BatchStructureSetConversion doesn't work with my dicom

[uffacci]

Dear SliceRT team,

I want to use your script to convert DICOM structures to surface mesh. Unfortunately, the conversion fails (the only empty folder is created). I checked that the Patient name, Patient ID and series instance UID fields were not empty; and also that there were no special characters in the filenames. I work with mac os 11, python 3.7.2 and Slicer 4.13. Could you possibly point me to a test file? Here is my bug:

`` % /Applications/Slicer.app/Contents/MacOS/Slicer --no-main-window --python-script Downloads/SlicerRT-master/BatchProcessing/BatchStructureSetConversion.py -i Desktop/DICOM_05161_rs -r Desktop/DICOM_05161_all_no_rs -o Desktop/output_mesh qSlicerSequencesModulePrivate::addToolBar: no main window is available, toolbar is not added Start batch RTSTRUCT conversion BatchStructureSet running in file mode Import reference anatomy DICOM data from Desktop/DICOM_05161_all_no_rs Switching to temporary DICOM database: /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150005_TempDICOMDatabase TagCacheDatabase adding table

E: DcmElement: CommandField (0000,0100) larger (828667202) than remaining bytes in file Could not load "Desktop/DICOM_05161_all_no_rs/.DS_Store" DCMTK says: I/O suspension or premature end of stream Could not read DICOM file:Desktop/DICOM_05161_all_no_rs/.DS_Store "DICOM indexer has successfully inserted 400 files [0.16s]" "DICOM indexer has successfully processed 401 files [0.49s]" "DICOM indexer has updated display fields for 400 files [0.07s]" Could not load "/private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150005_TempDICOMDatabase/Desktop/DICOM_05161_all_no_rs/_Anon_CT.75073429_285.dcm" DCMTK says: No such file or directory File /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150005_TempDICOMDatabase/Desktop/DICOM_05161_all_no_rs/_Anon_CT.75073429_285.dcm could not be initialized. Could not load "/private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150005_TempDICOMDatabase/Desktop/DICOM_05161_all_no_rs/_Anon_CT.75073429_291.dcm" DCMTK says: No such file or directory File /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150005_TempDICOMDatabase/Desktop/DICOM_05161_all_no_rs/_Anon_CT.75073429_291.dcm could not be initialized. Could not load "/private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150005_TempDICOMDatabase/Desktop/DICOM_05161_all_no_rs/_Anon_CT.75073429_246.dcm" DCMTK says: No such file or directory .... .... .... ....

Could not load "/private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150006_TempDICOMDatabase/Desktop/DICOM_05161_rs/_AnonRS.75073429.dcm" DCMTK says: No such file or directory File /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150006_TempDICOMDatabase/Desktop/DICOM_05161_rs/_AnonRS.75073429.dcm could not be initialized. Could not load "/private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150006_TempDICOMDatabase/Desktop/DICOM_05161_rs/_AnonRS.75073429.dcm" DCMTK says: No such file or directory File /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150006_TempDICOMDatabase/Desktop/DICOM_05161_rs/_AnonRS.75073429.dcm could not be initialized. Loading with imageIOName: GDCM vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150006_TempDICOMDatabase/Desktop/DICOM_05161_rs/_AnonRS.75073429.dcm does not exist.

Algorithm vtkITKArchetypeImageSeriesVectorReaderFile(0x7fae0e221d20) returned failure for request: vtkInformation (0x7fae0e224850) Debug: Off Modified Time: 143250 Reference Count: 1 Registered Events: (none) Request: REQUEST_INFORMATION ALGORITHM_AFTER_FORWARD: 1 FORWARD_DIRECTION: 0

Could not read scalar volume using GDCM approach. Error is: FileNotFoundError Loading with imageIOName: DCMTK vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /private/var/folders/vg/7xz3x48s4hl2fl4t3l2qbn0m0000gn/T/Slicer-winnieiii/20210914_150006_TempDICOMDatabase/Desktop/DICOM_05161_rs/_AnonRS.75073429.dcm does not exist.

Algorithm vtkITKArchetypeImageSeriesVectorReaderFile(0x7fae0e225e80) returned failure for request: vtkInformation (0x7fae0e226e40) Debug: Off Modified Time: 143356 Reference Count: 1 Registered Events: (none) Request: REQUEST_INFORMATION ALGORITHM_AFTER_FORWARD: 1 FORWARD_DIRECTION: 0

Could not read scalar volume using DCMTK approach. Error is: FileNotFoundError Convert loaded structure set to labelmap volumes Save labelmaps to directory Desktop/output_mesh/1 DONE

[cpinter]

Does the script have the necessary privileges to access the file itself? Maybe if you try to run it with sudo?

[uffacci]

Thanks for your answer! Even with 'sudo' I get the same error again. I tried to extract the mesh via GUI, and it seems to work, so it shouldn't be a problem of DICOM. I don't understand if there is something that I have to also set at the database level, maybe change some permissions ...Any idea? Thanks a lot!

[uffacci]

I think I have fix my bug. If I run the script directly from inside the folder ... so without path it works ... I think there is some problem reading the absolute paths, or maybe it is a specific problem of mac os 11

[cpinter]

Interesting, thanks for the update! I'll try the script on Linux (don't have access to Mac but path handling should be the same on the two), and fix if I find the issue.

[cpinter]

Sorry for the extremely long delay... I just tried it, and this command works on Ubuntu 20.04.4

./Slicer --no-main-window --python-script /home/csaba/Slicer/_Extensions/SlicerRT/BatchProcessing/BatchStructureSetConversion.py --input-folder /home/csaba/Data/20220325_BatchProcessingTest --output-folder /home/csaba/Data/20220325_BatchProcessingTestOut

[cpinter]

Closing due to long inactivity.