = (e.g.) ['1', '0', '0', '0', '1', '0'] but that has not helped.

Here's a dump of the DICOM metadata:

Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length  UL: 210
(0002, 0001) File Meta Information Version       OB: b'\x00\x01'
(0002, 0002) Media Storage SOP Class UID         UI: Secondary Capture Image Storage
(0002, 0003) Media Storage SOP Instance UID      UI: 1.2.826.0.1.3680043.10.511.3.40792569118819711334400295680320982
(0002, 0010) Transfer Syntax UID                 UI: Explicit VR Little Endian
(0002, 0012) Implementation Class UID            UI: 1.2.826.0.1.3680043.9.7433.1.1
(0002, 0013) Implementation Version Name         SH: 'highdicom0.21.1'
-------------------------------------------------
(0008, 0008) Image Type                          CS: ['DERIVED', 'SECONDARY', 'OTHER']
(0008, 0016) SOP Class UID                       UI: Secondary Capture Image Storage
(0008, 0018) SOP Instance UID                    UI: 1.2.826.0.1.3680043.10.511.3.40792569118819711334400295680320982
(0008, 0020) Study Date                          DA: None
(0008, 0023) Content Date                        DA: "20230807"
(0008, 0030) Study Time                          TM: None
(0008, 0033) Content Time                        TM: "131553.080334"
(0008, 0050) Accession Number                    SH: None
(0008, 0060) Modality                            CS: 'OT'
(0008, 0064) Conversion Type                     CS: 'DI'
(0008, 0070) Manufacturer                        LO: 'Manufacturer'
(0008, 0090) Referring Physician's Name          PN: None
(0010, 0010) Patient's Name                      PN: None
(0010, 0020) Patient ID                          LO: None
(0010, 0030) Patient's Birth Date                DA: None
(0010, 0040) Patient's Sex                       CS: None
(0018, 1012) Date of Secondary Capture           DA: "20230807"
(0018, 1014) Time of Secondary Capture           TM: "131553.080376"
(0020, 000d) Study Instance UID                  UI: 1.2.826.0.1.3680043.10.511.3.47134193835689979621889364632875485
(0020, 000e) Series Instance UID                 UI: 1.2.826.0.1.3680043.10.511.3.30353553887687175567028695251528949
(0020, 0010) Study ID                            SH: None
(0020, 0011) Series Number                       IS: '100'
(0020, 0013) Instance Number                     IS: '129'
(0020, 0020) Patient Orientation                 CS: ['L', 'P']
(0020, 0035) Image Orientation                   DS: [1, 0, 0, 0, 1, 0]
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0010) Rows                                US: 146
(0028, 0011) Columns                             US: 146
(0028, 0030) Pixel Spacing                       DS: [1.0, 1.0]
(0028, 0100) Bits Allocated                      US: 16
(0028, 0101) Bits Stored                         US: 16
(0028, 0102) High Bit                            US: 15
(0028, 0103) Pixel Representation                US: 0
(7fe0, 0010) Pixel Data                          OW: Array of 42632 elements

Thanks in advance.