Which DICOM attribute gives the number of slices in a sequence

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Which DICOM attribute gives the number of slices in a sequence

Murat Maga

Hi,

 

I am working with a clinical dataset, some of which came from archives.

 

There is a concern that original number of slices reconstructed does not match what’s retrieved from the archive. There are at least four datasets like that (there are fewer slices that they supposed to have).

Is there a field in the dicom metadata that will tell me this value? I am going through a bunch of attributes as reported by Slicer, and I can’t seem to find a value that corresponds to the number of slices.

 

 

 


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Re: Which DICOM attribute gives the number of slices in a sequence

Andrey Fedorov-2
Murat, there is no such attribute. Unfortunately, to the best of my
knowledge, it is impossible to determine if a slice is missing from a
series in the cases when slices are stored in separate files. You can
check for geometric consistency by ordering slices spatially, and
calculating distances between the slices, but this of course will not
help if you have every other slice missing, or missing slices at the
edges.

Enhanced multi-frame DICOM object types keep all slices (frames) in a
single object (file) and do not have this problem, but they are not so
commonly produced by the imaging equipment, and are not always
supported by the PACS viewers.

On Fri, Feb 17, 2017 at 1:47 PM, Murat Maga <[hidden email]> wrote:

> Hi,
>
>
>
> I am working with a clinical dataset, some of which came from archives.
>
>
>
> There is a concern that original number of slices reconstructed does not
> match what’s retrieved from the archive. There are at least four datasets
> like that (there are fewer slices that they supposed to have).
>
> Is there a field in the dicom metadata that will tell me this value? I am
> going through a bunch of attributes as reported by Slicer, and I can’t seem
> to find a value that corresponds to the number of slices.
>
>
>
>
>
>
>
>
> _______________________________________________
> 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: Which DICOM attribute gives the number of slices in a sequence

Murat Maga
In reply to this post by Murat Maga
Ouch!

M

-----Original Message-----
From: Andrey Fedorov [mailto:[hidden email]]
Sent: Friday, February 17, 2017 11:00 AM
To: Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Which DICOM attribute gives the number of slices in a sequence

Murat, there is no such attribute. Unfortunately, to the best of my knowledge, it is impossible to determine if a slice is missing from a series in the cases when slices are stored in separate files. You can check for geometric consistency by ordering slices spatially, and calculating distances between the slices, but this of course will not help if you have every other slice missing, or missing slices at the edges.

Enhanced multi-frame DICOM object types keep all slices (frames) in a single object (file) and do not have this problem, but they are not so commonly produced by the imaging equipment, and are not always supported by the PACS viewers.

On Fri, Feb 17, 2017 at 1:47 PM, Murat Maga <[hidden email]> wrote:

> Hi,
>
>
>
> I am working with a clinical dataset, some of which came from archives.
>
>
>
> There is a concern that original number of slices reconstructed does
> not match what’s retrieved from the archive. There are at least four
> datasets like that (there are fewer slices that they supposed to have).
>
> Is there a field in the dicom metadata that will tell me this value? I
> am going through a bunch of attributes as reported by Slicer, and I
> can’t seem to find a value that corresponds to the number of slices.
>
>
>
>
>
>
>
>
> _______________________________________________
> 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: Which DICOM attribute gives the number of slices in a sequence

Sharp, Gregory C.
In reply to this post by Murat Maga

Sorry Murat, no dice.  My suggestions:

 

-          Look for gaps in data elements that might be sequentially numbered, such as Instance Number or SOP Instance UID

-          If the scan was done at uniform slice spacing you can look for gaps in Image Position Patient

 

I usually use the latter heuristic.  But neither heuristic will tell you if slices are missing from the end.

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: Friday, February 17, 2017 1:47 PM
To: SPL Slicer Users
Subject: [slicer-users] Which DICOM attribute gives the number of slices in a sequence

 

Hi,

 

I am working with a clinical dataset, some of which came from archives.

 

There is a concern that original number of slices reconstructed does not match what’s retrieved from the archive. There are at least four datasets like that (there are fewer slices that they supposed to have).

Is there a field in the dicom metadata that will tell me this value? I am going through a bunch of attributes as reported by Slicer, and I can’t seem to find a value that corresponds to the number of slices.

 

 

 


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Re: Which DICOM attribute gives the number of slices in a sequence

Murat Maga
In reply to this post by Murat Maga

In all four instances that was exactly the case (missing from the end of the sequence). Double ouch.

M

 

From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Friday, February 17, 2017 11:07 AM
To: Murat Maga <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: RE: [slicer-users] Which DICOM attribute gives the number of slices in a sequence

 

Sorry Murat, no dice.  My suggestions:

 

  • Look for gaps in data elements that might be sequentially numbered, such as Instance Number or SOP Instance UID
  • If the scan was done at uniform slice spacing you can look for gaps in Image Position Patient

 

I usually use the latter heuristic.  But neither heuristic will tell you if slices are missing from the end.

 

From: slicer-users [[hidden email]] On Behalf Of Murat Maga
Sent: Friday, February 17, 2017 1:47 PM
To: SPL Slicer Users
Subject: [slicer-users] Which DICOM attribute gives the number of slices in a sequence

 

Hi,

 

I am working with a clinical dataset, some of which came from archives.

 

There is a concern that original number of slices reconstructed does not match what’s retrieved from the archive. There are at least four datasets like that (there are fewer slices that they supposed to have).

Is there a field in the dicom metadata that will tell me this value? I am going through a bunch of attributes as reported by Slicer, and I can’t seem to find a value that corresponds to the number of slices.

 

 

 

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