Could not load series as a scalar volume

Support
1

Operating system: Mac OS
Slicer version: 5.2.2
Expected behavior: Load DICOM series as a scalar volume
Actual behavior: Does’nt load anything

So I have a MRI DWI dicom series for which a mask was created (saved as a DICOM series) using HOROS, so I only have these exported series, not the original ones. They seem to load without any problem in Horos. I would like to load the series and the mask in slicer, but it keeps throwing errors. From previous posts that were comparable I tried to install the extensions SlicerDMRI and SlicerDcm2nii but it doesn’t solve the problem, just adds more lines of failed attempts to the error. I tried loading it outside the DCM reader, this was unsuccessful. I tried the DICOM patcher, didn’t work.

The error as a pop-up: Could not load: 100: FU DWI as a Scalar Volume

And in the python console:
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-31382/SlicerDcm2nii/lib/Slicer-5.2/qt-scripted-modules/Dcm2niixPlugin.py”, line 119, in examineFiles
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[’/Applications/Slicer.app/Contents/Extensions-31382/SlicerDcm2nii/lib/Slicer-5.2/qt-scripted-modules/Resources/bin/dcm2niix’, ‘-n’, ‘-1’, ‘-s’, ‘y’, ‘-f’, ‘%p_%t_%s’, ‘-i’, ‘y’, ‘-o’, ‘/private/var/folders/4q/3ch44qxj07x_zvqj8yp635nc0000gn/T/Slicer-username/tmp5vfeq8vm’, ‘/private/var/folders/4q/3ch44qxj07x_zvqj8yp635nc0000gn/T/Slicer-username/tmp5vfeq8vm/input-dicom-files.txt’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/lib/Slicer-5.2/qt-scripted-modules/DICOMLib/DICOMUtils.py”, line 748, in getLoadablesFromFileLists
loadablesByPlugin[plugin] = plugin.examine(fileLists)
File “/Applications/Slicer.app/Contents/Extensions-31382/SlicerDcm2nii/lib/Slicer-5.2/qt-scripted-modules/Dcm2niixPlugin.py”, line 29, in examine
loadables += self.examineFiles(files)
File “/Applications/Slicer.app/Contents/Extensions-31382/SlicerDcm2nii/lib/Slicer-5.2/qt-scripted-modules/Dcm2niixPlugin.py”, line 121, in examineFiles
logging.debug(“Failed to examine files using dcm2niix: {0}”.format(e.message))
AttributeError: ‘CalledProcessError’ object has no attribute ‘message’
[Python] DICOM Plugin failed: ‘CalledProcessError’ object has no attribute ‘message’
[VTK] Unhandled PixelFormat: SamplesPerPixel :1
[VTK] BitsAllocated :15
[VTK] BitsStored :15
[VTK] HighBit :14
[VTK] PixelRepresentation:1
[VTK] ScalarType found :UNKNOWN
[VTK] Algorithm vtkITKArchetypeImageSeriesScalarReader(0x7fccd2f0fe30) returned failure for request: vtkInformation (0x6000037c2d80)
[VTK] Debug: Off
[VTK] Modified Time: 238615
[VTK] Reference Count: 1
[VTK] Registered Events: (none)
[VTK] Request: REQUEST_INFORMATION
[VTK] ALGORITHM_AFTER_FORWARD: 1
[VTK] FORWARD_DIRECTION: 0
[Python] Could not read scalar volume using GDCM approach. Error is: FileFormatError
[VTK] Unhandled PixelFormat: SamplesPerPixel :1
[VTK] BitsAllocated :15
[VTK] BitsStored :15
[VTK] HighBit :14
[VTK] PixelRepresentation:1
[VTK] ScalarType found :UNKNOWN
[VTK] Algorithm vtkITKArchetypeImageSeriesScalarReader(0x7fcd155b3680) returned failure for request: vtkInformation (0x6000034f8f00)
[VTK] Debug: Off
[VTK] Modified Time: 238710
[VTK] Reference Count: 1
[VTK] Registered Events: (none)
[VTK] Request: REQUEST_INFORMATION
[VTK] ALGORITHM_AFTER_FORWARD: 1
[VTK] FORWARD_DIRECTION: 0
[Python] Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[Python] Could not load: 100: FU DWI as a Scalar Volume

The metadata:

[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10
[0008,0008] ImageType ORIGINAL CS 8
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.4 UI 26
[0008,0018] SOPInstanceUID 1.2.826.0.1.3680043.8.498.38959781551086868487592517682093160443 UI 64
[0008,0020] StudyDate 20010101 DA 8
[0008,0021] SeriesDate 20010101 DA 8
[0008,0022] AcquisitionDate 20010101 DA 8
[0008,0030] StudyTime 120000 TM 6
[0008,0031] SeriesTime 120000 TM 6
[0008,0032] AcquisitionTime 120000 TM 6
[0008,0050] AccessionNumber 0 SH 2
[0008,0060] Modality MR CS 2
[0008,0070] Manufacturer StrokeCenter LO 20
[0008,1030] StudyDescription FU DWI LO 6
[0008,103e] SeriesDescription FU DWI LO 6
[0010,0010] PatientName UHL071 PN 6
[0010,0020] PatientID UHL071 LO 6
[0010,0030] PatientBirthDate 20010101 DA 8
[0010,0040] PatientSex M CS 2
[0018,0020] ScanningSequence RM CS 2
[0018,0021] SequenceVariant NONE CS 4
[0018,0050] SliceThickness DS 0
[0018,5100] PatientPosition HFS CS 4
[0020,000d] StudyInstanceUID 1.2.826.0.1.3680043.8.498.55099949773984100432982975104017035658 UI 64
[0020,000e] SeriesInstanceUID 1.2.826.0.1.3680043.8.498.75684090443619204850010177854450728722 UI 64
[0020,0011] SeriesNumber 100 IS 4
[0020,0013] InstanceNumber 38 IS 2
[0020,0032] ImagePositionPatient [3] -100.0, -100.0, 14.0 DS 18
[0020,0037] ImageOrientationPatient [6] 1.0, 0.0, 0.0, 0.0, 1.0, 0.0 DS 24
[0020,0052] FrameOfReferenceUID 1.2.826.0.1.3680043.8.498.25150985547740653771167800120409132909 UI 64
[0028,0002] SamplesPerPixel 1 US 2
[0028,0004] PhotometricInterpretation MONOCHROME2 CS 12
[0028,0010] Rows 512 US 2
[0028,0011] Columns 512 US 2
[0028,0030] PixelSpacing [2] 0.44726562, 0.44726562 DS 22
[0028,0100] BitsAllocated 15 US 2
[0028,0101] BitsStored 15 US 2
[0028,0102] HighBit 16 US 2
[0028,0103] PixelRepresentation 1 US 2
[0028,1052] RescaleIntercept 0.0 DS 4
[0028,1053] RescaleSlope 1.0 DS 4
[7fe0,0010] PixelData 0000 OW 524288

I have an entire dataset with this same problem. Any suggestions?

2

I noticed the SliceThickness tag had None as value, so I set it to 3 (which I checked with ImagePositionPatient, but this didn’t solve the problem

3

Be sure to check the suggestions here:

https://slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html#troubleshooting

4

Thank you for the reply but I think I tried everything on that page already. Or was there something specific you would suggest based on the errors? The only thing I didn’t post already above that was in the error logs was this:

DICOMTID1500PluginClass : Using cached files

[‘/Applications/Slicer.app/Contents/Extensions-31382/SlicerDcm2nii/lib/Slicer-5.2/qt-scripted-modules/Resources/bin/dcm2niix’, ‘-n’, ‘-1’, ‘-s’, ‘y’, ‘-f’, ‘%p_%t_%s’, ‘-i’, ‘y’, ‘-o’, ‘/private/var/folders/4q/3ch44qxj07x_zvqj8yp635nc0000gn/T/Slicer-username/tmp2sdb7xa1’, ‘/private/var/folders/4q/3ch44qxj07x_zvqj8yp635nc0000gn/T/Slicer-username/tmp2sdb7xa1/input-dicom-files.txt’]

Compression will be faster with ‘pigz’ installed Install pigz on Mac OSX - Mac App Store

Chris Rorden’s dcm2niiX version v1.0.20230210 (JP2:OpenJPEG) (JP-LS:CharLS) Clang10.0.0 x86-64 (64-bit MacOS)

Found 50 files in ‘/private/var/folders/4q/3ch44qxj07x_zvqj8yp635nc0000gn/T/Slicer-username/tmp2sdb7xa1/input-dicom-files.txt’

Found 50 DICOM file(s)

Unable to determine slice thickness: please check voxel size (was printed 50 times)

Warning: Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor.

Unsupported DICOM bit-depth 15 with 1 samples per pixel

But I’m not sure what I should do with this, if I search it I can’t find it. My apologies is a trivial problem or already answered problem but I’m rather new to slicer and can’t find the solution.

5

This seems to be the issue that makes all three, commonly used, independently developed DICOM readers (GDCM, DCMTK, dcm2niix) fail to read the image.

Most likely that HOROS created an invalid image, but at least so “special” that none of the commmonly used DICOM toolkits support it. If you upload anonymized files somewhere and post the link here then we can have a look.

If you want to save a binary mask then currently, the most appropriate DICOM format for that is Segmentation information object. I would recommend to request HOROS developers to support this information object type and use that for saving your mask.

6

If you would be willing to have a look at it that would be really helpful.
You can find a test series here: Dropbox - test_dicom - Simplify your life