Issue loading DICOM segmentation storage

[matteo-bastico]

I am trying to use the data of CTPEL dataset (https://datahub.aida.scilifelab.se/10.23698/aida/ctpel) which are stored in DICOM files. I can load sucessufully the CT images with monai.transforms.LoadImage but I get a ValueError as in the following, when I try to load the DICOM segmentation storage.

ValueError                                Traceback (most recent call last)
Input In [34], in <cell line: 1>()
----> 1 label = label_loader('0A44743795D421F7/im_3/x0000.dcm')

File ~/anaconda3/envs/segmentation/lib/python3.10/site-packages/monai/transforms/io/array.py:266, in LoadImage.__call__(self, filename, reader)
    258     raise RuntimeError(
    259         f"{self.__class__.__name__} cannot find a suitable reader for file: {filename}.\n"
    260         "    Please install the reader libraries, see also the installation instructions:\n"
    261         "    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies.\n"
    262         f"   The current registered: {self.readers}.\n{msg}"
    263     )
    265 img_array: NdarrayOrTensor
--> 266 img_array, meta_data = reader.get_data(img)
    267 img_array = convert_to_dst_type(img_array, dst=img_array, dtype=self.dtype)[0]
    268 if not isinstance(meta_data, dict):

File ~/anaconda3/envs/segmentation/lib/python3.10/site-packages/monai/data/image_reader.py:600, in PydicomReader.get_data(self, data)
    598 for d in data:
    599     if hasattr(d, "SegmentSequence"):
--> 600         data_array, metadata = self._get_seg_data(d)
    601     else:
    602         data_array = self._get_array_data(d)

File ~/anaconda3/envs/segmentation/lib/python3.10/site-packages/monai/data/image_reader.py:787, in PydicomReader._get_seg_data(self, img)
    785         metadata["labels"][class_name] = i
    786     class_num = metadata["labels"][class_name]
--> 787     all_segs[..., class_num] = frames
    789 all_segs = all_segs.transpose([1, 2, 0, 3])
    790 metadata[MetaKeys.SPATIAL_SHAPE] = all_segs.shape[:-1]

ValueError: could not broadcast input array from shape (112,512,512) into shape (176,512,512)

Is there a way to load properly that file with MONAI or do I need to convert it to another format?

Thank you for the help !

[wyli]

there's only limited DICOMsegs support, could you please try LoadImage(reader="itkreader", ...), if it doesn't work I'd recommend converting it to nifti.

(just checked that itkreader is not available on python 3.10 at the moment)

[matteo-bastico]

The itkreader does not work either, I proceeded with the conversion to NIfTI. Thank you!