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