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How to edit DICOM Image Series without loosing metadata?

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How to edit DICOM Image Series without loosing metadata?

Rhino Cracker
Hi all,
 
I have problems in editing DICOM Image Series:
I am trying to edit an MRI scan. I want to re-paint some bad recorded structures to prevent ITKsnap from running out of a striucture I'm trying to segment.
 
I have imported the series as ImageStack, which worked very well in ImageJ. But I was not able to save it in the format I've loaded it.
 
So I placed Tudor's DICOM Tools PlugIns in ImageJ's plugin dir.
When I use File --> Save As --> Save DICOM and even uncheck all "remove *" checkboxes, it unevitably removes all Metadata and saves as a single *.dcm file instead of an image series.
This file, loaded by ITKsnap , contains all images, but is completely out of voxel-shape.
 
How can I make ImageJ saving the series as it has been loaded, without removing all metadata?
 
Thanks in advance and best regards,
Rhino Cracker
 
 
 


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Re: How to edit DICOM Image Series without loosing metadata?

Michael Doube-4
Hi,

> I have problems in editing DICOM Image Series:
> I have imported the series as ImageStack, which worked very well in ImageJ. But I was not able to save it in the format I've loaded it.

Save your working image as a TIFF stack (the default when you hit 's' on the keyboard). ImageJ will retain all the metadata, including DICOM headers. Your changes will get saved in the TIFF. It works this way to prevent you from accidentally damaging your raw data.

Michael


<http://www.rvc.ac.uk>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

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Re: How to edit DICOM Image Series without loosing metadata?

Rhino Cracker
Hi and thanks for your answere.

Am 13.01.2017 um 13:31 schrieb Michael Doube:
> It works this way to prevent you from accidentally damaging your raw data.
Don't worry, I'm working on a copy of the raw data.

Unfortunately ITK-Snap doesn't support TIFF stacks. It only supports:


I would rather like to manipulate the raw image data itself, without
re-encoding all images or changing any format encoding, etc.
Is that possible?

Best regards,
Rhino

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Re: How to edit DICOM Image Series without loosing metadata?

Rhino Cracker
In reply to this post by Michael Doube-4
Hi and thanks for your answere.

Am 13.01.2017 um 13:31 schrieb Michael Doube:
> It works this way to prevent you from accidentally damaging your raw data.
Don't worry, I'm working on a copy of the raw data.

Unfortunately ITK-Snap doesn't support TIFF stacks. It only supports:


I would rather like to manipulate the raw image data itself, without
re-encoding all images or changing any format encoding, etc.
Is that possible?

Best regards,
Rhino

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Re: How to edit DICOM Image Series without loosing metadata?

Rhino Cracker
In reply to this post by Rhino Cracker
Hi again,

thanks to some help from Salim K., who messaged me in private, I found
and managed to use a different tool for DICOM-Writing:

Pet/Ct Viewer by Ilian Tal and Salim Kanoun: http://petctviewer.org/

It's usually for Fiji and can be installed there using the update
manager (more detailed description on the page above):

In ImageJ I had to manually download the files
Pet_Ct_Viewer.jar, infovis.jar, japng.jar, vecmath-1.5.2.jar and
Gastric_Emptying.jar from the repository
https://sourceforge.net/projects/bifijiplugins/files/?source=navbar 
(some of them are in the libs directory)
and place them together in a seperate folder in ...\ImageJ\PlugIns\.

The option "Save As... --> myDICOM" then creates an imagestack (seperate
files), where the necessary tags
"0018,0050 [DS] Slice Thickness: 0.078125" and
"0028,0030 [DS] Pixel Spacing: 0.0625/0.0625" are still present.
(According to the DICOM Header Viewer delivered with Tudor's DICOM
Tools, the latter one was missing in the files created by Tudor's DICOM
Tools and is necessary to keep the voxel dimensions).

I hope this might help someone facing the same problems as I did.
Best regards,
Rhino Cracker


Am 13.01.2017 um 11:12 schrieb Rhino Cracker:

> Hi all,
>  
> I have problems in editing DICOM Image Series:
> I am trying to edit an MRI scan. I want to re-paint some bad recorded structures to prevent ITKsnap from running out of a striucture I'm trying to segment.
>  
> I have imported the series as ImageStack, which worked very well in ImageJ. But I was not able to save it in the format I've loaded it.
>  
> So I placed Tudor's DICOM Tools PlugIns in ImageJ's plugin dir.
> When I use File --> Save As --> Save DICOM and even uncheck all "remove *" checkboxes, it unevitably removes all Metadata and saves as a single *.dcm file instead of an image series.
> This file, loaded by ITKsnap , contains all images, but is completely out of voxel-shape.
>  
> How can I make ImageJ saving the series as it has been loaded, without removing all metadata?
>  
> Thanks in advance and best regards,
> Rhino Cracker
>  
>  
>  
>
>
> ---
> Die Bundesliga hat begonnen! Alle Tore, alle Ergebnisse, alle News: Pocket Liga jetzt im AppStore oder Google Play Store herunterladen - kostenlos!
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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