import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

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import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
This post has NOT been accepted by the mailing list yet.
Hi,
I have tried to import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips), generated by Qlab. After patching, I have followed the steps reported in this forum: “To load DICOM images to Slicer, drag-and-drop the folder that contains the DICOM file and choose “Load directory into DICOM database” to import. To load the image into Slicer, choose the image in the DICOM browser and click “Load” button. There is a small bug in the DICOM loader for cardiac 4D US files, which causes a popup window to remain on the screen after loading is completed – just click”
The problem is that the popup windows remain at the 0%, the process doesn’t go on.
This is the log file :
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - database filename for  "2.25.130781512219424787854096217494124025481"  is empty - we should insert on top of it
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - This looks like a different patient from last insert:  "2.25.130781512377881112886188365886368831113"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted: 4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted as :  4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Going to insert this instance with dbPatientID:  4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new study:  "2.25.130781512457109275397335086637865555593"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Study Added
[WARNING][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Statement: SELECT * FROM Series WHERE SeriesInstanceUID = ?
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new series:  "2.25.130781512536337437913842779795793434249"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Series Added
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Maybe add Instance
[DEBUG][Qt] 13.01.2017 10:33:54 [] (unknown:0) - Instance Added
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:392) - MultiVolumeImportPlugin::examine
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:432) - DICOMMultiVolumePlugin found 0 multivolumes!
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:105) - MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:110) - DICOMMultiVolumePlugin found 0 multivolumes!
[WARNING][VTK] 13.01.2017 10:34:00 [vtkMRMLSequenceBrowserNode (0000014166C9D1E0)] (c:\d\n\s462-e-b\sequences\sequencebrowser\mrml\vtkMRMLSequenceBrowserNode.h:178) - vtkMRMLSequenceBrowserNode::GetVirtualOutputDataNode is deprecated, use vtkMRMLSequenceBrowserNode::GetProxyNode method instead
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program Files\Slicer 4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 712, in loadCheckedLoadables
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     self.proceedWithReferencedLoadablesSelection()
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program Files\Slicer 4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 762, in proceedWithReferencedLoadablesSelection
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     if not plugin.load(loadable):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py", line 116, in load
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     return self.loadAsSequence(loadable)
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py", line 187, in loadAsSequence
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     outputSequenceBrowserNode.ScalarVolumeAutoWindowLevelOff() # for performance optimization
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - AttributeError: 'vtkCommonCorePython.vtkMRMLSequenceBrowserNode' object has no attribute 'ScalarVolumeAutoWindowLevelOff'
Could you help me? 
Thanks!
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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
Hi,
I have tried to import in 3d slicer a Cartesian dicom file (cardiac 4D US -
philips), generated by Qlab. After patching, I have followed the steps
reported in this forum: “To load DICOM images to Slicer, drag-and-drop the
folder that contains the DICOM file and choose “Load directory into DICOM
database” to import. To load the image into Slicer, choose the image in the
DICOM browser and click “Load” button. There is a small bug in the DICOM
loader for cardiac 4D US files, which causes a popup window to remain on the
screen after loading is completed – just click”
The problem is that the popup windows remain at the 0%, the process doesn’t
go on.
This is the log file :
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - database filename for
"2.25.130781512219424787854096217494124025481"  is empty - we should insert
on top of it
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - This looks like a different
patient from last insert:  "2.25.130781512377881112886188365886368831113"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted: 4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted as :
4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Going to insert this
instance with dbPatientID:  4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new study:
"2.25.130781512457109275397335086637865555593"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Study Added
[WARNING][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Statement: SELECT * FROM
Series WHERE SeriesInstanceUID = ?
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new series:
"2.25.130781512536337437913842779795793434249"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Series Added
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Maybe add Instance
[DEBUG][Qt] 13.01.2017 10:33:54 [] (unknown:0) - Instance Added
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:392) -
MultiVolumeImportPlugin::examine
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:432) -
DICOMMultiVolumePlugin found 0 multivolumes!
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:105) -
MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:110) -
DICOMMultiVolumePlugin found 0 multivolumes!
[WARNING][VTK] 13.01.2017 10:34:00 [vtkMRMLSequenceBrowserNode
(0000014166C9D1E0)]
(c:\d\n\s462-e-b\sequences\sequencebrowser\mrml\vtkMRMLSequenceBrowserNode.h:178)
- vtkMRMLSequenceBrowserNode::GetVirtualOutputDataNode is deprecated, use
vtkMRMLSequenceBrowserNode::GetProxyNode method instead
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - Traceback (most
recent call last):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program
Files\Slicer
4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line
712, in loadCheckedLoadables
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -    
self.proceedWithReferencedLoadablesSelection()
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program
Files\Slicer
4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line
762, in proceedWithReferencedLoadablesSelection
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     if not
plugin.load(loadable):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File
"C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py",
line 116, in load
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     return
self.loadAsSequence(loadable)
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File
"C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py",
line 187, in loadAsSequence
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -    
outputSequenceBrowserNode.ScalarVolumeAutoWindowLevelOff() # for performance
optimization
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - AttributeError:
'vtkCommonCorePython.vtkMRMLSequenceBrowserNode' object has no attribute
'ScalarVolumeAutoWindowLevelOff'
Could you help me? 
Thanks!




--
View this message in context: http://slicer-users.65878.n3.nabble.com/import-in-3d-slicer-a-Cartesian-dicom-file-cardiac-4D-US-philips-tp4031565p4031566.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
This post has NOT been accepted by the mailing list yet.
In reply to this post by GIOVIVI
Hi,
I have tried to import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips), generated by Qlab. After patching, I have followed the steps reported in this forum: “To load DICOM images to Slicer, drag-and-drop the folder that contains the DICOM file and choose “Load directory into DICOM database” to import. To load the image into Slicer, choose the image in the DICOM browser and click “Load” button. There is a small bug in the DICOM loader for cardiac 4D US files, which causes a popup window to remain on the screen after loading is completed – just click”
The problem is that the popup windows remain at the 0%, the process doesn’t go on.
This is the log file :
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - database filename for  "2.25.130781512219424787854096217494124025481"  is empty - we should insert on top of it
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - This looks like a different patient from last insert:  "2.25.130781512377881112886188365886368831113"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted: 4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted as :  4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Going to insert this instance with dbPatientID:  4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new study:  "2.25.130781512457109275397335086637865555593"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Study Added
[WARNING][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Statement: SELECT * FROM Series WHERE SeriesInstanceUID = ?
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new series:  "2.25.130781512536337437913842779795793434249"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Series Added
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Maybe add Instance
[DEBUG][Qt] 13.01.2017 10:33:54 [] (unknown:0) - Instance Added
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:392) - MultiVolumeImportPlugin::examine
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:432) - DICOMMultiVolumePlugin found 0 multivolumes!
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:105) - MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer 4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:110) - DICOMMultiVolumePlugin found 0 multivolumes!
[WARNING][VTK] 13.01.2017 10:34:00 [vtkMRMLSequenceBrowserNode (0000014166C9D1E0)] (c:\d\n\s462-e-b\sequences\sequencebrowser\mrml\vtkMRMLSequenceBrowserNode.h:178) - vtkMRMLSequenceBrowserNode::GetVirtualOutputDataNode is deprecated, use vtkMRMLSequenceBrowserNode::GetProxyNode method instead
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program Files\Slicer 4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 712, in loadCheckedLoadables
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     self.proceedWithReferencedLoadablesSelection()
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program Files\Slicer 4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 762, in proceedWithReferencedLoadablesSelection
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     if not plugin.load(loadable):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py", line 116, in load
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     return self.loadAsSequence(loadable)
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py", line 187, in loadAsSequence
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     outputSequenceBrowserNode.ScalarVolumeAutoWindowLevelOff() # for performance optimization
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - AttributeError: 'vtkCommonCorePython.vtkMRMLSequenceBrowserNode' object has no attribute 'ScalarVolumeAutoWindowLevelOff'
Could you help me? 
Thanks!
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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Andras Lasso-2
In reply to this post by GIOVIVI
In the patcher there is an option to save the image as .nrrd file. We almost exclusively use that because the only additional metadata that the DICOM file stores is the patient/study/image name. You can load the .nrrd file as a volume sequence using Sequences extension.

Use a recent (not older than a few weeks) nightly version of Slicer. Let us know if you run into any problem.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of GIOVIVI
Sent: January 13, 2017 8:31
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Hi,
I have tried to import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips), generated by Qlab. After patching, I have followed the steps reported in this forum: “To load DICOM images to Slicer, drag-and-drop the folder that contains the DICOM file and choose “Load directory into DICOM database” to import. To load the image into Slicer, choose the image in the DICOM browser and click “Load” button. There is a small bug in the DICOM loader for cardiac 4D US files, which causes a popup window to remain on the screen after loading is completed – just click”
The problem is that the popup windows remain at the 0%, the process doesn’t go on.
This is the log file :
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - database filename for "2.25.130781512219424787854096217494124025481"  is empty - we should insert on top of it [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - This looks like a different patient from last insert:  "2.25.130781512377881112886188365886368831113"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted: 4 [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted as :
4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Going to insert this instance with dbPatientID:  4 [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new study:
"2.25.130781512457109275397335086637865555593"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Study Added [WARNING][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Statement: SELECT * FROM Series WHERE SeriesInstanceUID = ?
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new series:
"2.25.130781512536337437913842779795793434249"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Series Added [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Maybe add Instance [DEBUG][Qt] 13.01.2017 10:33:54 [] (unknown:0) - Instance Added [DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:392) - MultiVolumeImportPlugin::examine [DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:432) - DICOMMultiVolumePlugin found 0 multivolumes!
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:105) - MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:110) - DICOMMultiVolumePlugin found 0 multivolumes!
[WARNING][VTK] 13.01.2017 10:34:00 [vtkMRMLSequenceBrowserNode (0000014166C9D1E0)]
(c:\d\n\s462-e-b\sequences\sequencebrowser\mrml\vtkMRMLSequenceBrowserNode.h:178)
- vtkMRMLSequenceBrowserNode::GetVirtualOutputDataNode is deprecated, use vtkMRMLSequenceBrowserNode::GetProxyNode method instead [CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program
Files\Slicer
4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 712, in loadCheckedLoadables
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -    
self.proceedWithReferencedLoadablesSelection()
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program
Files\Slicer
4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 762, in proceedWithReferencedLoadablesSelection
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     if not
plugin.load(loadable):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File
"C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py",
line 116, in load
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     return
self.loadAsSequence(loadable)
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File
"C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py",
line 187, in loadAsSequence
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -    
outputSequenceBrowserNode.ScalarVolumeAutoWindowLevelOff() # for performance optimization [CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - AttributeError:
'vtkCommonCorePython.vtkMRMLSequenceBrowserNode' object has no attribute 'ScalarVolumeAutoWindowLevelOff'
Could you help me? 
Thanks!




--
View this message in context: http://slicer-users.65878.n3.nabble.com/import-in-3d-slicer-a-Cartesian-dicom-file-cardiac-4D-US-philips-tp4031565p4031566.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Andras Lasso-2
I've just tested and patched 4D ultrasound DICOM files can be loaded correctly into Slicer. Make sure to:
1. Have SlicerHeart and Sequences extension installed
2. To import, drag-and-drop the directory that contains the DICOM file(s) and not an individual DICOM file

At some point there was an error in loading, so use a recent version of Slicer.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andras Lasso
Sent: January 13, 2017 10:14
To: GIOVIVI <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

In the patcher there is an option to save the image as .nrrd file. We almost exclusively use that because the only additional metadata that the DICOM file stores is the patient/study/image name. You can load the .nrrd file as a volume sequence using Sequences extension.

Use a recent (not older than a few weeks) nightly version of Slicer. Let us know if you run into any problem.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of GIOVIVI
Sent: January 13, 2017 8:31
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Hi,
I have tried to import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips), generated by Qlab. After patching, I have followed the steps reported in this forum: “To load DICOM images to Slicer, drag-and-drop the folder that contains the DICOM file and choose “Load directory into DICOM database” to import. To load the image into Slicer, choose the image in the DICOM browser and click “Load” button. There is a small bug in the DICOM loader for cardiac 4D US files, which causes a popup window to remain on the screen after loading is completed – just click”
The problem is that the popup windows remain at the 0%, the process doesn’t go on.
This is the log file :
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - database filename for "2.25.130781512219424787854096217494124025481"  is empty - we should insert on top of it [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - This looks like a different patient from last insert:  "2.25.130781512377881112886188365886368831113"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted: 4 [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - New patient inserted as :
4
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Going to insert this instance with dbPatientID:  4 [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new study:
"2.25.130781512457109275397335086637865555593"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Study Added [WARNING][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Statement: SELECT * FROM Series WHERE SeriesInstanceUID = ?
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Need to insert new series:
"2.25.130781512536337437913842779795793434249"
[DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Series Added [DEBUG][Qt] 13.01.2017 10:33:53 [] (unknown:0) - Maybe add Instance [DEBUG][Qt] 13.01.2017 10:33:54 [] (unknown:0) - Instance Added [DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:392) - MultiVolumeImportPlugin::examine [DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:432) - DICOMMultiVolumePlugin found 0 multivolumes!
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:105) - MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 13.01.2017 10:33:58 [Python] (C:/Program Files/Slicer
4.6.2/lib/Slicer-4.6/qt-scripted-modules/MultiVolumeImporterPlugin.py:110) - DICOMMultiVolumePlugin found 0 multivolumes!
[WARNING][VTK] 13.01.2017 10:34:00 [vtkMRMLSequenceBrowserNode (0000014166C9D1E0)]
(c:\d\n\s462-e-b\sequences\sequencebrowser\mrml\vtkMRMLSequenceBrowserNode.h:178)
- vtkMRMLSequenceBrowserNode::GetVirtualOutputDataNode is deprecated, use vtkMRMLSequenceBrowserNode::GetProxyNode method instead [CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program
Files\Slicer
4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 712, in loadCheckedLoadables
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -    
self.proceedWithReferencedLoadablesSelection()
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File "C:\Program
Files\Slicer
4.6.2\lib\Slicer-4.6\qt-scripted-modules\DICOMLib\DICOMWidgets.py", line 762, in proceedWithReferencedLoadablesSelection
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     if not
plugin.load(loadable):
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File
"C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py",
line 116, in load
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -     return
self.loadAsSequence(loadable)
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -   File
"C:/Users/BCL_XPS/AppData/Roaming/NA-MIC/Extensions-25516/SlicerHeart/lib/Slicer-4.6/qt-scripted-modules/DicomUltrasoundPlugin.py",
line 187, in loadAsSequence
[CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) -    
outputSequenceBrowserNode.ScalarVolumeAutoWindowLevelOff() # for performance optimization [CRITICAL][Stream] 13.01.2017 10:34:00 [] (unknown:0) - AttributeError:
'vtkCommonCorePython.vtkMRMLSequenceBrowserNode' object has no attribute 'ScalarVolumeAutoWindowLevelOff'
Could you help me? 
Thanks!




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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
Thanks a lot for your help!
Installing the new release, I resolved the problem!
Now, I have another questions!
I have a sequence ( 3D volume + time(112 frames))...
can I export the dicom file relative to a specific frame (for example the
5th frame)??
In other words, is it possible to extract, from a 4d series US, a 3d dicom
file?
Thank you for the help!!



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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
This post has NOT been accepted by the mailing list yet.
In reply to this post by Andras Lasso-2
Thanks a lot for your help!
Installing the new release, I resolved the problem!
Now, I have another questions!
I have a sequence ( 3D volume + time(112 frames))...
can I export the dicom file relative to a specific frame (for example the 5th frame)??
In other words, is it possible to extract, from a 4d series US, a 3d dicom file?
Thank you for the help!!
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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Andras Lasso-2
In reply to this post by GIOVIVI
It's doable, but correct DICOM export is not simple. What software you would like to load the data into?

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of GIOVIVI
Sent: January 18, 2017 5:40
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Thanks a lot for your help!
Installing the new release, I resolved the problem!
Now, I have another questions!
I have a sequence ( 3D volume + time(112 frames))...
can I export the dicom file relative to a specific frame (for example the 5th frame)??
In other words, is it possible to extract, from a 4d series US, a 3d dicom file?
Thank you for the help!!



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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
This post has NOT been accepted by the mailing list yet.
I would process the single frames in Matlab, or, anyway, I wount separate the frames!

The original file (4D US from Philips IE33) is a Cartesian DICOM (exported from QLAB). When I import it in 3D Slicer, the Metadata-file shows these informations:

- rows 112
- columns 128
- number of frames 112
- Unknown Tag & Data 208 (that should be the number of slices)

I would like to obtain 112 DICOM files, each of which 112X128X208

...is it possibile?
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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
In reply to this post by Andras Lasso-2
I would process the single frames in Matlab, or, anyway, I wount separate the
frames!

The original file (4D US from Philips IE33) is a Cartesian DICOM (exported
from QLAB). When I import it in 3D Slicer, the Metadata-file shows these
informations:

- rows 112
- columns 128
- number of frames 112
- Unknown Tag & Data 208 (that should be the number of slices)

I would like to obtain 112 DICOM files, each of which 112X128X208

...is it possibile?



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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Andrey Fedorov-2
In reply to this post by Andras Lasso-2
This task is best solved outside of Slicer. With 3d + time there typically is some (platform and sequence dependent) attribute that is used to identify individual time points. You can use that attribute to subset your DICOM instances. The specifics cannot be clarified without having access to the data.

On Jan 18, 2017 08:34, "Andras Lasso" <[hidden email]> wrote:
It's doable, but correct DICOM export is not simple. What software you would like to load the data into?

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of GIOVIVI
Sent: January 18, 2017 5:40
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Thanks a lot for your help!
Installing the new release, I resolved the problem!
Now, I have another questions!
I have a sequence ( 3D volume + time(112 frames))...
can I export the dicom file relative to a specific frame (for example the 5th frame)??
In other words, is it possible to extract, from a 4d series US, a 3d dicom file?
Thank you for the help!!



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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Andras Lasso-2
In reply to this post by Andras Lasso-2

The Cartesion DICOM files that QLab exports are “fake” DICOM files. They use a private SOP class UID and only store patient name, ID, image spacing, and frame timestamps. We don’t lose any information by saving them as NRRD files, so I would recommend the NRRD format in this case.

 

For accessing frames in Matlab, I would suggest to import the data into Slicer and save as nrrd (you can save to NRRD directly in the Philips DICOM patcher module).

 

To read the 4D nrrd files (as a 4D matrix into Matlab) using our NRRD reader:

https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/nrrdread.m

 

In Slicer you can also save the current 3D frame as a NRRD file. You can use the same reader as above, it’ll read pixel data as a 3D matrix.

 

You can also use MatlabBridge extension to run you Matlab functions directly from Slicer and visualize results directly in Slicer. See more details here:

https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge

 

We are working on developing valve annulus contouring, leaflet segmentation, quantification modules. These modules will be publicly released as they get published.

 

Andras

 

From: Andrey Fedorov [mailto:[hidden email]]
Sent: January 18, 2017 9:32
To: Andras Lasso <[hidden email]>
Cc: [hidden email]; GIOVIVI <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

 

This task is best solved outside of Slicer. With 3d + time there typically is some (platform and sequence dependent) attribute that is used to identify individual time points. You can use that attribute to subset your DICOM instances. The specifics cannot be clarified without having access to the data.

 

On Jan 18, 2017 08:34, "Andras Lasso" <[hidden email]> wrote:

It's doable, but correct DICOM export is not simple. What software you would like to load the data into?

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of GIOVIVI
Sent: January 18, 2017 5:40
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Thanks a lot for your help!
Installing the new release, I resolved the problem!
Now, I have another questions!
I have a sequence ( 3D volume + time(112 frames))...
can I export the dicom file relative to a specific frame (for example the 5th frame)??
In other words, is it possible to extract, from a 4d series US, a 3d dicom file?
Thank you for the help!!



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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
I have imported the data into Slicer and saved as nrrd; but when i import
nrrd file in the matlab workspace (using filename = uigetfile('*.nrrd')) and
call the function
nrrdread that you have suggested, there is an error:

Error in nrrdread>readData (line 152)
switch (meta.encoding)

Output argument "data" (and maybe others) not assigned during call to
"C:\...\nrrdread.m>readData".

Error in nrrdread (line 94)
data = readData(fid, img.metaData, datatype);


Could you tell me where am I wrong??

(excuse my clumsiness! I'm starting to work with these tools for the first
time!!)





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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

GIOVIVI
This post has NOT been accepted by the mailing list yet.
In reply to this post by Andras Lasso-2
I have imported the data into Slicer and saved as nrrd; but when i import
nrrd file in the matlab workspace (using filename = uigetfile('*.nrrd')) and call the function
nrrdread that you have suggested, there is an error:

Error in nrrdread>readData (line 152)
switch (meta.encoding)

Output argument "data" (and maybe others) not assigned during call to
"C:\...\nrrdread.m>readData".

Error in nrrdread (line 94)
data = readData(fid, img.metaData, datatype);


Could you tell me where am I wrong??

(excuse my clumsiness! I'm starting to work with these tools for the first
time!!)

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Re: import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

Andras Lasso-2
In reply to this post by GIOVIVI
4D image sequences may be too large to fit in default Java heap space in Matlab while being uncompressed. Either increase Java heap space in Matlab preferences or save the 4D image sequence file as uncompressed nrrd file.

To re-save a nrrd file without compression:
* Load sequence nrrd file into Slicer
* Open Save data dialog
* Click "Show options" in the top-right corner
* Uncheck "Compress" in the line of the ultrasound seq.nrrd file's row
* Click Save

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of GIOVIVI
Sent: January 18, 2017 16:27
To: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] import in 3d slicer a Cartesian dicom file (cardiac 4D US - philips)

I have imported the data into Slicer and saved as nrrd; but when i import nrrd file in the matlab workspace (using filename = uigetfile('*.nrrd')) and call the function nrrdread that you have suggested, there is an error:

Error in nrrdread>readData (line 152)
switch (meta.encoding)

Output argument "data" (and maybe others) not assigned during call to "C:\...\nrrdread.m>readData".

Error in nrrdread (line 94)
data = readData(fid, img.metaData, datatype);


Could you tell me where am I wrong??

(excuse my clumsiness! I'm starting to work with these tools for the first
time!!)





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