I need help: Encountered "Could not load ... as a scalar volume" when loading MRI sequence

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1

Dear developer,
Hello~
When I loaded the MRI image sequence today, the software kept reporting errors, “Could not load: 23: t1_quick3d_tra_fs_bh_P_MPRTRA as a Scalar Volume”, but there was no problem when loading CT images. The specific log is as follows. I have searched but failed to solve the problem, I hope you can get help, thank you!

[INFO][Python] 04.10.2023 13:24:06 [Python] (F:/3D SLICER/Slicer 5.0.2/bin/…/lib/Slicer-5.0/qt-scripted-modules/DICOMScalarVolumePlugin.py:391) - Loading with imageIOName: GDCM
[ERROR][Python] 04.10.2023 13:24:06 [Python] (F:/3D SLICER/Slicer 5.0.2/bin/…/lib/Slicer-5.0/qt-scripted-modules/DICOMScalarVolumePlugin.py:397) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Python] 04.10.2023 13:24:06 [Python] (F:/3D SLICER/Slicer 5.0.2/bin/…/lib/Slicer-5.0/qt-scripted-modules/DICOMScalarVolumePlugin.py:391) - Loading with imageIOName: DCMTK
[ERROR][Python] 04.10.2023 13:24:06 [Python] (F:/3D SLICER/Slicer 5.0.2/bin/…/lib/Slicer-5.0/qt-scripted-modules/DICOMScalarVolumePlugin.py:397) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[WARNING][Python] 04.10.2023 13:24:06 [Python] (F:\3D SLICER\Slicer 5.0.2\bin\Python\slicer\util.py:2610) - Could not load: 23: t1_quick3d_tra_fs_bh_P_MPRTRA as a Scalar Volume
[INFO][Stream] 04.10.2023 13:24:06 (unknown:0) - Loading with imageIOName: GDCM
[ERROR][VTK] 04.10.2023 13:24:06 [vtkITKArchetypeImageSeriesScalarReader (0000024173E28540)] (D:\D\S\S-0\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:517) - vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/2023-6 影像收集/何宏硕20210119 间隔时间长/20200408腹部MRI/51DT35BB/UTBCMUPO/I4100000. ITK exception info: error in unknown: ITK ERROR: Pixel type larger than output type
[ERROR][VTK] 04.10.2023 13:24:06 [vtkCompositeDataPipeline (000002417DC7DA40)] (D:\D\S\S-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:741) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000024173E28540) returned failure for request: vtkInformation (00000241166BD3F0)
Debug: Off
Modified Time: 71921732
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 04.10.2023 13:24:06 (unknown:0) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Stream] 04.10.2023 13:24:06 (unknown:0) - Loading with imageIOName: DCMTK
[ERROR][VTK] 04.10.2023 13:24:06 [vtkITKArchetypeImageSeriesScalarReader (0000024173E29440)] (D:\D\S\S-0\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:517) - vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/2023-6 影像收集/何宏硕20210119 间隔时间长/20200408腹部MRI/51DT35BB/UTBCMUPO/I4100000. ITK exception info: error in unknown: ITK ERROR: Pixel type larger than output type
[ERROR][VTK] 04.10.2023 13:24:06 [vtkCompositeDataPipeline (000002417DC7DC40)] (D:\D\S\S-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:741) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000024173E29440) returned failure for request: vtkInformation (00000241166C0460)
Debug: Off
Modified Time: 71921838
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 04.10.2023 13:24:06 (unknown:0) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[CRITICAL][Stream] 04.10.2023 13:24:06 (unknown:0) - Could not load: 23: t1_quick3d_tra_fs_bh_P_MPRTRA as a Scalar Volume

2

It seems that the data set is invalid. The issue looks very similar to this one:

Probably the image has not come straight from the scanner but it was processed/anonymized, which corrupted its content.

1 Like
3

Thank you very much !
However, I am very sorry that I am still a rookie in using 3Dslicer. May I ask where I can find the repair tool “dcmodify.exe”? Do I run every file in the dicom folder?

4

dcmodify is part of the dcmtk set of DICOM tools https://dicom.offis.de/dcmtk.php.en and you will need to run it for all affected files.

You could also try using gdcmconv from the gdcm DICOM toolkit https://sourceforge.net/projects/gdcm/ as it can automatically correct some issues during conversion. The Ubuntu man page has a section on usage Ubuntu Manpage: gdcmconv - Tool to convert DICOM to DICOM.

1 Like
5

Thank you! I will try it.