Contoured Structures look like parrallel plates

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Contoured Structures look like parrallel plates

Guangming Ma
Hi Slicer users,

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

Regards,
Guangming

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Re: Contoured Structures look like parrallel plates

Sharp, Gregory C.
Hi Guangming,
 
Do you mean there are gaps between the "parallel plates"?
 
And do the labelmaps show corresponding gaps?
 
A screenshot may help.
 
Greg


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

Regards,
Guangming

_______________________________________________
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/4.2/FAQ
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Re: Contoured Structures look like parrallel plates

Guangming Ma
Hi Greg,

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

Kind regards,
Guangming


On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Guangming,
 
Do you mean there are gaps between the "parallel plates"?
 
And do the labelmaps show corresponding gaps?
 
A screenshot may help.
 
Greg


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

Regards,
Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



_______________________________________________
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/4.2/FAQ

parralel plates instead of a whole volume.jpg (240K) Download Attachment
normal whole volume.jpg (216K) Download Attachment
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Re: Contoured Structures look like parrallel plates

Csaba Pinter
Hi Guangming,

The "plates" with the gaps between those are most probably the symptom of a wrong slice thickness value for the structure. The way it ended up being wrong, especially that you were able to read it right the next time, is a good question.

If you experience the same problem again, please send us the errors you find in the Error Log, mainly the ones that originate from any vtkSlicerDicomRtImport* class after double-checking that the slice thickness value in the DICOM file is indeed right.

Cheers,
csaba


On 8/28/2013 15:43, Guangming Ma wrote:
Hi Greg,

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

Kind regards,
Guangming


On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Guangming,
 
Do you mean there are gaps between the "parallel plates"?
 
And do the labelmaps show corresponding gaps?
 
A screenshot may help.
 
Greg


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

Regards,
Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




_______________________________________________
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/4.2/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/4.2/FAQ
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Re: Contoured Structures look like parrallel plates

Guangming Ma
In reply to this post by Guangming Ma
Hi all,

the same problem happens again.

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

The Error log indicates following information:
"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507
vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

Best regards,
Guangming


On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:
Hi Greg,

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

Kind regards,
Guangming


On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Guangming,
 
Do you mean there are gaps between the "parallel plates"?
 
And do the labelmaps show corresponding gaps?
 
A screenshot may help.
 
Greg


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

Regards,
Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

closed surface.png (127K) Download Attachment
error log.png (117K) Download Attachment
indexedLabelmap.png (140K) Download Attachment
ribbon.png (197K) Download Attachment
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Re: Contoured Structures look like parrallel plates

Csaba Pinter-2

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: Contoured Structures look like parrallel plates

Guangming Ma
Hi Csaba,

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

By the way, where can I find the "dcmdump" in slicer?

Regards, 
Guangming


On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 



_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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Re: Contoured Structures look like parrallel plates

Csaba Pinter-2

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 

 


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: Contoured Structures look like parrallel plates

Guangming Ma
Hi Csaba,

those UIDs above mentioned except (0008,1155) can't be found in the dicom header of CT volume, which is in the same study as the structure set. In other words, only (0008,1155) can be found in the dicom header.

I am wondering, if it is possible to change the slicer value from 2 (default) to 4. Thanks a lot.

Best,
Guangming


On Mon, Dec 9, 2013 at 5:11 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 

 



_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Contoured Structures look like parrallel plates

Csaba Pinter-2

Hi Guangming,

 

I'm not sure if I understand what you described. The tag referencing the CT slice SOP instance UID should not be in the CT at all. What we expect is if the structure set has an entry like this:

              (fffe,e000) na (Item with explicit length #=2)          #  94, 1 Item

                (0008,1150) UI =CTImageStorage                          #  26, 1 ReferencedSOPClassUID

                (0008,1155) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 ReferencedSOPInstanceUID

              (fffe,e00d) na (ItemDelimitationItem for re-encoding)   #   0, 0 ItemDelimitationItem

 

then there should be a CT slice with a header entry

    (0008,0018) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 SOPInstanceUID

 

Does this apply for your dataset? If yes, then I need to see your data to find out why the slice thickness cannot be determined. If no, then it is not a bug in SlicerRT, so we need to find another solution.

 

About changing the default slice thickness, I don't think it is a good solution, as what works for you doesn't necessarily work for someone else (our 2.5mm default thickness came from our very first sample data).

The only reason why we still have a default slice thickness is to be able to display "something" even without the correct slice thickness, as without converting the contour points to ribbon, virtually nothing could be seen of it in the 3D view.

 

The proper long-term solution would be a robust slice thickness computation algorithm, that (in absence of the referenced value) would compute the slice thickness based on the contour point data in the structure set. However, we don't have the capacity to implement this within the next month or so.

 

A possible short-term solution could be an option in the Contours module that would allow the user to re-ribbonize the contour data using a specific thickness value, or an entry in the Slicer...ini file specifying the default slice thickness. We could implement either option quite quickly.

Andras, Adam, everyone, what do you think?

 

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 11:40
To: Csaba Pinter
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

those UIDs above mentioned except (0008,1155) can't be found in the dicom header of CT volume, which is in the same study as the structure set. In other words, only (0008,1155) can be found in the dicom header.

 

I am wondering, if it is possible to change the slicer value from 2 (default) to 4. Thanks a lot.

 

Best,

Guangming

 

On Mon, Dec 9, 2013 at 5:11 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 

 

 


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: Contoured Structures look like parrallel plates

Guangming Ma
Hi Csaba,

thank you so much! But I know almost nothing about DICOM headers etc. So don't be confused by my misleading description. 

I would love to send you the information in "DICOM tag inspector", but it is too long to fit into screenshot. And I cannot copy or save it. 

Just looked into the lengthy header information of the structure set, I didn't find an entry exactly match what you described in your previous respond. 

Hopefully we can find a solution soon. Thanks a lot!

Regards,
Guangming


On Mon, Dec 9, 2013 at 6:26 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

I'm not sure if I understand what you described. The tag referencing the CT slice SOP instance UID should not be in the CT at all. What we expect is if the structure set has an entry like this:

              (fffe,e000) na (Item with explicit length #=2)          #  94, 1 Item

                (0008,1150) UI =CTImageStorage                          #  26, 1 ReferencedSOPClassUID

                (0008,1155) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 ReferencedSOPInstanceUID

              (fffe,e00d) na (ItemDelimitationItem for re-encoding)   #   0, 0 ItemDelimitationItem

 

then there should be a CT slice with a header entry

    (0008,0018) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 SOPInstanceUID

 

Does this apply for your dataset? If yes, then I need to see your data to find out why the slice thickness cannot be determined. If no, then it is not a bug in SlicerRT, so we need to find another solution.

 

About changing the default slice thickness, I don't think it is a good solution, as what works for you doesn't necessarily work for someone else (our 2.5mm default thickness came from our very first sample data).

The only reason why we still have a default slice thickness is to be able to display "something" even without the correct slice thickness, as without converting the contour points to ribbon, virtually nothing could be seen of it in the 3D view.

 

The proper long-term solution would be a robust slice thickness computation algorithm, that (in absence of the referenced value) would compute the slice thickness based on the contour point data in the structure set. However, we don't have the capacity to implement this within the next month or so.

 

A possible short-term solution could be an option in the Contours module that would allow the user to re-ribbonize the contour data using a specific thickness value, or an entry in the Slicer...ini file specifying the default slice thickness. We could implement either option quite quickly.

Andras, Adam, everyone, what do you think?

 

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 11:40
To: Csaba Pinter


Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

those UIDs above mentioned except (0008,1155) can't be found in the dicom header of CT volume, which is in the same study as the structure set. In other words, only (0008,1155) can be found in the dicom header.

 

I am wondering, if it is possible to change the slicer value from 2 (default) to 4. Thanks a lot.

 

Best,

Guangming

 

On Mon, Dec 9, 2013 at 5:11 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 

 

 



_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: Contoured Structures look like parrallel plates

Csaba Pinter-2

Hi Guangming,

 

It is very strange that the CT has no SOP instance UID, as it is one of the most basic tags there is, and without it the CT is invalid.

Can you share the files themselves with me? If the dataset is anonymized it should be OK.

 

The command-line program dcmdump, which I described earlier is does a very similar thing as the tags inspector in the DICOM browser, so if you use that then you get a text file with all the tags, and you can send it easily. However at this point the data itself would be more helpful.

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 13:10
To: Csaba Pinter
Cc: [hidden email]; Andras Lasso; Adam Rankin
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thank you so much! But I know almost nothing about DICOM headers etc. So don't be confused by my misleading description. 

 

I would love to send you the information in "DICOM tag inspector", but it is too long to fit into screenshot. And I cannot copy or save it. 

 

Just looked into the lengthy header information of the structure set, I didn't find an entry exactly match what you described in your previous respond. 

 

Hopefully we can find a solution soon. Thanks a lot!

 

Regards,

Guangming

 

On Mon, Dec 9, 2013 at 6:26 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

I'm not sure if I understand what you described. The tag referencing the CT slice SOP instance UID should not be in the CT at all. What we expect is if the structure set has an entry like this:

              (fffe,e000) na (Item with explicit length #=2)          #  94, 1 Item

                (0008,1150) UI =CTImageStorage                          #  26, 1 ReferencedSOPClassUID

                (0008,1155) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 ReferencedSOPInstanceUID

              (fffe,e00d) na (ItemDelimitationItem for re-encoding)   #   0, 0 ItemDelimitationItem

 

then there should be a CT slice with a header entry

    (0008,0018) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 SOPInstanceUID

 

Does this apply for your dataset? If yes, then I need to see your data to find out why the slice thickness cannot be determined. If no, then it is not a bug in SlicerRT, so we need to find another solution.

 

About changing the default slice thickness, I don't think it is a good solution, as what works for you doesn't necessarily work for someone else (our 2.5mm default thickness came from our very first sample data).

The only reason why we still have a default slice thickness is to be able to display "something" even without the correct slice thickness, as without converting the contour points to ribbon, virtually nothing could be seen of it in the 3D view.

 

The proper long-term solution would be a robust slice thickness computation algorithm, that (in absence of the referenced value) would compute the slice thickness based on the contour point data in the structure set. However, we don't have the capacity to implement this within the next month or so.

 

A possible short-term solution could be an option in the Contours module that would allow the user to re-ribbonize the contour data using a specific thickness value, or an entry in the Slicer...ini file specifying the default slice thickness. We could implement either option quite quickly.

Andras, Adam, everyone, what do you think?

 

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 11:40
To: Csaba Pinter


Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

those UIDs above mentioned except (0008,1155) can't be found in the dicom header of CT volume, which is in the same study as the structure set. In other words, only (0008,1155) can be found in the dicom header.

 

I am wondering, if it is possible to change the slicer value from 2 (default) to 4. Thanks a lot.

 

Best,

Guangming

 

On Mon, Dec 9, 2013 at 5:11 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 

 

 

 


_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: Contoured Structures look like parrallel plates

Guangming Ma
Hi Csaba,

you are absolutely right. My structure set and the images were from different sources, therefore they were inconsistent. No wonder Slicer couldn't find the reference image. 

I exported the structure set together with the images again, and the structures are now shown without gaps in slicer. That is to say, the problem was caused by the inconsistancy of my dicom dataset. And from my point of view, it is solved. 

Of course, SlicerRT could be improved on this issue. I will be happy to test it when the it comes to a better solution in the future. Thank you so much for the help!

Best regards,
Guangming


On Mon, Dec 9, 2013 at 7:15 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

It is very strange that the CT has no SOP instance UID, as it is one of the most basic tags there is, and without it the CT is invalid.

Can you share the files themselves with me? If the dataset is anonymized it should be OK.

 

The command-line program dcmdump, which I described earlier is does a very similar thing as the tags inspector in the DICOM browser, so if you use that then you get a text file with all the tags, and you can send it easily. However at this point the data itself would be more helpful.

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 13:10
To: Csaba Pinter
Cc: [hidden email]; Andras Lasso; Adam Rankin


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thank you so much! But I know almost nothing about DICOM headers etc. So don't be confused by my misleading description. 

 

I would love to send you the information in "DICOM tag inspector", but it is too long to fit into screenshot. And I cannot copy or save it. 

 

Just looked into the lengthy header information of the structure set, I didn't find an entry exactly match what you described in your previous respond. 

 

Hopefully we can find a solution soon. Thanks a lot!

 

Regards,

Guangming

 

On Mon, Dec 9, 2013 at 6:26 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

I'm not sure if I understand what you described. The tag referencing the CT slice SOP instance UID should not be in the CT at all. What we expect is if the structure set has an entry like this:

              (fffe,e000) na (Item with explicit length #=2)          #  94, 1 Item

                (0008,1150) UI =CTImageStorage                          #  26, 1 ReferencedSOPClassUID

                (0008,1155) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 ReferencedSOPInstanceUID

              (fffe,e00d) na (ItemDelimitationItem for re-encoding)   #   0, 0 ItemDelimitationItem

 

then there should be a CT slice with a header entry

    (0008,0018) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 SOPInstanceUID

 

Does this apply for your dataset? If yes, then I need to see your data to find out why the slice thickness cannot be determined. If no, then it is not a bug in SlicerRT, so we need to find another solution.

 

About changing the default slice thickness, I don't think it is a good solution, as what works for you doesn't necessarily work for someone else (our 2.5mm default thickness came from our very first sample data).

The only reason why we still have a default slice thickness is to be able to display "something" even without the correct slice thickness, as without converting the contour points to ribbon, virtually nothing could be seen of it in the 3D view.

 

The proper long-term solution would be a robust slice thickness computation algorithm, that (in absence of the referenced value) would compute the slice thickness based on the contour point data in the structure set. However, we don't have the capacity to implement this within the next month or so.

 

A possible short-term solution could be an option in the Contours module that would allow the user to re-ribbonize the contour data using a specific thickness value, or an entry in the Slicer...ini file specifying the default slice thickness. We could implement either option quite quickly.

Andras, Adam, everyone, what do you think?

 

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 11:40
To: Csaba Pinter


Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

those UIDs above mentioned except (0008,1155) can't be found in the dicom header of CT volume, which is in the same study as the structure set. In other words, only (0008,1155) can be found in the dicom header.

 

I am wondering, if it is possible to change the slicer value from 2 (default) to 4. Thanks a lot.

 

Best,

Guangming

 

On Mon, Dec 9, 2013 at 5:11 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

 

 

 

 



_______________________________________________
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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: Contoured Structures look like parrallel plates

Csaba Pinter-2

Hi Guangming,

 

Indeed, in the case when the structure set and the CT belong to different studies, currently there is no way in SlicerRT to find the reference CT and thus the slice thickness automatically (nor manually as a matter of fact). Your only option now was the one you chose, to export them together and import them from the new dataset.

 

You are right, this should be handled in SlicerRT, as your use case is not unique, and others will also need to load and handle together data from different sources. We are thinking on possible solutions for this problem, and I think the upcoming Subject Hierarchy is the good place to solve this, as it can handle and create connections between data (as it already does in the Patient Hierarchy). I will make sure that the RT plugin in the Subject Hierarchy supports this feature. I created a ticket for this, in which you can track the progress:

https://www.assembla.com/spaces/slicerrt/tickets/485-allow-manual-association-of-anatomical-volume-and-contour#/activity/ticket:

 

Cheers,

csaba

 

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 12, 2013 03:32
To: Csaba Pinter
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

you are absolutely right. My structure set and the images were from different sources, therefore they were inconsistent. No wonder Slicer couldn't find the reference image. 

 

I exported the structure set together with the images again, and the structures are now shown without gaps in slicer. That is to say, the problem was caused by the inconsistancy of my dicom dataset. And from my point of view, it is solved. 

 

Of course, SlicerRT could be improved on this issue. I will be happy to test it when the it comes to a better solution in the future. Thank you so much for the help!

 

Best regards,

Guangming

 

On Mon, Dec 9, 2013 at 7:15 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

It is very strange that the CT has no SOP instance UID, as it is one of the most basic tags there is, and without it the CT is invalid.

Can you share the files themselves with me? If the dataset is anonymized it should be OK.

 

The command-line program dcmdump, which I described earlier is does a very similar thing as the tags inspector in the DICOM browser, so if you use that then you get a text file with all the tags, and you can send it easily. However at this point the data itself would be more helpful.

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 13:10
To: Csaba Pinter
Cc: [hidden email]; Andras Lasso; Adam Rankin


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thank you so much! But I know almost nothing about DICOM headers etc. So don't be confused by my misleading description. 

 

I would love to send you the information in "DICOM tag inspector", but it is too long to fit into screenshot. And I cannot copy or save it. 

 

Just looked into the lengthy header information of the structure set, I didn't find an entry exactly match what you described in your previous respond. 

 

Hopefully we can find a solution soon. Thanks a lot!

 

Regards,

Guangming

 

On Mon, Dec 9, 2013 at 6:26 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

I'm not sure if I understand what you described. The tag referencing the CT slice SOP instance UID should not be in the CT at all. What we expect is if the structure set has an entry like this:

              (fffe,e000) na (Item with explicit length #=2)          #  94, 1 Item

                (0008,1150) UI =CTImageStorage                          #  26, 1 ReferencedSOPClassUID

                (0008,1155) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 ReferencedSOPInstanceUID

              (fffe,e00d) na (ItemDelimitationItem for re-encoding)   #   0, 0 ItemDelimitationItem

 

then there should be a CT slice with a header entry

    (0008,0018) UI [1.2.840.113619.2.55.3.671756986.106.1316467036.466.1] #  52, 1 SOPInstanceUID

 

Does this apply for your dataset? If yes, then I need to see your data to find out why the slice thickness cannot be determined. If no, then it is not a bug in SlicerRT, so we need to find another solution.

 

About changing the default slice thickness, I don't think it is a good solution, as what works for you doesn't necessarily work for someone else (our 2.5mm default thickness came from our very first sample data).

The only reason why we still have a default slice thickness is to be able to display "something" even without the correct slice thickness, as without converting the contour points to ribbon, virtually nothing could be seen of it in the 3D view.

 

The proper long-term solution would be a robust slice thickness computation algorithm, that (in absence of the referenced value) would compute the slice thickness based on the contour point data in the structure set. However, we don't have the capacity to implement this within the next month or so.

 

A possible short-term solution could be an option in the Contours module that would allow the user to re-ribbonize the contour data using a specific thickness value, or an entry in the Slicer...ini file specifying the default slice thickness. We could implement either option quite quickly.

Andras, Adam, everyone, what do you think?

 

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 11:40
To: Csaba Pinter


Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

those UIDs above mentioned except (0008,1155) can't be found in the dicom header of CT volume, which is in the same study as the structure set. In other words, only (0008,1155) can be found in the dicom header.

 

I am wondering, if it is possible to change the slicer value from 2 (default) to 4. Thanks a lot.

 

Best,

Guangming

 

On Mon, Dec 9, 2013 at 5:11 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

If you built Slicer from source, then dcmdump is in the folder Slicer4_R64-bin\DCMTK-build\bin\Release\dcmdump.exe, otherwise you can download the dcmtk package from the internet. However, the DICOM tag inspector works fine, so you don't need to do that.

 

It seems that the referenced UID is there. Can you check if those UIDs can be found in the anatomical volume (CT/MR...) that is the same study as your structure set?

 

Thanks,

csaba

 

 

From: Guangming Ma [mailto:[hidden email]]
Sent: December 9, 2013 10:53
To: Csaba Pinter; [hidden email]


Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi Csaba,

 

thanks! I attach here two screenshots of the DICOM hearder, hopeful it is helps for the diagnostics. 

 

By the way, where can I find the "dcmdump" in slicer?

 

Regards, 

Guangming

 

On Mon, Dec 9, 2013 at 4:24 PM, Csaba Pinter <[hidden email]> wrote:

Hi Guangming,

 

In the current version, the slice thickness is acquired from the SliceThickness (0018,0050) tag in the referenced volume, which means that you need a reference volume, and that specific tag in it. Unfortunately this approach is not fail-safe, because the SliceThickness tag is not mandatory, and also deemed not reliable. We are working on this issue, see [1].

 

However, your error message implies that the reference volume could not be found at all. The way the referenced volume is now found is:

ReferencedFrameOfReferenceSequence (3006,0010) -> first item -> RTReferencedStudySequence (3006,0012) -> first item -> RTReferencedSeriesSequence (3006,0014) -> first item -> ContourImageSequence (3006,0016)  -> first item -> ReferencedSOPInstanceUID (0008,1155).

 

Please check the DICOM header in your RTSS file to see if it's there (you can use dcmdump for this).

It would help a great deal if you could send us the dcmdump of the RTSS and the CT (removing all the sensitive information such as patient name etc).

 

Thanks,

csaba

 

 

[1]: https://www.assembla.com/spaces/slicerrt/tickets/456#/activity/ticket:

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: December 9, 2013 01:25
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Contoured Structures look like parrallel plates

 

Hi all,

 

the same problem happens again.

 

Serveral months ago (August 2013), I reported the structures are shown in Slicer as "parrallel plates", which meaned there were gaps between the plates. But then the problem disappeared by itself.

 

Now, I have a totally new patient study and using Slicer 4.3.0, the same problem happens again, shown in the attached files. All three formats of the contours (ribbon, closed surface, indexedLabelmap) have the same problem.

 

The Error log indicates following information:

"ERROR: In ..\..\..\..\SlicerRT\DicomRtImport\Logic\vtkSlicerDicomRtReader.cxx, line 507

vtkSlicerDicomRtReader (000000001FA95970): GetSliceThickness: No referenced image file is found, default slice thickness is used for contour import"

 

How could I solve this problem, then? Where to change the Slice Thickness? Thanks!

 

Best regards,

Guangming

 

On Wed, Aug 28, 2013 at 9:43 PM, Guangming Ma <[hidden email]> wrote:

Hi Greg,

 

yes, I meant the gaps between the "parallel plates", like in the attachment "parralel plates instead of a whole volume.jpg". 

 

In order to make sure whether the same problem would happend again, I imported the contour again after Slicer is freshly started. Surprisingly, the volume are fine now, in all three formats: Ribbon, IndexedLabelmap, and ClosedSurface. The same organ, but this time in normal volume without gaps, is shown in attachment "normal whole volume.jpg".

 

What could be the reason, then? I will report it, if this problem happens in the future again. Thanks!

 

Kind regards,

Guangming

 

On Wed, Aug 28, 2013 at 3:54 PM, Sharp, Gregory C. <[hidden email]> wrote:

Hi Guangming,

 

Do you mean there are gaps between the "parallel plates"?

 

And do the labelmaps show corresponding gaps?

 

A screenshot may help.

 

Greg

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Guangming Ma
Sent: Wednesday, August 28, 2013 4:30 AM
To: [hidden email]
Subject: [slicer-users] Contoured Structures look like parrallel plates

Hi Slicer users,

 

some of contoured structures which I have got from clinical physician look strange. In closedSurfaceModel, the structures (CTV and OARs) look like parrallel plates instead of whole volume!

 

Some other contoured structures do look like a whole volume, although the sharp change of different slices are easily seen.

 

I guess this is because the contour slice depth are not well tuned. Could I edit the contours somewhere in Slicer, so that the structures look as whole volume?

 

Regards,

Guangming

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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