Fwd: [slicer-users] LOGIQ E9 Volume Slices Processing

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Fwd: [slicer-users] LOGIQ E9 Volume Slices Processing

Steve Pieper-2
FYI I updated CTK with a fix for the RunttimeError in footnote [1].

-Steve

---------- Forwarded message ----------
From: Csaba Pinter <[hidden email]>
Date: Thu, Mar 30, 2017 at 9:20 AM
Subject: Re: [slicer-users] LOGIQ E9 Volume Slices Processing
To: Chris <[hidden email]>, SPL Slicer Users <[hidden email]>


Hi Chris,

Thanks for the data!

Importing seemed fine (except for a python error about offering extensions, for developers: [1]).

When loading, DWI seemed to take over (seems to happen now more often, also it's slow to examine - now that the processing classes are out in an extension, maybe the DICOM plugin could be in the extension too, like for other special DICOM formats), and maybe scalar volume was invoked next when DWI failed. When I explicitly selected the scalar volume loadable in the advanced option (the loadable had a warning about geometry [2] which is sometimes harmless) however, there was an actual VTK error:
"UpdateFromSeries: Unsupported number of components: 1 != 3
ReadData: Not a scalar volume file: C:/Users/Csaba/Downloads/Temp/20170330_DICOM_EXPORT/DICOM_EXPORT/GEMS_IMG/2017_MAR/28/TT121224/H3SCD68C"

Is this some kind of multiparametric ultrasound image? The reader expects simple grayscale image.

csaba

[1]
>>> Imported a DICOM directory, checking for extensions
Traceback (most recent call last):
  File "C:/d/S4R/Slicer-build/lib/Slicer-4.7/qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 408, in timerCallback
    self.promptForExtensions()
  File "C:/d/S4R/Slicer-build/lib/Slicer-4.7/qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 413, in promptForExtensions
    extensionsToOffer = self.checkForExtensions()
  File "C:/d/S4R/Slicer-build/lib/Slicer-4.7/qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 478, in checkForExtensions
    sopClassUID = slicer.dicomDatabase.fileValue(instance0, sopClassUIDTag)
RuntimeError: std::logic_error: Calling methods on uninitialized ctkDICOMItem

[2] Warning in DICOM plugin Scalar Volume when examining loadable 1: Unnamed Series: Reference image in series does not contain geometry information.  Please use caution.

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Chris
Sent: Thursday, March 30, 2017 08:15
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] LOGIQ E9 Volume Slices Processing

Hi,

this is the link to a zip on dropbox containing the the Exported Directory:

https://www.dropbox.com/s/ezxwpj2li3qnilk/DICOM_EXPORT.zip?dl=0

The data is anonymized with Dicom Anonym 1.1.6.1


I can import it to the DICOM Browser but cannot load and get this error
message:

Could not load: 1: Unnamed Series as a Scalar Volume"


This is the error Log of 3DSlicer

______

Session start time .......: 2017-03-30 14:12:36 Slicer version ...........: 4.6.2 (revision 25516) macosx-amd64 - installed Operating system .........: Mac OS X / 10.11.6 / 15G1421 - 64-bit Memory ...................: 8192 MB physical, 0 MB virtual
CPU ......................: GenuineIntel Intel(R) Core(TM)2 Duo CPU
T9550  @ 2.66GHz, 2 cores, 2 logical processors Developer mode enabled ...: no Prefer executable CLI ....: yes Additional module paths ..: (none) Number of registered modules: 133 Number of instantiated modules: 133 When loading module  "CLIEventTest" , the dependency "CLI4Test" failed to be loaded.
Initializing terminology mapping for map file /Applications/Slicer.app/Contents/share/Slicer-4.6/ColorFiles/Terminology//GenericAnatomyColors-SNOMED.csv
288 terms were read for Slicer LUT GenericAnatomyColors When loading module  "TwoCLIsInARowTest" , the dependency "CLI4Test"
failed to be loaded.
When loading module  "TwoCLIsInParallelTest" , the dependency "CLI4Test"
failed to be loaded.
Number of loaded modules: 130
Switch to module:  "Welcome"
Switch to module:  "DICOM"
MultiVolumeImportPlugin::examine
DICOMMultiVolumePlugin found 1 multivolumes!
MultiVolumeImportPlugin:examineMultiseries
DICOMMultiVolumePlugin found 0 multivolumes!
MultiVolumeImportPlugin::examine
DICOMMultiVolumePlugin found 1 multivolumes!
MultiVolumeImportPlugin:examineMultiseries
DICOMMultiVolumePlugin found 0 multivolumes!
MultiVolumeImportPlugin::examine
DICOMMultiVolumePlugin found 1 multivolumes!
MultiVolumeImportPlugin:examineMultiseries
DICOMMultiVolumePlugin found 0 multivolumes!
MultiVolumeImportPlugin::examine
DICOMMultiVolumePlugin found 1 multivolumes!
MultiVolumeImportPlugin:examineMultiseries
DICOMMultiVolumePlugin found 0 multivolumes!
UpdateFromSeries: Unsupported number of components: 1 != 3




ReadData: Not a scalar volume file:
/Users/ole/Desktop/logiq/DICOM_EXPORT/GEMS_IMG/2017_MAR/28/TT121224/H3SCD68C




2017-03-30 14:13:18.315 Slicer[2756:115813] IMKClient Stall detected, *please Report* your user scenario attaching a spindump (or sysdiagnose) that captures the problem - (imkxpc_attributesForCharacterIndex:reply:)
block performed very slowly (4.07 secs).
2017-03-30 14:13:18.315 Slicer[2756:115813] IMKClient Stall detected, *please Report* your user scenario attaching a spindump (or sysdiagnose) that captures the problem - (imkxpc_windowLevelWithReply:) block performed very slowly (2.07 secs).


Could not load: 1: Unnamed Series as a Scalar Volume


Could not load: 1: Unnamed Series as a Scalar Volume
2017-03-30 14:13:19.868 Slicer[2756:115813] modalSession has been exited prematurely - check for a reentrant call to endModalSession:


-----



On 30/03/17 11:33, Chris wrote:
>    Hi Everyone,
>
> For a student project I was assigned the Task to prototype an Ultrasound
> Learning App based on
> Ultrasound Volumes obtained by a GE LOGIQ E9.
>
> The assignment is: Create a standalone App that allows you to swipe
> through the Volume Image Slices.
>
> We have access to a LOGIQ E9 and I got a Volume Scan done and exported a
> directory to my USB drive of about 570 MB.
>
> I have Slicer installed and tried to load the Dicom Directory but it
> gives me an error:
> "Could not load: 1: Unnamed Series as a Scalar Volume"
>
> Does anyone have experience on how to open or use the LOGIQ E9 Data or
> know what I am doing wrong?
>
> If it helps I am willing to upload such Directory to e.g. dropbox if it
> helps - the Dataset contains no Private Information, is anonymized and I
> am allowed to share it.
>
>
> Best Regards,
>
> Chris Hansen
>
> Student of Medical Information Technology at the University of Applied
> Sciences Bremerhaven
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ