Hi,
Recently I started using Slicer (4.10.2) to extract some radiomics features from MRI images using the radiomics module, but every time I try to import some DICOMs through the DICOM manager, I get a lot of warnings; then if I load the exam, a list of “could not load as scalar volume” comes out. I already tried DICOM patcher and nothing changed. I tried GDCM, DCMTK and Archetype. Files aren’t anonymized, since I read it was another possible issue. I know that another things is that they could be corrupted, but if that’s the case, that would mean that every exported exam is the same.
Hi, since I’m actually travelling back and forth for my work, I cannot always access to all my data, that’s the reason I was this late in answering.
The error data log is the following, and it seems it repeats a lot, this is only part of it since the whole thing is exceeding the word limit of the post.
[ERROR][Python] 21.07.2019 12:52:39 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:38 [] (unknown:0) - Loading with imageIOName: GDCM
[ERROR][VTK] 21.07.2019 12:52:39 [vtkITKArchetypeImageSeriesScalarReader (0000000010174DC0)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000406. ITK exception info: error in unknown: Could not create IO object for reading file G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000406
Tried to create one of the following:
BMPImageIO
BioRadImageIO
DCMTKImageIO
GDCMImageIO
GiplImageIO
JPEGImageIO
LSMImageIO
MGHImageIO
MINCImageIO
MRCImageIO
MetaImageIO
NiftiImageIO
NrrdImageIO
PNGImageIO
StimulateImageIO
TIFFImageIO
VTKImageIO
MRMLIDImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
[ERROR][VTK] 21.07.2019 12:52:39 [vtkCompositeDataPipeline (000000001674DF90)] (D:\D\S\Slicer-4102-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:782) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000000010174DC0) returned failure for request: vtkInformation (0000000015D7A750)
Debug: Off
Modified Time: 338830
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 21.07.2019 12:52:39 [] (unknown:0) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:39 [] (unknown:0) - Loading with imageIOName: DCMTK
[ERROR][VTK] 21.07.2019 12:52:39 [vtkITKArchetypeImageSeriesScalarReader (0000000010175170)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000406. ITK exception info: error in unknown: Could not create IO object for reading file G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000406
Tried to create one of the following:
BMPImageIO
BioRadImageIO
DCMTKImageIO
GDCMImageIO
GiplImageIO
JPEGImageIO
LSMImageIO
MGHImageIO
MINCImageIO
MRCImageIO
MetaImageIO
NiftiImageIO
NrrdImageIO
PNGImageIO
StimulateImageIO
TIFFImageIO
VTKImageIO
MRMLIDImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
[ERROR][VTK] 21.07.2019 12:52:39 [vtkCompositeDataPipeline (0000000016749DF0)] (D:\D\S\Slicer-4102-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:782) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000000010175170) returned failure for request: vtkInformation (0000000015D7DD60)
Debug: Off
Modified Time: 338913
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 21.07.2019 12:52:39 [] (unknown:0) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Python] 21.07.2019 12:52:39 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: GDCM
[ERROR][Python] 21.07.2019 12:52:39 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Python] 21.07.2019 12:52:39 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: DCMTK
[ERROR][Python] 21.07.2019 12:52:40 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:39 [] (unknown:0) - Loading with imageIOName: GDCM
[ERROR][VTK] 21.07.2019 12:52:39 [vtkITKArchetypeImageSeriesScalarReader (0000000010174DC0): vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/000000D7. ITK exception info: error in unknown: itk::ERROR: GDCMImageIO(00000000107B4A60)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - Cannot read requested file
[ERROR][VTK] 21.07.2019 12:52:39 [vtkCompositeDataPipeline (0000000016750510)] (D:\D\S\Slicer-4102-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:782) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000000010174DC0) returned failure for request: vtkInformation (0000000015D7E850)
Debug: Off
Modified Time: 340155
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 21.07.2019 12:52:39 [] (unknown:0) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:39 [] (unknown:0) - Loading with imageIOName: DCMTK
[ERROR][VTK] 21.07.2019 12:52:40 [vtkITKArchetypeImageSeriesScalarReader (0000000010175170): vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/000000D7. ITK exception info: error in unknown: itk::ERROR: GDCMImageIO(00000000107B4610)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - Cannot read requested file
[ERROR][VTK] 21.07.2019 12:52:40 [vtkCompositeDataPipeline (00000000167536C0)] (D:\D\S\Slicer-4102-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:782) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000000010175170) returned failure for request: vtkInformation (0000000015D7D720)
Debug: Off
Modified Time: 340249
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 21.07.2019 12:52:40 [] (unknown:0) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Python] 21.07.2019 12:52:40 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: GDCM
[ERROR][Python] 21.07.2019 12:52:40 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Python] 21.07.2019 12:52:40 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: DCMTK
[ERROR][Python] 21.07.2019 12:52:40 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:40 [] (unknown:0) - Loading with imageIOName: GDCM
[ERROR][VTK] 21.07.2019 12:52:40 [vtkITKArchetypeImageSeriesScalarReader (0000000010174DC0): vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000282. ITK exception info: error in unknown: itk::ERROR: GDCMImageIO(00000000107B4A60)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - Cannot read requested file
[ERROR][VTK] 21.07.2019 12:52:40 [vtkCompositeDataPipeline (00000000167538A0)] (D:\D\S\Slicer-4102-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:782) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000000010174DC0) returned failure for request: vtkInformation (0000000015D7F020)
Debug: Off
Modified Time: 340342
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 21.07.2019 12:52:40 [] (unknown:0) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:40 [] (unknown:0) - Loading with imageIOName: DCMTK
[ERROR][VTK] 21.07.2019 12:52:40 [vtkITKArchetypeImageSeriesScalarReader (0000000010175170): vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000282. ITK exception info: error in unknown: itk::ERROR: GDCMImageIO(00000000107B4610)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - Cannot read requested file
[ERROR][VTK] 21.07.2019 12:52:40 [vtkCompositeDataPipeline (0000000016753A80)] (D:\D\S\Slicer-4102-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:782) - Algorithm vtkITKArchetypeImageSeriesScalarReader(0000000010175170) returned failure for request: vtkInformation (0000000015D7D6D0)
Debug: Off
Modified Time: 340436
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
[CRITICAL][Stream] 21.07.2019 12:52:40 [] (unknown:0) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Python] 21.07.2019 12:52:40 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: GDCM
[ERROR][Python] 21.07.2019 12:52:41 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using GDCM approach. Error is: FileFormatError
[INFO][Python] 21.07.2019 12:52:41 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: DCMTK
[ERROR][Python] 21.07.2019 12:52:41 [Python] (G:/3d Slicer/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:309) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError
[INFO][Stream] 21.07.2019 12:52:40 [] (unknown:0) - Loading with imageIOName: GDCM
[ERROR][VTK] 21.07.2019 12:52:41 [vtkITKArchetypeImageSeriesScalarReader (0000000010174DC0)] (D:\D\S\Slicer-4102\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx:408) - vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000408. ITK exception info: error in unknown: Could not create IO object for reading file G:/1 Pre-PT/Avila 29-10-2018/DICOMOBJ/00000408
This may be very trivial but could you try using a directory that does not have a space in the path? I see that there are a few like “1 Pre-PT” and “Avila 29-10-2018”, and space may be a problem, similarly to how special characters are a problem.
Thank you for the suggestion, but it doesn’t seems to work. I noticed (opening up the DICOMs in another reader) that some mri sequences folders (for example T2) are empty, but there other folders named differently which contains the data. If I look at advanced settings in Dicom importer in slicer, I can select these series (that are unselected by default) and this seems to solve the problem in some cases.