fedorov
commented
2 years ago What is the reason you manipulate the data? You don't need to have everything in a single series to load a multivolume.
Closed ignaciordc closed 2 years ago
fedorov
commented
2 years ago What is the reason you manipulate the data? You don't need to have everything in a single series to load a multivolume.
ignaciordc
commented
2 years ago -->Hi, Andrey.Thanks for your quick answer.
The data is contained in 9 different series, 4 of them are axial, from different, contiguous sections of the abdomen, the other 5 are sagittal and coronal. If I load the directory (and 9 subdirs) with these (9)series, only one axial section is displayed. So, what the manipulation is doing is taking the 4 axial series and creating a unique series, with some of the metadata modified and sorted by SliceLocation, which affects the naming of the files.The modified tags are documented in the bug report. When loading the resulting series (only 1 directory, not 9 as before), the axial view contains all the axial images, not just one series. This works most of the times, but with certain patients, it breaks with the mentioned error message.
Would that work if I load just the 4 axial series? What could the most logical reason for this behavior? All the data is previously anonymized , with virtual patient names , history, ids,… so I could share info if needed to debug. Thanks, Ignacio
ignaciordc
commented
2 years ago Andrey,
By the way, I get the error using the standard 3DSlicer, I have not installed the plugin, which does not show in the Extensions Manager.
I assume the MultiVolumeImporter plugin is now part of the standard Slicer v 4.11
[image: error_3d_001.png] [image: error_3d_003.png] [image: error_3d_002.png]
El sáb, 25 sept 2021 a las 17:01, Ignacio @.***>) escribió:
Hi, Andrey.
Thanks for your quick answer.
The data is contained in 9 different series, 4 of them are axial, from different, contiguous sections of the abdomen, the other 5 are sagittal and coronal.
If I load the directory with these (9)series, only one axial section is displayed.
So, what the manipulation is doing is taking the 4 axial series and creating a unique series, with some of the metadata modified and sorted by SliceLocation, which affects the naming of the files.
The modified tags are documented in the bug report.
When loading the resulting series (only 1 directory, not 9 as before), the axial view contains all the axial images, not just one series. This works most of the times, but with certain patients, it breaks with the mentioned error message.
Would that work if I load just the 4 axial series?
What could the most logical reason for this behavior?
All the data is previously anonymized , with virtual patient names , history, ids,… so I could share info if needed to debug.
Thanks,
Ignacio
From: Andrey Fedorov @.> Sent: Saturday, September 25, 2021 5:12 AM To: fedorov/MultiVolumeImporter @.> Cc: Ignacio Ruiz de Conejo @.>; Author @.> Subject: Re: [fedorov/MultiVolumeImporter] "Could not load
- as a 3 frames MultiVolume by B.standard value" (#48) What is the reason you manipulate the data? You don't need to have everything in a single series to load a multivolume.
ignaciordc
commented
2 years ago 
lassoan
commented
2 years ago Please use the very latest Slicer Preview Release and follow the steps below:
ignaciordc
commented
2 years ago Here you have the log Hope this helps. Thanks a lot! Ignacio
[DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Session start time .......: 2021-09-25 23:44:28 [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Slicer version ...........: 4.13.0-2021-09-23 (revision 30243 / 4eed607) win-amd64 - installed release [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Operating system .........: Windows / Professional / (Build 18363, Code Page 65001) - 64-bit [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Memory ...................: 32574 MB physical, 37438 MB virtual [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - CPU ......................: GenuineIntel , 8 cores, 8 logical processors [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, TBB threading [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Qt configuration .........: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile) [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Developer mode enabled ...: no [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Application path .........: C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin [DEBUG][Qt] 25.09.2021 23:44:28 [] (unknown:0) - Additional module paths ..: (none) [DEBUG][Python] 25.09.2021 23:44:31 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations [DEBUG][Python] 25.09.2021 23:44:32 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor [DEBUG][Python] 25.09.2021 23:44:32 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics [DEBUG][Qt] 25.09.2021 23:44:32 [] (unknown:0) - Switch to module: "Welcome" [DEBUG][Qt] 25.09.2021 23:44:44 [] (unknown:0) - Switch to module: "DICOM" [DEBUG][Qt] 26.09.2021 00:11:32 [] (unknown:0) - "DICOM indexer has successfully inserted 552 files [0.78s]" [DEBUG][Qt] 26.09.2021 00:11:32 [] (unknown:0) - "DICOM indexer has successfully processed 552 files [1.53s]" [DEBUG][Qt] 26.09.2021 00:11:32 [] (unknown:0) - "DICOM indexer has updated display fields for 552 files [0.36s]" [INFO][Python] 26.09.2021 00:11:32 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMBrowser.py:252) - Imported a DICOM directory, checking for extensions [INFO][Stream] 26.09.2021 00:11:32 [] (unknown:0) - Imported a DICOM directory, checking for extensions [DEBUG][Python] 26.09.2021 00:11:48 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMEnhancedUSVolumePlugin [DEBUG][Python] 26.09.2021 00:11:48 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMGeAbusPlugin [DEBUG][Python] 26.09.2021 00:11:49 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMImageSequencePlugin [DEBUG][Python] 26.09.2021 00:11:50 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMImageSequencePlugin.py:196) - Only one or few different trigger times found ({''}) - assuming this series is not a cine MRI [DEBUG][Python] 26.09.2021 00:11:50 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMScalarVolumePlugin [WARNING][Python] 26.09.2021 00:11:53 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:11:53 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:11:53 [] (unknown:0) - [DEBUG][Python] 26.09.2021 00:11:53 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMSlicerDataBundlePlugin [DEBUG][Python] 26.09.2021 00:11:53 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMVolumeSequencePlugin [DEBUG][Python] 26.09.2021 00:11:53 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using MultiVolumeImporterPlugin [DEBUG][Python] 26.09.2021 00:11:53 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:471) - MultiVolumeImporterPlugin: examine [DEBUG][Python] 26.09.2021 00:11:56 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:512) - MultiVolumeImporterPlugin: found 3 multivolumes! [WARNING][Python] 26.09.2021 00:11:57 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:11:57 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:11:58 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:11:59 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [DEBUG][Python] 26.09.2021 00:12:03 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:180) - MultiVolumeImporterPlugin: examineMultiseries [DEBUG][Python] 26.09.2021 00:12:04 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:187) - MultiVolumeImporterPlugin: found 1 multivolumes! [WARNING][Python] 26.09.2021 00:12:05 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:12:06 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [DEBUG][Python] 26.09.2021 00:12:11 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:168) - MultiVolumeImporterPlugin: found 4 loadables in 552 files in 18.4sec. [CRITICAL][Stream] 26.09.2021 00:11:57 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:11:57 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:11:57 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:11:57 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:11:58 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:11:58 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:11:59 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:11:59 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:12:05 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:12:05 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:12:06 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:12:06 [] (unknown:0) - [INFO][Python] 26.09.2021 00:12:13 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:384) - Loading with imageIOName: GDCM [ERROR][Python] 26.09.2021 00:12:14 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:390) - Could not read scalar volume using GDCM approach. Error is: FileFormatError [INFO][Python] 26.09.2021 00:12:14 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:384) - Loading with imageIOName: DCMTK [ERROR][Python] 26.09.2021 00:12:15 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:390) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError [ERROR][Python] 26.09.2021 00:12:15 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:748) - Failed to read a multivolume: Volume frame 0 is invalid - [WARNING][Python] 26.09.2021 00:12:15 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\bin\Python\slicer\util.py:2296) - Could not load: _COMP - as a 3 frames MultiVolume by Standard.B-value as a MultiVolume [INFO][Stream] 26.09.2021 00:12:13 [] (unknown:0) - Loading with imageIOName: GDCM [ERROR][VTK] 26.09.2021 00:12:14 [vtkITKArchetypeImageSeriesScalarReader (000002AF3ABFDE80): Exception from vtkITK MegaMacro: itk::ExceptionObject (000000EE045C87C8) Location: "unknown" File: D:\D\P\Slicer-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx Line: 356 Description: ITK ERROR: ImageSeriesReader(000002AF3BA06340)] (D:\D\P\Slicer-0\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx:260) - Size mismatch! The size of C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/1000001.dcm is [224, 224, 1] and does not match the required size [176, 176, 1] from file C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/4000001.dcm [ERROR][VTK] 26.09.2021 00:12:14 [vtkCompositeDataPipeline (000002AF3F15D940)] (D:\D\P\Slicer-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:753) - Algorithm vtkITKArchetypeImageSeriesScalarReader(000002AF3ABFDE80) returned failure for request: vtkInformation (000002AF3AFEBDA0) Debug: Off Modified Time: 260597 Reference Count: 1 Registered Events: (none) Request: REQUEST_DATA FORWARD_DIRECTION: 0 ALGORITHM_AFTER_FORWARD: 1 FROM_OUTPUT_PORT: 0 [CRITICAL][Stream] 26.09.2021 00:12:14 [] (unknown:0) - Could not read scalar volume using GDCM approach. Error is: FileFormatError [INFO][Stream] 26.09.2021 00:12:14 [] (unknown:0) - Loading with imageIOName: DCMTK [ERROR][VTK] 26.09.2021 00:12:15 [vtkITKArchetypeImageSeriesScalarReader (000002AF3AC00040): Exception from vtkITK MegaMacro: itk::ExceptionObject (000000EE045C87C8) Location: "unknown" File: D:\D\P\Slicer-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx Line: 356 Description: ITK ERROR: ImageSeriesReader(000002AF3BA06C40)] (D:\D\P\Slicer-0\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx:260) - Size mismatch! The size of C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/1000001.dcm is [224, 224, 1] and does not match the required size [176, 176, 1] from file C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/4000001.dcm [ERROR][VTK] 26.09.2021 00:12:15 [vtkCompositeDataPipeline (000002AF3F15CE40)] (D:\D\P\Slicer-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:753) - Algorithm vtkITKArchetypeImageSeriesScalarReader(000002AF3AC00040) returned failure for request: vtkInformation (000002AF4386DB00) Debug: Off Modified Time: 260830 Reference Count: 1 Registered Events: (none) Request: REQUEST_DATA FORWARD_DIRECTION: 0 ALGORITHM_AFTER_FORWARD: 1 FROM_OUTPUT_PORT: 0 [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - Failed to read a multivolume: Volume frame 0 is invalid - [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - Traceback (most recent call last): [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - File "C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py", line 639, in load [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - raise OSError(f"Volume frame {frameNumber} is invalid - {svLoadables[0].warning}") [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - OSError: Volume frame 0 is invalid - [CRITICAL][Stream] 26.09.2021 00:12:15 [] (unknown:0) - Could not load: _COMP - as a 3 frames MultiVolume by Standard.B-value as a MultiVolume [DEBUG][Qt] 26.09.2021 00:14:31 [] (unknown:0) - SQLITE: removing seriesInstanceUID 1.2.276.0.7230010.3.75593522985655176054883451027381860234 [DEBUG][Qt] 26.09.2021 00:14:48 [] (unknown:0) - "DICOM indexer has successfully inserted 552 files [1.42s]" [DEBUG][Qt] 26.09.2021 00:14:48 [] (unknown:0) - "DICOM indexer has successfully processed 552 files [2.22s]" [DEBUG][Qt] 26.09.2021 00:14:48 [] (unknown:0) - "DICOM indexer has updated display fields for 552 files [0.31s]" [INFO][Python] 26.09.2021 00:14:48 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMBrowser.py:252) - Imported a DICOM directory, checking for extensions [INFO][Stream] 26.09.2021 00:14:48 [] (unknown:0) - Imported a DICOM directory, checking for extensions [DEBUG][Python] 26.09.2021 00:14:56 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMEnhancedUSVolumePlugin [DEBUG][Python] 26.09.2021 00:14:56 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMGeAbusPlugin [DEBUG][Python] 26.09.2021 00:14:56 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMImageSequencePlugin [DEBUG][Python] 26.09.2021 00:14:57 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMImageSequencePlugin.py:196) - Only one or few different trigger times found ({''}) - assuming this series is not a cine MRI [DEBUG][Python] 26.09.2021 00:14:57 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMScalarVolumePlugin [DEBUG][Python] 26.09.2021 00:14:57 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMSlicerDataBundlePlugin [DEBUG][Python] 26.09.2021 00:14:57 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using DICOMVolumeSequencePlugin [DEBUG][Python] 26.09.2021 00:14:57 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:711) - Examine for import using MultiVolumeImporterPlugin [DEBUG][Python] 26.09.2021 00:14:57 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:471) - MultiVolumeImporterPlugin: examine [DEBUG][Python] 26.09.2021 00:15:00 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:512) - MultiVolumeImporterPlugin: found 3 multivolumes! [WARNING][Python] 26.09.2021 00:15:00 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:15:01 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:15:01 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:15:02 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [DEBUG][Python] 26.09.2021 00:15:05 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:180) - MultiVolumeImporterPlugin: examineMultiseries [DEBUG][Python] 26.09.2021 00:15:06 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:187) - MultiVolumeImporterPlugin: found 1 multivolumes! [WARNING][Python] 26.09.2021 00:15:07 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [WARNING][Python] 26.09.2021 00:15:07 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\lib\Slicer-4.13\qt-scripted-modules\DICOMLib\DICOMUtils.py:667) - Geometric issues were found with 1 of the series. Please use caution. [DEBUG][Python] 26.09.2021 00:15:11 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:168) - MultiVolumeImporterPlugin: found 4 loadables in 552 files in 14.1sec. [CRITICAL][Stream] 26.09.2021 00:15:00 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:15:00 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:15:01 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:15:01 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:15:01 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:15:01 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:15:02 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:15:02 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:15:07 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:15:07 [] (unknown:0) - [CRITICAL][Stream] 26.09.2021 00:15:07 [] (unknown:0) - Geometric issues were found with 1 of the series. Please use caution. [CRITICAL][Stream] 26.09.2021 00:15:07 [] (unknown:0) - [INFO][Python] 26.09.2021 00:15:12 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:384) - Loading with imageIOName: GDCM [ERROR][Python] 26.09.2021 00:15:13 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:390) - Could not read scalar volume using GDCM approach. Error is: FileFormatError [INFO][Python] 26.09.2021 00:15:13 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:384) - Loading with imageIOName: DCMTK [ERROR][Python] 26.09.2021 00:15:14 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/DICOMScalarVolumePlugin.py:390) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError [ERROR][Python] 26.09.2021 00:15:14 [Python] (C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py:748) - Failed to read a multivolume: Volume frame 0 is invalid - [WARNING][Python] 26.09.2021 00:15:14 [Python] (C:\Users\ignac\Programs\Slicer 4.13.0-2021-09-23\bin\Python\slicer\util.py:2296) - Could not load: _COMP - as a 3 frames MultiVolume by Standard.B-value as a MultiVolume [INFO][Stream] 26.09.2021 00:15:12 [] (unknown:0) - Loading with imageIOName: GDCM [ERROR][VTK] 26.09.2021 00:15:13 [vtkITKArchetypeImageSeriesScalarReader (000002AF3AE93FD0): Exception from vtkITK MegaMacro: itk::ExceptionObject (000000EE045C87C8) Location: "unknown" File: D:\D\P\Slicer-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx Line: 356 Description: ITK ERROR: ImageSeriesReader(000002AF3AB0FBE0)] (D:\D\P\Slicer-0\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx:260) - Size mismatch! The size of C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/1000001.dcm is [224, 224, 1] and does not match the required size [176, 176, 1] from file C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/4000001.dcm [ERROR][VTK] 26.09.2021 00:15:13 [vtkCompositeDataPipeline (000002AF3B9101B0)] (D:\D\P\Slicer-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:753) - Algorithm vtkITKArchetypeImageSeriesScalarReader(000002AF3AE93FD0) returned failure for request: vtkInformation (000002AF601C6460) Debug: Off Modified Time: 265844 Reference Count: 1 Registered Events: (none) Request: REQUEST_DATA FORWARD_DIRECTION: 0 ALGORITHM_AFTER_FORWARD: 1 FROM_OUTPUT_PORT: 0 [CRITICAL][Stream] 26.09.2021 00:15:13 [] (unknown:0) - Could not read scalar volume using GDCM approach. Error is: FileFormatError [INFO][Stream] 26.09.2021 00:15:13 [] (unknown:0) - Loading with imageIOName: DCMTK [ERROR][VTK] 26.09.2021 00:15:14 [vtkITKArchetypeImageSeriesScalarReader (000002AF3AE94390): Exception from vtkITK MegaMacro: itk::ExceptionObject (000000EE045C87C8) Location: "unknown" File: D:\D\P\Slicer-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx Line: 356 Description: ITK ERROR: ImageSeriesReader(000002AF3AB0FA60)] (D:\D\P\Slicer-0\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx:260) - Size mismatch! The size of C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/1000001.dcm is [224, 224, 1] and does not match the required size [176, 176, 1] from file C:/Users/ignac/DocumentsC/HUB/PRECIMET/ANONIMIZADOS/DICOMS/id6rm4w/DWI_COMP2/4000001.dcm [ERROR][VTK] 26.09.2021 00:15:14 [vtkCompositeDataPipeline (000002AF3B90F2B0)] (D:\D\P\Slicer-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx:753) - Algorithm vtkITKArchetypeImageSeriesScalarReader(000002AF3AE94390) returned failure for request: vtkInformation (000002AF4363D6C0) Debug: Off Modified Time: 266090 Reference Count: 1 Registered Events: (none) Request: REQUEST_DATA FORWARD_DIRECTION: 0 ALGORITHM_AFTER_FORWARD: 1 FROM_OUTPUT_PORT: 0 [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - Could not read scalar volume using DCMTK approach. Error is: FileFormatError [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - Failed to read a multivolume: Volume frame 0 is invalid - [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - Traceback (most recent call last): [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - File "C:/Users/ignac/Programs/Slicer 4.13.0-2021-09-23/bin/../lib/Slicer-4.13/qt-scripted-modules/MultiVolumeImporterPlugin.py", line 639, in load [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - raise OSError(f"Volume frame {frameNumber} is invalid - {svLoadables[0].warning}") [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - OSError: Volume frame 0 is invalid - [CRITICAL][Stream] 26.09.2021 00:15:14 [] (unknown:0) - Could not load: _COMP - as a 3 frames MultiVolume by Standard.B-value as a MultiVolume
ignaciordc
commented
2 years ago Reading the log has given me a good hint for the error, i think. As I explained, I am"stitching" 4 series. When the images of the 4 series were scanned at the same size (i.e., 224x224), the stitching works well. However, when one of the series contains images scanned at a different size (176x176), then the program breaks. In other word, the DICOM series is poorly defined, since alll the images should be of the same size.
Please, confirm what I am suggesting. thanks,
Ignacio
lassoan
commented
2 years ago You understood it right. All image slices must have the same size to load it directly as a time series.
If you have a more complex reconstruction task (varying image size, rotating slices, etc.) then you can load the images as a series of 2D slices and reconstruct using Volume Reconstructor module in SlicerIGSIO extension.
ignaciordc
commented
2 years ago Thanks, therefore, it is not a a bug (great!), but a poor implementation of the scanning tasks, for DICOM file series contain images of varying sizes. I'll check the extension you are mentioning. Thanks for your help.
I think you can close the issue. ;-)
fedorov
commented
2 years ago Would that work if I load just the 4 axial series?
You could try selecting just the 4 axial series that you want to load as a multivolume with Shift+click, and then clicking "Examine". The plugin will attempt to parse them. It already utilizes some heuristic to parse b-values and handle trace DWI.
The MultiVolumeImporterPlugin breaks when trying to load the data. Sometimes only.
The data has been 'manipulated' to stitch 4 different sections with 138 images each. This process of stitching generates a directory with all the images (138x4) as a single sequence. Loading these generated directories as data, sometimes works and sometimes breaks, which might mean that the stitching process is weak and does not check well that the tags modified contained proper information. The only fields I am modifying in the DICOM files in the stitching process are ['Image Type', 'Series Time', 'Series Description', 'Series Instance UID', 'Series Number', 'Instance Number', 'SAR', 'Frame of Reference UID', 'Slice Location'] I do not discard that the original, unmodified files have tags with missing information for the 3D volume....
========================
The three 2D views are displayed. This is working well with 70% of the data files I am loading...
Environment [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Session start time .......: 2021-09-25 02:21:14 [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Slicer version ...........: 4.11.20210226 (revision 29738 / 7a593c8) win-amd64 - installed release [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Operating system .........: Windows / Professional / (Build 18363, Code Page 65001) - 64-bit [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Memory ...................: 32574 MB physical, 37438 MB virtual [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - CPU ......................: GenuineIntel , 8 cores, 8 logical processors [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, TBB threading [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Qt configuration .........: version 5.15.1, with SSL, requested OpenGL 3.2 (compatibility profile) [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Developer mode enabled ...: no [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Prefer executable CLI ....: yes [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Application path .........: C:/Users/ignac/AppData/Local/NA-MIC/Slicer 4.11.20210226/bin [DEBUG][Qt] 25.09.2021 02:21:14 [] (unknown:0) - Additional module paths ..: NA-MIC/Extensions-29738/SlicerOpenCV/lib/Slicer-4.11/qt-loadable-modules, NA-MIC/Extensions-29738/DeepInfer/lib/Slicer-4.11/qt-scripted-modules, NA-MIC/Extensions-29738/SlicerJupyter/lib/Slicer-4.11/qt-loadable-modules, NA-MIC/Extensions-29738/SlicerJupyter/lib/Slicer-4.11/qt-scripted-modules, NA-MIC/Extensions-29738/SlicerDMRI/lib/Slicer-4.11/cli-modules, NA-MIC/Extensions-29738/SlicerDMRI/lib/Slicer-4.11/qt-loadable-modules, NA-MIC/Extensions-29738/SlicerDMRI/lib/Slicer-4.11/qt-scripted-modules, NA-MIC/Extensions-29738/UKFTractography/lib/Slicer-4.11/cli-modules, NA-MIC/Extensions-29738/UKFTractography/lib/Slicer-4.11/qt-loadable-modules, NA-MIC/Extensions-29738/UKFTractography/lib/Slicer-4.11/qt-scripted-modules [DEBUG][Python] 25.09.2021 02:21:16 [Python] (C:\Users\ignac\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Python\Lib\site-packages\pydicom\datadict.py:432) - Reversing DICOM dictionary so can look up tag from a keyword... [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - Traceback (most recent call last): [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - File "", line 1, in [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - File "C:\Users\ignac\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Python\Lib\imp.py", line 170, in load_source [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - module = _exec(spec, sys.modules[name]) [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - File "", line 618, in _exec [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - File "", line 678, in exec_module [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - File "", line 219, in _call_with_frames_removed [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - File "C:/Users/ignac/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/DeepInfer/lib/Slicer-4.11/qt-scripted-modules/DeepInfer.py", line 1, in [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - import Queue [CRITICAL][Stream] 25.09.2021 02:21:17 [] (unknown:0) - ModuleNotFoundError: No module named 'Queue' [CRITICAL][Qt] 25.09.2021 02:21:17 [] (unknown:0) - loadSourceAsModule - Failed to load file "C:/Users/ignac/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/DeepInfer/lib/Slicer-4.11/qt-scripted-modules/DeepInfer.py" as module "DeepInfer" ! [CRITICAL][Qt] 25.09.2021 02:21:17 [] (unknown:0) - Fail to instantiate module "DeepInfer" [CRITICAL][Qt] 25.09.2021 02:21:17 [] (unknown:0) - The following modules failed to be instantiated: [CRITICAL][Qt] 25.09.2021 02:21:17 [] (unknown:0) - DeepInfer [DEBUG][Python] 25.09.2021 02:21:18 [Python] (C:\Users\ignac\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations [DEBUG][Python] 25.09.2021 02:21:20 [Python] (C:\Users\ignac\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor [DEBUG][Python] 25.09.2021 02:21:20 [Python] (C:\Users\ignac\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics [DEBUG][Qt] 25.09.2021 02:21:20 [] (unknown:0) - Switch to module: "Welcome" [DEBUG][Qt] 25.09.2021 02:21:41 [] (unknown:0) - Switch to module: ""