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IDProjectCategoryView StatusDate SubmittedLast Update
0004624Slicer4Module DICOMpublic2018-10-09 01:192018-10-17 20:28
Reporterrlucas.bsn Assigned Topieper  
PriorityurgentSeveritymajorReproducibilityalways
Status closedResolutionno change required 
Product VersionSlicer 4.8.1 
Target VersionFixed in Version 
Summary0004624: Dicom images not loading
Description

I've recently downloaded Slicer so that I can convert Dicom images into nrrd files for 3d printing to assist with surgical planning.
Whenever I have tried to load the dicom files, they don't load and I can't get onto the next step in the process as described by the tutorials.

What if anything am I doing wrong, and can it be fixed?

Cheers
Richard

Here are the error codes:
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Session start time .......: 2018-10-09 13:00:25
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Slicer version ...........: 4.8.1 (revision 26813) win-amd64 - installed
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Operating system .........: Windows / Personal / (Build 9200) - 64-bit
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Memory ...................: 7980 MB physical, 16172 MB virtual
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - CPU ......................: GenuineIntel , 4 cores, 16 logical processors
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Developer mode enabled ...: no
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Prefer executable CLI ....: yes
[DEBUG][Qt] 09.10.2018 13:00:25 [] (unknown:0) - Additional module paths ..: (none)
[DEBUG][Python] 09.10.2018 13:00:35 [Python] (C:\Program Files\Slicer 4.8.1\lib\Python\Lib\site-packages\git\cmd.py:719) - Popen(%s, cwd=%s, universal_newlines=%s, shell=%s)
[DEBUG][Python] 09.10.2018 13:00:37 [Python] (C:\Program Files\Slicer 4.8.1\lib\Python\Lib\site-packages\git\cmd.py:719) - Popen(%s, cwd=%s, universal_newlines=%s, shell=%s)
[DEBUG][Python] 09.10.2018 13:00:49 [Python] (C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Python] 09.10.2018 13:00:53 [Python] (C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 09.10.2018 13:00:53 [Python] (C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 09.10.2018 13:00:26 [] (unknown:0) - Number of registered modules: 135
[DEBUG][Qt] 09.10.2018 13:00:40 [] (unknown:0) - Number of instantiated modules: 135
[DEBUG][Qt] 09.10.2018 13:00:53 [] (unknown:0) - Number of loaded modules: 135
[DEBUG][Qt] 09.10.2018 13:00:53 [] (unknown:0) - Switch to module: "Welcome"
[DEBUG][Qt] 09.10.2018 13:01:49 [] (unknown:0) - Switch to module: "DICOM"
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 327, in setup
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - self.detailsPopup = self.getSavedDICOMDetailsWidgetType()()
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - File "C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 1004, in init
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - super(DICOMDetailsWindow, self).init(dicomBrowser, parent)
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - File "C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 973, in init
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - DICOMDetailsBase.init(self, dicomBrowser)
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - File "C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 86, in init
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - self.promptForDatabaseDirectory()
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - File "C:\Program Files\Slicer 4.8.1\lib\Slicer-4.8\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 529, in promptForDatabaseDirectory
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - os.makedirs(databaseDirectory)
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Python/Lib\os.py", line 157, in makedirs
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - mkdir(name, mode)
[CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - WindowsError: [Error 5] Access is denied: 'SlicerDICOMDatabase'
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 268, in enter
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - self.onOpenDetailsPopup()
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 368, in onOpenDetailsPopup
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - if not isinstance(self.detailsPopup, self.getSavedDICOMDetailsWidgetType()):
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - AttributeError: DICOMWidget instance has no attribute 'detailsPopup'
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 201, in dropEvent
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - dicomWidget.detailsPopup.dicomBrowser.importDirectories(self.directoriesToAdd)
[CRITICAL][Stream] 09.10.2018 13:01:50 [] (unknown:0) - AttributeError: DICOMWidget instance has no attribute 'detailsPopup'
[DEBUG][Qt] 09.10.2018 13:04:51 [] (unknown:0) - Switch to module: "Data"
[CRITICAL][Stream] 09.10.2018 13:04:51 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 09.10.2018 13:04:51 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 271, in exit
[CRITICAL][Stream] 09.10.2018 13:04:51 [] (unknown:0) - if not self.detailsPopup.browserPersistent:
[CRITICAL][Stream] 09.10.2018 13:04:51 [] (unknown:0) - AttributeError: DICOMWidget instance has no attribute 'detailsPopup'
[DEBUG][Qt] 09.10.2018 13:05:08 [] (unknown:0) - Switch to module: "DICOM"
[CRITICAL][Stream] 09.10.2018 13:05:08 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 09.10.2018 13:05:08 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 268, in enter
[CRITICAL][Stream] 09.10.2018 13:05:08 [] (unknown:0) - self.onOpenDetailsPopup()
[CRITICAL][Stream] 09.10.2018 13:05:08 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 368, in onOpenDetailsPopup
[CRITICAL][Stream] 09.10.2018 13:05:08 [] (unknown:0) - if not isinstance(self.detailsPopup, self.getSavedDICOMDetailsWidgetType()):
[CRITICAL][Stream] 09.10.2018 13:05:08 [] (unknown:0) - AttributeError: DICOMWidget instance has no attribute 'detailsPopup'
[DEBUG][Qt] 09.10.2018 13:05:15 [] (unknown:0) - Switch to module: "Welcome"
[CRITICAL][Stream] 09.10.2018 13:05:15 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 09.10.2018 13:05:15 [] (unknown:0) - File "C:/Program Files/Slicer 4.8.1/lib/Slicer-4.8/qt-scripted-modules/DICOM.py", line 271, in exit
[CRITICAL][Stream] 09.10.2018 13:05:15 [] (unknown:0) - if not self.detailsPopup.browserPersistent:
[CRITICAL][Stream] 09.10.2018 13:05:15 [] (unknown:0) - AttributeError: DICOMWidget instance has no attribute 'detailsPopup'

TagsNo tags attached.

Activities

pieper

pieper

2018-10-09 08:16

administrator   ~0016095

Looks like you have the dicom database set to a place you cannot access:

CRITICAL][Stream] 09.10.2018 13:01:49 [] (unknown:0) - WindowsError: [Error 5]
Access is denied: 'SlicerDICOMDatabase'

Try deleting your settings file and when you run slicer you should be able to pick a location. The default would be your Documents folder, which should be writable.

https://www.slicer.org/wiki/Documentation/Nightly/SlicerApplication/ApplicationSettings#Settings_file_location
rlucas.bsn

rlucas.bsn

2018-10-09 10:29

reporter   ~0016096

G'Day Pieper

I've deleted the settings file as described in the link you sent but it still won't work.
I copied the file containing the dicom images to a file in my Documents file, but when I try and load the images it comes up with a dialogue box which says: Select a reader to use for your data? Load Directory into DICOM database
If I hit OK for this the program then stops and comes up with a message saying non responsive or nothing happens at all. It never goes to open the Dicom browser as happens in all the tutorials and I have copied exactly what the tutorials say to do!
What's next?
I'm sure there must be something simple, ie that isn't turned on?
Cheers
Richard
pieper

pieper

2018-10-09 11:37

administrator   ~0016099

Hi -

It sounds like there's still some kind of configuration issues.

Are you able to do the steps in this tutorial? https://www.slicer.org/wiki/Documentation/4.8/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications

I suggest you use the data from the tutorial and try to follow step by step. Then post a screenshot of the first place where it doesn't work exactly like the tutorial. This should narrow down what's going on.

Best,
Steve
rlucas.bsn

rlucas.bsn

2018-10-09 22:24

reporter   ~0016105

G'Day Steve
I started the tutorial, dragged the files into Slicer, said OK to "Load Directory into DICOM database" the Left screen changes to the Dicom module screen but then nothing happens.
It doesn't do anything more. The Dicom browser window never opens and the program just sits there.
A screen shot would just show the Dicom module window with nothing else on there.

What next?
I think you are 12 hours behind my time zone so I'll wait for your reply patiently! I'm in West Australia UTC + 8hrs.
Cheers
Richard

ps I have uninstalled and reinstalled Slicer and the same thing keeps happening.
pieper

pieper

2018-10-10 12:25

administrator   ~0016106

Good Day (Night) Richard -

I suspect it's still the same issue - that the database directory is being set to a location that you cannot access. Is this an institutional PC with some sort of constraints to the home directory? In any case one thing to try is editing the settings file and pointing to a directory where you know you have read/write access to (perhaps on a c: or d: drive).

There should be a line that looks like this and you can change the path to something valid:

[General]
DatabaseDirectory=/Volumes/encrypted/data/cardiacatlas/AMRG-db

Or even better, try the most recent nightly build from download.slicer.org of the 4.9 pre-release and see if you still have the same issue. If so add info here about the configuration of your PC.

Regards from UTC-5,
Steve
rlucas.bsn

rlucas.bsn

2018-10-11 05:48

reporter   ~0016108

G'Day Steve,

Tried loading 4.9 and it did download and seemed to install but when I tried to open the program it wouldn't open. The initial box opened and it had the scripts flashing on and off (eg Loading modules etc) but then it disappeared and the program didn't open.
I've had my daughter load Slicer 4.8.1 on her computer with similar spec as mine and it opened and she was able to follow the tutorial fine.
So therefore there is something in my computer setup that is miss aligning things!
Should I take my laptop to a local computer tech to get them to check the settings as the next step?
Cheers
Richard
pieper

pieper

2018-10-11 15:31

administrator   ~0016111

Interesting - if your laptop is an older model it may not be working with the very latest slicer version, but generally we are pretty compatible. It would help to see if you can get the log file related to the runs where slicer failed to open (they should be in the same folder as the logs for the older Slicer version).

But the new version not starting should be unrelated to the Access Denied issue for the dicom module. I still think it's something to do with the default directory not being writeable for some reason. Yes, maybe a computer tech could help troubleshoot that...?
rlucas.bsn

rlucas.bsn

2018-10-17 19:56

reporter   ~0016166

G'Day again Steve,
I actually went and bought a current model laptop with much better specs than my old one, installed Slicer and it worked!
I've created y first orthopaedic models and sent the files away to be 3d printed. Now I am happy!
I do think there was something a bit screwy with my old laptop as there were other times when it couldn't find the right directory for other programs too.
At least now I have a shiny new laptop and Slicer!
Thanks for all your assistance.
Cheers
Richard
pieper

pieper

2018-10-17 20:28

administrator   ~0016167

Sounds great Richard - happy printing!

Issue History

Date Modified Username Field Change
2018-10-09 01:19 rlucas.bsn New Issue
2018-10-09 01:19 rlucas.bsn Status new => assigned
2018-10-09 01:19 rlucas.bsn Assigned To => pieper
2018-10-09 08:16 pieper Status assigned => feedback
2018-10-09 08:16 pieper Note Added: 0016095
2018-10-09 10:29 rlucas.bsn Note Added: 0016096
2018-10-09 10:29 rlucas.bsn Status feedback => assigned
2018-10-09 11:37 pieper Note Added: 0016099
2018-10-09 22:24 rlucas.bsn Note Added: 0016105
2018-10-10 12:25 pieper Note Added: 0016106
2018-10-11 05:48 rlucas.bsn Note Added: 0016108
2018-10-11 15:31 pieper Note Added: 0016111
2018-10-17 19:56 rlucas.bsn Note Added: 0016166
2018-10-17 20:28 pieper Status assigned => closed
2018-10-17 20:28 pieper Resolution open => no change required
2018-10-17 20:28 pieper Note Added: 0016167