# How load diffusionTensorImages from Dicom? **URL:** \ **Category:** Support\ **Tags:** extensions-manager, diffusion, dicom\ **Created:** [April 9, 2018, 4:02pm UTC](https://discourse.slicer.org/t/how-load-diffusiontensorimages-from-dicom/2544 "2018-04-09T16:02:14Z")\ **Posts on this page:** 3\ **Page:** 1

**Author:** ![ElonKou](https://avatars.discourse-cdn.com/v4/letter/e/e19b73/32.png) [@ElonKou](https://discourse.slicer.org/u/ElonKou)\ **Post date:** [April 9, 2018, 4:02pm UTC](https://discourse.slicer.org/t/how-load-diffusiontensorimages-from-dicom/2544/1 "2018-04-09T16:02:14Z")

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. ![Screenshot%20from%202018-04-09%2018-31-29](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/4/34c6d161d507706755bf537a0c0c70853ee33fae.png) I select the checkbox named “DICOMScalarVolumePlugin” + “MultiVolumeImportedPlugin” + “DicomRtimportPlugin”. ![Screenshot%20from%202018-04-09%2018-30-02](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/9/4969c1fa7c8bcafadff21f7bcd4ca4adecd268e5.png) 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 ========= ![Screenshot%20from%202018-04-09%2018-35-23](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/1/7164d8edf462fd885c496d62908da05d743fc3a2.png) so , what should i do ,anyone who can help me ? ---

**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\ **Post date:** [April 10, 2018, 4:33pm UTC](https://discourse.slicer.org/t/how-load-diffusiontensorimages-from-dicom/2544/2 "2018-04-10T16:33:58Z")

A post was merged into an existing topic: [Is there any method to convert volume to DiffusionTensorvolume?](https://discourse.slicer.org/t/is-there-any-method-to-convert-volume-to-diffusiontensorvolume/2553) ---