Metadata exists in .nrrd files?

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Metadata exists in .nrrd files?

arumiat
It seems that if I save a dicom series as an .nrrd, there's no way to access
the metadata like you can with the DICOM series:


Does the  <http://slicer-users.65878.n3.nabble.com/file/n4031408/nrrd.png>

Does conversion to .nrrd strip this information? Thanks, T



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Re: Metadata exists in .nrrd files?

Andrey Fedorov-2
> Does conversion to .nrrd strip [DICOM metadata] information?

yes it does


On Thu, Dec 8, 2016 at 1:19 PM, arumiat <[hidden email]> wrote:

> It seems that if I save a dicom series as an .nrrd, there's no way to access
> the metadata like you can with the DICOM series:
>
>
> Does the  <http://slicer-users.65878.n3.nabble.com/file/n4031408/nrrd.png>
>
> Does conversion to .nrrd strip this information? Thanks, T
>
>
>
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Re: Metadata exists in .nrrd files?

arumiat
Thanks Andrey, and it is the same case for .niftis?
Are there any similar formats that maintain this data?



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Re: Metadata exists in .nrrd files?

arumiat
This post has NOT been accepted by the mailing list yet.
In reply to this post by Andrey Fedorov-2
Thanks Andrey, and it is the same case for .niftis?
Are there any similar formats that maintain this data?
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Re: Metadata exists in .nrrd files?

Andrey Fedorov-2
In reply to this post by arumiat
On Thu, Dec 8, 2016 at 3:24 PM, arumiat <[hidden email]> wrote:
> Thanks Andrey, and it is the same case for .niftis?
> Are there any similar formats that maintain this data?
>

I will leave it to the expects in those other formats to comment. I am
not an advocate of any other formats as a complete replacement for
DICOM.


>
>
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Re: Metadata exists in .nrrd files?

Andras Lasso-2
NRRD can only store a flat list of key/value string pairs. Metadata in a DICOM series can contain hierarchical structures, large binary blobs, etc., so you cannot easily serialize all that to key/value pairs and most often you don't want to.

If you tell a bit about what you would like to achieve then we may be able to recommend solutions.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: December 8, 2016 17:36
To: arumiat <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Metadata exists in .nrrd files?

On Thu, Dec 8, 2016 at 3:24 PM, arumiat <[hidden email]> wrote:
> Thanks Andrey, and it is the same case for .niftis?
> Are there any similar formats that maintain this data?
>

I will leave it to the expects in those other formats to comment. I am not an advocate of any other formats as a complete replacement for DICOM.


>
>
> --
> View this message in context:
> http://slicer-users.65878.n3.nabble.com/Metadata-exists-in-nrrd-files-
> tp4031409p4031411.html Sent from the slicer-users mailing list archive
> at Nabble.com.
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Re: Metadata exists in .nrrd files?

inorton
In reply to this post by arumiat
Generally speaking, if you need DICOM metadata ... why not just stay with DICOM?
 
Are there any similar formats that maintain this data?

It depends on the goal and area of research. Some in the brain imaging community are pushing [1] which builds on [2] (or vice-versa). In MR research, there is a ISMRM format initiative [3] (I have no idea if anyone actually uses it, might be a one-off thing).

Reduction of metadata has in some ways been considered a benefit in the past because it decreases the risk of propagation of protected information that is not necessary for research (not a complete anonymization solution, of course). On the other hand, loss of metadata complicates reproducible research and can hinder advanced reconstruction techniques.

[1] http://bids.neuroimaging.io/
[2] http://www.nitrc.org/projects/cifti/
[3] https://github.com/ismrmrd/ismrmrd



On Thu, Dec 8, 2016 at 3:24 PM, arumiat <[hidden email]> wrote:
Thanks Andrey, and it is the same case for .niftis?
Are there any similar formats that maintain this data?



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Re: Metadata exists in .nrrd files?

arumiat
In reply to this post by arumiat
- we're building a custom online medical image data viewer.
-  currently it is made to work with the .nifti file format
- this is for viewing CT and MRI (standard studies)
- something the imagers I'm working with want is to be able to query the associated metadata
- I will have to find out if we can convert the program so that we have the ability to read the DICOM files instead, - it just seems easier to work with a single file, such as .nrrd or .nifti (and that was how the system was initially implemented)
Thanks for any tips :)


------------------------------------
V A L A design
+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2
IVALA LTD.   REG NO.7931234


On 9 December 2016 at 04:09, Isaiah Norton <[hidden email]> wrote:
Generally speaking, if you need DICOM metadata ... why not just stay with DICOM?
 
Are there any similar formats that maintain this data?

It depends on the goal and area of research. Some in the brain imaging community are pushing [1] which builds on [2] (or vice-versa). In MR research, there is a ISMRM format initiative [3] (I have no idea if anyone actually uses it, might be a one-off thing).

Reduction of metadata has in some ways been considered a benefit in the past because it decreases the risk of propagation of protected information that is not necessary for research (not a complete anonymization solution, of course). On the other hand, loss of metadata complicates reproducible research and can hinder advanced reconstruction techniques.

[1] http://bids.neuroimaging.io/
[2] http://www.nitrc.org/projects/cifti/
[3] https://github.com/ismrmrd/ismrmrd



On Thu, Dec 8, 2016 at 3:24 PM, arumiat <[hidden email]> wrote:
Thanks Andrey, and it is the same case for .niftis?
Are there any similar formats that maintain this data?



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Re: Metadata exists in .nrrd files?

Andrey Fedorov-2
You could maintain nifti representation in parallel to DICOM for quick
loading. It is usually a good idea to keep the original data, if you
have an option.

On Fri, Dec 9, 2016 at 12:06 PM, Taimur Alavi <[hidden email]> wrote:

> - we're building a custom online medical image data viewer.
> -  currently it is made to work with the .nifti file format
> - this is for viewing CT and MRI (standard studies)
> - something the imagers I'm working with want is to be able to query the
> associated metadata
> - I will have to find out if we can convert the program so that we have the
> ability to read the DICOM files instead, - it just seems easier to work with
> a single file, such as .nrrd or .nifti (and that was how the system was
> initially implemented)
> Thanks for any tips :)
>
>
> ------------------------------------
> I V A L A design
> WWW.IVALADESIGN.COM
> [hidden email]
> + 4 4 (0) 2 0 3 6 3 7 0 0 6 2
> IVALA LTD.   REG NO.7931234
> uk.linkedin.com/pub/taimur-alavi/71/72/b38/
>
>
>
> On 9 December 2016 at 04:09, Isaiah Norton <[hidden email]> wrote:
>>
>> Generally speaking, if you need DICOM metadata ... why not just stay with
>> DICOM?
>>
>>>
>>> Are there any similar formats that maintain this data?
>>
>>
>> It depends on the goal and area of research. Some in the brain imaging
>> community are pushing [1] which builds on [2] (or vice-versa). In MR
>> research, there is a ISMRM format initiative [3] (I have no idea if anyone
>> actually uses it, might be a one-off thing).
>>
>> Reduction of metadata has in some ways been considered a benefit in the
>> past because it decreases the risk of propagation of protected information
>> that is not necessary for research (not a complete anonymization solution,
>> of course). On the other hand, loss of metadata complicates reproducible
>> research and can hinder advanced reconstruction techniques.
>>
>> [1] http://bids.neuroimaging.io/
>> [2] http://www.nitrc.org/projects/cifti/
>> [3] https://github.com/ismrmrd/ismrmrd
>>
>>
>>
>> On Thu, Dec 8, 2016 at 3:24 PM, arumiat <[hidden email]> wrote:
>>>
>>> Thanks Andrey, and it is the same case for .niftis?
>>> Are there any similar formats that maintain this data?
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://slicer-users.65878.n3.nabble.com/Metadata-exists-in-nrrd-files-tp4031409p4031411.html
>>> Sent from the slicer-users mailing list archive at Nabble.com.
>>> _______________________________________________
>>> slicer-users mailing list
>>> [hidden email]
>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>> To unsubscribe: send email to [hidden email] with
>>> unsubscribe as the subject
>>> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>>
>>
>
>
> _______________________________________________
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Re: Metadata exists in .nrrd files?

Andras Lasso-2
In reply to this post by arumiat

What do you mean by “online”? Where the data comes from? How do you use Slicer?

 

If you only use Slicer for DICOM->nrrd conversion then you can create a simple module that stores metadata fields in volume node attributes. If you set the volume’s storage node to be a vtkMRMLNRRDStorageNode then when you save the volume as nrrd, all node attributes will be saved into the file.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Taimur Alavi
Sent: December 9, 2016 12:07
To: Isaiah Norton <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Metadata exists in .nrrd files?

 

- we're building a custom online medical image data viewer.

-  currently it is made to work with the .nifti file format

- this is for viewing CT and MRI (standard studies)

- something the imagers I'm working with want is to be able to query the associated metadata

- I will have to find out if we can convert the program so that we have the ability to read the DICOM files instead, - it just seems easier to work with a single file, such as .nrrd or .nifti (and that was how the system was initially implemented)

Thanks for any tips :)

 


------------------------------------

I V A L A design

+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2

IVALA LTD.   REG NO.7931234

  •  

 

On 9 December 2016 at 04:09, Isaiah Norton <[hidden email]> wrote:

Generally speaking, if you need DICOM metadata ... why not just stay with DICOM?
 

Are there any similar formats that maintain this data?

 

It depends on the goal and area of research. Some in the brain imaging community are pushing [1] which builds on [2] (or vice-versa). In MR research, there is a ISMRM format initiative [3] (I have no idea if anyone actually uses it, might be a one-off thing).


Reduction of metadata has in some ways been considered a benefit in the past because it decreases the risk of propagation of protected information that is not necessary for research (not a complete anonymization solution, of course). On the other hand, loss of metadata complicates reproducible research and can hinder advanced reconstruction techniques.

[1] http://bids.neuroimaging.io/
[2] http://www.nitrc.org/projects/cifti/
[3] https://github.com/ismrmrd/ismrmrd

 

 

On Thu, Dec 8, 2016 at 3:24 PM, arumiat <[hidden email]> wrote:

Thanks Andrey, and it is the same case for .niftis?
Are there any similar formats that maintain this data?



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