Failed to Fetch Sample from MONAI Label Server

[landynfrancis]

Hello all,

I have previously used MONAI Label several times for Active Learning and assisted annotation of 3D images within 3D Slicer. I am revisiting my previous setup, now working with 2D TIFF files.

When I try to retrieve a sample from the MONAI Label server, 3D Slicer reports that it failed to fetch the sample. After some initial research I thought it was the file format, so I converted my files to NRRDs then to NIfTIs. I am still getting the same error, see below:

There is more than one file, use the vtkITKArchetypeImageSeriesReader instead


Exception from vtkITK MegaMacro: 
itk::InvalidRequestedRegionError (0x17392150)
Location: "unknown" 
File: /work/Stable/Slicer-0-build/ITK/Modules/Core/Common/src/itkDataObject.cxx
Line: 367
Description: Requested region is (at least partially) outside the largest possible region.





Algorithm vtkITKArchetypeImageSeriesScalarReader (0x144065b0) returned failure for request: vtkInformation (0x173a3990)
  Debug: Off
  Modified Time: 211076
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0




vtkMRMLStorageNode::ReadData: Failed to read node FILENAME (vtkMRMLMultiVolumeNode1) from filename=PATH


ReadData: This is not a nrrd file


vtkMRMLStorageNode::ReadData: Failed to read node FILENAME  (vtkMRMLDiffusionWeightedVolumeNode1) from filename=PATH


vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read file as a volume of type DiffusionTensorVolume [fullName = PATH]: FileFormatError. Number of files listed in the node = 0. File reader says it was able to read 530 files. File reader used the archetype file name of PATH [reader 0th file name = PATH].


vtkMRMLStorageNode::ReadData: Failed to read node FILENAME (vtkMRMLDiffusionTensorVolumeNode1) from filename=PATH


ReadData: This is not a nrrd file


vtkMRMLStorageNode::ReadData: Failed to read node FILENAME (vtkMRMLVectorVolumeNode1) from filename=PATH


vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Failed to instantiate a file reader


vtkMRMLStorageNode::ReadData: Failed to read node FILENAME (vtkMRMLVectorVolumeNode2) from filename=PATH


vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read file as a volume of type Volume [fullName = PATH]: FileFormatError. Number of files listed in the node = 0. File reader says it was able to read 530 files. File reader used the archetype file name of PATH [reader 0th file name = PATH].


vtkMRMLStorageNode::ReadData: Failed to read node FILENAME (vtkMRMLScalarVolumeNode1) from filename=PATH

I have redacted full filenames and file paths for privacy reasons, but they are all files named as follows {NAME}-{133-650}. It seems like Slicer is trying to load the entire series of images in the folder instead of the single one MONAI Label is providing.

MONAI Label's output looks like:

[2025-01-16 09:07:24,825] [28630] [MainThread] [INFO] (monailabel.endpoints.activelearning:44) - Active Learning Request: {'strategy': 'random', 'client_id': 'user-xyz'}

[2025-01-16 09:07:24,840] [28630] [MainThread] [INFO] (monailabel.tasks.activelearning.random:47) - Random: Selected Image: FILENAME; Weight: 1737036444

[2025-01-16 09:07:24,846] [28630] [MainThread] [INFO] (monailabel.endpoints.activelearning:60) - Next sample: {'id': 'FILENAME', 'weight': 1737036444, 'path': PATH, 'ts': 1737036220, 'name': FILENAME}

Any help with solving this bug would be appreciated, as MONAI Label is an incredibly useful tool, made useless if I can't fetch samples.