Operating system : ubuntu 16.04
Slicer version:4.8.1
Expected behavior:Load DTI data from dicom files.
Actual behavior:
Hi,I am new to 3dSlicer , and I failed to load DTI files which from Hospital’s DVD(from Manufacturer SIEMENS).
the file structure is like this:
dicom
|-----18032098/
|------58020000
| |----dcm1
| |----dcm2
| |----dcm...
|------58020001
| |----dcm1
| |----dcm2
| |----dcm...
I install slicerDMRI module and i want to load dti files to reconstruct Neural.
I select the checkbox named “DICOMScalarVolumePlugin” + “MultiVolumeImportedPlugin” + “DicomRtimportPlugin”.
when I Click the examine button to check all the files.It shows some warning: "Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. Reference image in series does not contain geometry information. Please use caution. "
------------------------------------------------error---------------------------------
all info about error in python interactor:
reg inside examine
Warning in DICOM plugin Scalar Volume when examining loadable 17: ep2d_diff_mddw_64_cor_TENSOR_TRACEW_MAP_BValue_700: Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. Reference image in series does not contain geometry information. Please use caution.
Warning in DICOM plugin Scalar Volume when examining loadable 16: ep2d_diff_mddw_64_cor_TENSOR_ADC_MAP: Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. Reference image in series does not contain geometry information. Please use caution.
Warning in DICOM plugin Scalar Volume when examining loadable 15: ep2d_diff_mddw_64_cor_TENSOR_FA_MAP: Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. Reference image in series does not contain geometry information. Please use caution.
Warning in DICOM plugin Scalar Volume when examining loadable 14: ep2d_diff_mddw_64_cor_TENSOR: Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. Reference image in series does not contain geometry information. Please use caution.
Warning in DICOM plugin Scalar Volume when examining loadable 9: ep2d_diff_mddw_64_cor: Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. Reference image in series does not contain geometry information. Please use caution.
Loading with imageIOName: GDCM
No geomtry information available for DICOM data, skipping corner calculations
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=636.0, width=1275.0) has been applied to volume 5: t1_vibe_cor_1.8mm
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 1.1314e-05 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
No geomtry information available for DICOM data, skipping corner calculations
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=55.0, width=145.0) has been applied to volume 11: ep2d_diff_mddw_64_cor_TRACEW
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 3.94772e-05 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Could not read scalar volume using GDCM approach. Error is: FileFormatError
Loading with imageIOName: DCMTK
Could not read scalar volume using DCMTK approach. Error is: FileFormatError
DICOM plugin failed to load '9: ep2d_diff_mddw_64_cor' as a 'Scalar Volume'.
Traceback (most recent call last):
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMLib/DICOMWidgets.py", line 856, in proceedWithReferencedLoadablesSelection
loadSuccess = plugin.load(loadable)
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 547, in load
addAcquisitionTransformIfNeeded=self.acquisitionGeometryRegularizationEnabled())
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 780, in createAcquisitionTransform
self.originalCorners = self.sliceCornersFromIJKToRAS(volumeNode)
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 754, in sliceCornersFromIJKToRAS
volumeNode.GetIJKToRASMatrix(ijkToRAS)
AttributeError: 'NoneType' object has no attribute 'GetIJKToRASMatrix'
Loading with imageIOName: GDCM
No geomtry information available for DICOM data, skipping corner calculations
Loading with imageIOName: GDCM
No geomtry information available for DICOM data, skipping corner calculations
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=127.0, width=328.0) has been applied to volume 6: t2_spc_stir_cor_p2_iso
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 0.000195456 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=632.0, width=1288.0) has been applied to volume 2: t2_tse_sag_384
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 3.84523e-05 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=315.0, width=814.0) has been applied to volume 8: t2_haste3d_fs_cor_iso_myelo_MIP_COR
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 7.35083e-06 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=819.0, width=1643.0) has been applied to volume 3: t2_tse_cor_384
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 2.52064e-05 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Could not read scalar volume using GDCM approach. Error is: FileFormatError
Loading with imageIOName: DCMTK
Could not read scalar volume using DCMTK approach. Error is: FileFormatError
Failed to read a multivolume: 'NoneType' object has no attribute 'GetIJKToRASMatrix'
Traceback (most recent call last):
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/MultiVolumeImporterPlugin.py", line 606, in load
frame = scalarVolumePlugin.load(svLoadables[0])
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 547, in load
addAcquisitionTransformIfNeeded=self.acquisitionGeometryRegularizationEnabled())
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 780, in createAcquisitionTransform
self.originalCorners = self.sliceCornersFromIJKToRAS(volumeNode)
File "/home/elonkou/MyProjects/Slicer-4.8.1-linux-amd64/lib/Slicer-4.8/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 754, in sliceCornersFromIJKToRAS
volumeNode.GetIJKToRASMatrix(ijkToRAS)
AttributeError: 'NoneType' object has no attribute 'GetIJKToRASMatrix'
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=1528.0, width=3140.0) has been applied to volume 10: ep2d_diff_mddw_64_cor_ADC
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 3.94772e-05 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=111.0, width=300.0) has been applied to volume 7: t2_haste3d_fs_cor_iso_myelo
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 0.000243026 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=500.0, width=1000.0) has been applied to volume 12: ep2d_diff_mddw_64_cor_FA
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 3.94772e-05 mm, tolerance threshold is 0.001 mm).
Loading with imageIOName: GDCM
Window/level found in DICOM tags (center=636.0, width=1340.0) has been applied to volume 4: t2_tse_tra
Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 8.01715e-05 mm, tolerance threshold is 0.001 mm).
Could not load: 9: ep2d_diff_mddw_64_cor as a Scalar Volume
Could not load: ep2d_diff_mddw_64_cor_ColFA - as a 26 frames MultiVolume by ImagePositionPatient+AcquisitionTime as a MultiVolume
it seems that the data is multi-frame image, so I check ed the file and found some DICOM file is a 3d-data (128 × 128 × 26)，what should i do to load these data?
and , I need the file of type nrrd, and I also failed to convert it to nrrd in DWIconveter moudule, it tells me
===================================================
Diffusion-weighted DICOM Import (DWIConvert) standard error:
Exception thrown while reading DICOM volume
itk::ExceptionObject (0x10e3c4c0)
Location: "unknown"
File: /home/kitware/Dashboards/Package/Slicer-481-package/ITKv4/Modules/IO/ImageBase/include/itkImageSeriesReader.hxx
Line: 370
Description: itk::ERROR: ImageSeriesReader(0x10e27750): Size mismatch! The size of /home/elonkou/Desktop/DTI/dicom/18032908/58020000/69462439 is [384, 384, 1] and does not match the required size [256, 256, 1] from file /home/elonkou/Desktop/DTI/dicom/18032908/58020000/69463693
Exception creating converter
itk::ExceptionObject (0x10e3c4c0)
Location: "unknown"
File: /home/kitware/Dashboards/Package/Slicer-481-package/ITKv4/Modules/IO/ImageBase/include/itkImageSeriesReader.hxx
Line: 370
Description: itk::ERROR: ImageSeriesReader(0x10e27750): Size mismatch! The size of /home/elonkou/Desktop/DTI/dicom/18032908/58020000/69462439 is [384, 384, 1] and does not match the required size [256, 256, 1] from file /home/elonkou/Desktop/DTI/dicom/18032908/58020000/69463693
Diffusion-weighted DICOM Import (DWIConvert) standard output:
======= DWI Convert Public Lib Ctest =========
===================================================
so , what should i do ,anyone who can help me ?