Operating system:Windows 10
Slicer version:4.8.1
Expected behavior: choose directory/fie to add.
Actual behavior: I choose the directory I wish to add and nothing happens. It does not show up on the dialog box. After a while a get a message that it is not responding and I have to shut it down.
Data that is already loaded I also cannot get to show up on the screen. I can select the file I want but when I press load it does not load.
The new data that I wanted to import is a patched DICOM file.
Drag-and-drop the folder that contains your files, choose to import as DICOM, then use DICOM module to load the image into the scene.
I tried that. But it is just sitting there, saying 0% done, for about the last hour.
Which directory should I try to load? I have DICOM/pa001. It is recognising it as a DICOM file.
Drag-and-drop pa001 folder. If it fails to load then please post the application log (menu: Help/Report a bug) or share the data set (make sure it is properly anonymized if it is human data).
I’ve seen this happen when a zombie Slicer process is still running. Close
your current instance, then check your task manager-> processes and kill
any lingerers.
Ton of error message
SQL failed
Bad SQL: SELECT InsertTimestamp FROM Images WHERE Filename == ?
Error text: database disk image is malformed Unable to fetch row
A later message is
C:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct000.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct001.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct002.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct003.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct004.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct005.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct006.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct007.dcmC:/Users/pg13t/Desktop/3D Ortho Prints/TROH84507_fixed/DICOM/pa001/st000/se000/ct008.dcmImported a DICOM directory, checking for extensions
The final one
Traceback (most recent call last):
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 413, in timerCallback
self.promptForExtensions()
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 418, in promptForExtensions
extensionsToOffer = self.checkForExtensions()
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 481, in checkForExtensions
instance0 = slicer.dicomDatabase.filesForSeries(series)[0]
IndexError: tuple index out of range
I cancel the import as it does not do anything. It doesn’t give me a %update on this one
If I use the DICOM button to load previously used data sets I get the message:
Traceback (most recent call last):
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 766, in loadCheckedLoadables
self.examineForLoading()
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 677, in examineForLoading
self.loadablesByPlugin, loadEnabled = self.getLoadablesFromFileLists(self.fileLists)
TypeError: ‘NoneType’ object is not iterable
Traceback (most recent call last):
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 766, in loadCheckedLoadables
self.examineForLoading()
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 677, in examineForLoading
self.loadablesByPlugin, loadEnabled = self.getLoadablesFromFileLists(self.fileLists)
TypeError: ‘NoneType’ object is not iterable
Traceback (most recent call last):
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 766, in loadCheckedLoadables
self.examineForLoading()
File “C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py”, line 677, in examineForLoading
self.loadablesByPlugin, loadEnabled = self.getLoadablesFromFileLists(self.fileLists)
TypeError: ‘NoneType’ object is not iterable
The DICOM database sem to be corrupted or in an incorrect location (not writeable by current user). Please try the solution described here: Why I can not import DICOM?
I tried patching it again, then importing. I can’t see any problem on the patch log, but the import log says this
W: DcmItem: Non-standard VR ’ ’ (0a\00) encountered while parsing element (0004,1130), assuming 2 byte length field
W: DcmItem: Non-standard VR ‘16’ (31\36) encountered while parsing element (5346,3959), assuming 2 byte length field
W: DcmItem: Length of element (5346,3959) is odd
W: DcmItem: Non-standard VR ’ 5’ (00\35) encountered while parsing element (0200,0000), assuming 2 byte length field
W: DcmItem: Length of element (0200,0000) is odd
W: DcmItem: Dataset not in ascending tag order, at element (0200,0000)
W: DcmItem: Non-standard VR ‘CO’ (43\4f) encountered while parsing element (0000,4944), assuming 4 byte length field
W: DcmItem: Length of element (0000,4944) is odd
E: DcmElement: Unknown Tag & Data (0000,4944) larger (808464467) than remaining bytes in file
W: DcmItem: Dataset not in ascending tag order, at element (0000,4944)
This seems like an invalid/corrupted DICOM file. What did produce this file?
It was produced by DICOM patcher
There were no error messages on the patched files. The problem came when I tried to load it.
Where does the original data comes from (that you feed into DICOM patcher)?
The DICOM patcher should not introduce those invalid tags that are reported to be found when you try to import the data.
You can also try all 3 available DICOM parsers (GDCM, DCMTK, archetype) and see if any of them is insensitive to the presence of invalid tags.
I’ve also tried to delete data sets from DICOM browser and it’s not letting me delete those. I try REMOVE or DELETE and neither works.
It seems to be DICOM browser that I’m specifically having problems with
If you have trouble deleting the DICOM database content then you can clear the DICOM database folder or choose an empty folder (DICOM browser, >> icon in the top-right, LocalDatabase).
I rebooted the computer and that has fixed a lot of the problems. I’m guessing there was a background process going on. Thanks for the help