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Tags for transcranial magnetic stimulation (TMS)
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hapap
Dec 1, 2022, 1:08:46 AM12/1/22
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Hi all,
I'm working with a transcranial magnetic stimulation (TMS) device and we are about to export various types of information into DICOM files and file series. The device works with 3D MR images and exporting the image data works already fine via ITK/GDCM. However, we would like to start exporting also other information such as
- 3D points of interest with custom RGB colors
- colored 2D/3D segmentations overlaid on the original MR data
- surface objects defined via nodes, triangular faces and face colors
In a previous work with radiation therapy device I used RT Structure Set module, which fullfilled my needs just fine. Now that we are dealing with TMS instead of RT, what would be the appropriate module to store points, segmentations and surfaces? To my understanding, there is no specific section for TMS in DICOM Standard, right? Is there are general Structure Set Module then that I could perhaps use for points/surfaces?
One thing we would like to export is the original MR data together with a collection of overlay layers. Currently I'm implementing this using Overlay Plane Module of MR Image CIOD, but I'm not sure if this is the best way to do this? I hope I can define custom RGB colors on these layers. I don't know if the overlay plane module is even widely supported by DICOM viewer softwares?
Obviously I could export the overlays as separate series of 2D RGB images, but this wouldn't be the most elegant solution. Also I don't want to export the points/surfaces in some custom format that might not be supported by other software, such as surgery planning tools.
Many thanks for your help!
/Harri Pölönen
I'm working with a transcranial magnetic stimulation (TMS) device and we are about to export various types of information into DICOM files and file series. The device works with 3D MR images and exporting the image data works already fine via ITK/GDCM. However, we would like to start exporting also other information such as
- 3D points of interest with custom RGB colors
- colored 2D/3D segmentations overlaid on the original MR data
- surface objects defined via nodes, triangular faces and face colors
In a previous work with radiation therapy device I used RT Structure Set module, which fullfilled my needs just fine. Now that we are dealing with TMS instead of RT, what would be the appropriate module to store points, segmentations and surfaces? To my understanding, there is no specific section for TMS in DICOM Standard, right? Is there are general Structure Set Module then that I could perhaps use for points/surfaces?
One thing we would like to export is the original MR data together with a collection of overlay layers. Currently I'm implementing this using Overlay Plane Module of MR Image CIOD, but I'm not sure if this is the best way to do this? I hope I can define custom RGB colors on these layers. I don't know if the overlay plane module is even widely supported by DICOM viewer softwares?
Obviously I could export the overlays as separate series of 2D RGB images, but this wouldn't be the most elegant solution. Also I don't want to export the points/surfaces in some custom format that might not be supported by other software, such as surgery planning tools.
Many thanks for your help!
/Harri Pölönen
David Clunie
Dec 4, 2022, 8:02:46 AM12/4/22
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Hi Harri
There are specific DICOM Segmentation objects for rasterized and surface segmentations respectively:
- http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.51.html
- http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.57.html
For points of interest, I suggest DICOM SR, with planar annotations; see the suggestions at:
- http://dx.doi.org/10.13140/RG.2.2.34520.62725
The use of overlays is discouraged, as opposed to segmentations that are semantically meaningful (and do not involve editing an image object or making an entire copy of it). See also:
- http://www.dclunie.com/papers/CMIMI_2018_David_Clunie_StandardizingAIAnnotationsDICOM.pdf
David
There are specific DICOM Segmentation objects for rasterized and surface segmentations respectively:
- http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.51.html
- http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.57.html
For points of interest, I suggest DICOM SR, with planar annotations; see the suggestions at:
- http://dx.doi.org/10.13140/RG.2.2.34520.62725
The use of overlays is discouraged, as opposed to segmentations that are semantically meaningful (and do not involve editing an image object or making an entire copy of it). See also:
- http://www.dclunie.com/papers/CMIMI_2018_David_Clunie_StandardizingAIAnnotationsDICOM.pdf
David
hapap
Dec 15, 2022, 3:49:57 AM12/15/22
to
Hi David,
and many thanks for the information! This will be very useful.
For your information, and to everyone who finds this thread later, I have continued the discussion at ITK forum regarding practical and technical issues of exporting points into DICOM SR format here: https://discourse.itk.org/t/export-itk-points-into-dicom-sr-planar-annotations/5555. There may be useful info to those who plan to implement DICOM SR into their software.
/Harri
and many thanks for the information! This will be very useful.
For your information, and to everyone who finds this thread later, I have continued the discussion at ITK forum regarding practical and technical issues of exporting points into DICOM SR format here: https://discourse.itk.org/t/export-itk-points-into-dicom-sr-planar-annotations/5555. There may be useful info to those who plan to implement DICOM SR into their software.
/Harri
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