# How to generate 4D cine MRI?

**URL:** <https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [August 13, 2022, 8:58pm UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743 "2022-08-13T20:58:35Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![KLNU](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/klnu/32/13600_2.png) [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Post date:** [August 13, 2022, 8:58pm UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743/1 "2022-08-13T20:58:35Z")

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Dear Dr, Lasso,

Currently, I have cine MRI images (25 phases a cardiac cycle, at 2-, 3-, 4 chamber and short-axis view (9 slices from the apex to the base) [total 300 pictures]. I tried to “Reconstruct 4D volume from cine-MRI frames” in 3D slicer (V.5.03). However, I have some questions regarding the workflow. I also watched the video on youtube, however it did not answer all my questions. Please see below.

- Import the cine-MRI acquisition using the DICOM module: switch to DICOM module and drag-and-drop the folder that contains the DICOM files to the application window  
Done.
- Load the cine-MRI data set by double-clicking on the cine-MRI series in the DICOM browser  
Done. There are 12 series loaded. One of them is “SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime”.
- Create an Annotation ROI node: click the down-arrow in the “Create and place” button on the toolbar, choose the “ROI” option at the top, then click in the middle of the region of interest in a slice view, then at a corner of a region of interest in the same slice view.  
This sentence is not clear. I installed Nvidiaannotation and find the “annotations” module and found the ROI. My question is which “slice views” should I work on it? 4-chamber? 2-chamber?or short-axis? and which slice? It seems that I could not pill out all slices on three windows (R, G ,Y). Only two clicks is enough? I selected 2-, 4- and a short-axis view at 3 windows and set an ROI covering the whole heart in three different views, is that right?
- Switch to “Reconstruct 4D cine-MRI” module  
Done.
- Select the loaded cine-MRI sequence as “Input sequence”  
When I switched to “Reconstruct 4D cine-MRI”, I was unable to find current cine MRI sequence under “input sequence”. Therefore, no “apply” showed.
- Select the created ROI node as “Input region”  
It showed “R”, right?

Thanks,

Kai

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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:** [August 13, 2022, 9:41pm UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743/2 "2022-08-13T21:41:55Z")

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> [@KLNU](#):
>
> There are 12 series loaded. One of them is “SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime”

This is the issue - the sequence is loaded as a `MultiVolume`. In the menu: Edit → Application settings → DICOM → Preferred multi-volume import format → select `volume sequence`. After you restart the application, the images will be loaded as volume sequence and they will appear in the node selector.

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**Author:** ![KLNU](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/klnu/32/13600_2.png) [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Post date:** [August 13, 2022, 10:35pm UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743/3 "2022-08-13T22:35:15Z")

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> [@KLNU](#):
>
> SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime

Thanks!  
Now it showed “SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime”  
“SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime\_1”  
“SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime\_2”

Is that normal? Do I need to just upload short-axis cine (to construct the volume) or do I need to also upload 2-, 3-, 4- chamber view? My ultimate goal is to extract radiomics features on each phase of the left ventricle.

Thanks!

Kai

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<div class="post-metadata">

**Author:** ![KLNU](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/klnu/32/13600_2.png) [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Post date:** [August 13, 2022, 10:57pm UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743/4 "2022-08-13T22:57:49Z")

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> [@KLNU](#):
>
> Thanks!  
> Now it showed “SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime”  
> “SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime\_1”  
> “SAX cine\_trufi\_retro\_invf - as a 25 frames MultiVolume by TriggerTime\_2”
> 
> Is that normal? Do I need to just upload short-axis cine (to construct the volume) or do I need to also upload 2-, 3-, 4- chamber view? My ultimate goal is to extract radiomics features on each phase of the left ventricle.
> 
> Thanks!
> 
> Kai

Sorry. The sequences should be:  
“SAX cine\_trufi\_retro\_invf - as a 25 frames Volume Sequence by TriggerTime [0]”  
“SAX cine\_trufi\_retro\_invf - as a 25 frames Volume Sequence by TriggerTime\_1 [0]”  
…  
My questions are:

1. Should I include 2-, 3-, 4- chambers images as well?
2. Where should I “Create an Annotation ROI node”? On which images?

Best,

Kai

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<div class="post-metadata">

**Author:** ![KLNU](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/klnu/32/13600_2.png) [@KLNU](https://discourse.slicer.org/u/KLNU)\
**Post date:** [August 17, 2022, 2:15am UTC](https://discourse.slicer.org/t/how-to-generate-4d-cine-mri/24743/5 "2022-08-17T02:15:10Z")

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Dear Dr. Lasso,

Finally I solved the problem in constructing 4D cine MRI. It is the problem of dicom format. The data I shared with you did not work.

I have another question. How can I load a sequence (such as 4-chamber view cine as separated images)? I want to get radiomics features on those 25 images one by one.

Thank you!