How to generate 4D cine MRI?

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
  • 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
  • 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?



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.

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.



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?



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!