# Working with 4D flow MRI data

**URL:** <https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214>\
**Category:** Support\
**Created:** [February 8, 2024, 6:07pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214 "2024-02-08T18:07:19Z")\
**Posts on this page:** 14\
**Page:** 1

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**Author:** ![sannpeterson](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sannpeterson/32/10892_2.png) [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Post date:** [February 8, 2024, 6:07pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/1 "2024-02-08T18:07:19Z")

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I’ve never worked with 4D flow MRI data (head) before and am wondering if it is possible to perform flow analysis in 3D Slicer. I’ve also attempted to segment the brain vessels but cannot capture any vessels apart from the ICA and even those are quite hard to make out. Any tips would be greatly appreciated.

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**Author:** ![roeg](https://avatars.discourse-cdn.com/v4/letter/r/8491ac/32.png) [@roeg](https://discourse.slicer.org/u/roeg)\
**Post date:** [February 9, 2024, 12:59pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/2 "2024-02-09T12:59:49Z")

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These topics have my attention too. They are 2 of my prime work related activities in 3D. I am currently working my way through the software, but the online tutorials are for an older software version.  
cheers  
john roeger  
3D Reconstruction  
VIR/INR Medical Radiation Technologist  
University Health Network

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 9, 2024, 3:01pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/3 "2024-02-09T15:01:07Z")

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We have developed a Slicer module for importing Siemens CS 4D flow images from DICOM, visualize it as a flow field, sample the speed with a plane (e.g., to get speed across a cross-section to be used as CFD simulation input), and experimenting with flow simulations. We plan to release the module publicly when corresponding paper is published (maybe in a couple of months).

If you have any specific questions then let us know.

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**Author:** ![sannpeterson](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sannpeterson/32/10892_2.png) [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Post date:** [February 9, 2024, 6:04pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/4 "2024-02-09T18:04:01Z")

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The data files for a study consists of these series: a 2D dataset, a 3D dataset (can’t figure out what this is in relation to other datasets), 3 magnitude datasets (3D), 3 phase datasets (3D). I don’t even really know what I’m looking at. I’ve gone through the metadata for the files but still having a hard time deciphering the images. I’m familiar with vessel segmentation for TOF MRA but cannot figure out how to do this for the files I have. Can you guide me please?

[files here](https://www.dropbox.com/scl/fi/tnkn5nsn0ylhxm69w1gzq/Archive.zip?rlkey=vkdlb4y4qdbgv2j631bygv5r9&dl=0)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 10, 2024, 4:51pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/5 "2024-02-10T16:51:07Z")

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These NRRD files do not contain all the metadata that is necessary to interpret the data. If you have Siemens CS 4D flow images then I can give advice on how to load them (maybe share some code in private before we publish). For other vendors or acquisition types you can dig into the specification and/or search for existing readers on github. We can also help with some advice here if you have specific questions.

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**Author:** ![sannpeterson](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sannpeterson/32/10892_2.png) [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Post date:** [February 12, 2024, 5:22pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/6 "2024-02-12T17:22:57Z")

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What do you mean about the files not containing all the metadata? Would it be better if I upload the original dicom files?

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 12, 2024, 5:25pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/7 "2024-02-12T17:25:50Z")

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The exported NRRD files only contain the voxel values and the position, orientation, spacing of the voxel grid of each component, which is not sufficient to reconstruct the 5D flow fields. Make sure to use phantom/animal data set or anonymize the DICOM data before sharing.

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**Author:** ![sannpeterson](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sannpeterson/32/10892_2.png) [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Post date:** [February 12, 2024, 5:47pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/8 "2024-02-12T17:47:59Z")

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Can you take a look?

[files here](https://www.dropbox.com/scl/fi/3nn3rrotf74xxiz8diqgc/dicom-anonymized.zip?rlkey=sxe722fzx6zng4i66oacogkef&dl=0)

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**Author:** ![klns23](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@klns23](https://discourse.slicer.org/u/klns23)\
**Post date:** [June 7, 2024, 4:39pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/9 "2024-06-07T16:39:37Z")

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Hi, I’m curious whether the Slicer module for working with 4D flow images has been released? The available commercial software does not seem very useful beyond visualization, and I would really like the ability to work with this type of data in Slicer.

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**Author:** ![klns23](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@klns23](https://discourse.slicer.org/u/klns23)\
**Post date:** [August 14, 2024, 4:07pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/10 "2024-08-14T16:07:11Z")

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Any news on the Slicer module for importing Siemens CS 4D flow images from DICOM? Is it now available via an extension? Thanks!

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [September 12, 2024, 2:42pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/11 "2024-09-12T14:42:53Z")

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We have the Siemens CS 4D flow image importer Slicer module and it works well. We’ll release it as soon as we get it published, which may take several months. You can check back here/comment on this topic later to get an update.

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**Author:** ![Onyxazure](https://avatars.discourse-cdn.com/v4/letter/o/3e96dc/32.png) [@Onyxazure](https://discourse.slicer.org/u/Onyxazure)\
**Post date:** [July 4, 2025, 7:07pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/12 "2025-07-04T19:07:20Z")

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Hi Andras,

I wanted to ask if you have published this plugin / paper by now? I would be really interested to use it. Thanks a lot.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 4, 2025, 7:24pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/13 "2025-07-04T19:24:26Z")

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We have made significant progress with the implementation (added bias correction, velocity phase unwrapping, motion compensation, flow metrics computation, etc.) but have not started writing the paper. So, publishing the software is probably still at least a few months away. Maybe we can share with you privately - you can contact me in private message to discuss.

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**Author:** ![Astree\_LEMORE](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/astree_lemore/32/82720_2.png) [@Astree\_LEMORE](https://discourse.slicer.org/u/Astree_LEMORE)\
**Post date:** [August 14, 2026, 3:45pm UTC](https://discourse.slicer.org/t/working-with-4d-flow-mri-data/34214/14 "2026-08-14T15:45:12Z")

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Hi Andras,

I wonder do you have published the plugin by now?

I would be very interested to be able to work with this type of data in Slicer.

Thanks !