Can't get axial, sagital, and coronal MRI slices to display together like in tutorial

Hello,
I got through the DICOM tutorial, but have hit a wall when loading in my own MRI data. In the tutorial, the series loads in and the 3 slices appear in the 3D viewer together, however when I load in my series, it seperates the 1 into 3 series and I can only see one of the slices at a time in my viewer (screenshots attached).

How can I reproduce the example given in the tutorial? I would be happy to provide a copy of the data since it’s not subject to HIPAA anyways.

I’m ultimately looking to reconstruct 3D volume of the heart from these images.

Yes, please share the data set (upload somewhere and post the download link here) then we can easily investigate.

Link expires on 12/7 but I can extend if needed!

The series contains slices with different orientations, Slicer separated them into 3 volumes by “image orientation (patient)” attribute. IMHO, very good. Original slices in series look in physical space like that:

AFAIK, it is possible to view slices from red, green and yellow windows at once, if eye symbol is checked in every window (one of 3 volumes at a time, one slice is original and 2 reconstructed)

1 Like

Thanks for the reply. I can’t figure out how you overlayed the volumes like in your first picture.

When I visualize of the 3 sets, it unchecks the other 2. Like I said earlier, I’m going to need the recreate the 3D volume of the endocardium from this dataset and I’m stuck as how to proceed.

I’m brand new to 3D visualization so thanks ahead of time for the patience!

1st screen is from another app, in Slicer it is possible to view several volumes at once (eye symbol for every volume in “Volume Rendering”), is is close to that view.

1 Like

If you click the eye icon in the data module then the volume is shown in all views. To show different volume in each slice view, you can click “Show view controls” then select the volume in “Background volume selector” - see documentation.

2 Likes

Thank you for the help! I’m one step closer!

I managed to set my ROI for the heart, where does one proceed from here for reconstructing a 3D mesh from endocardial volume? I’ve found the segmentations documentation: https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentations.html but am weary I’m missing something since this is my first time. Is there anything else I should be referencing to do this?

You can segment the endocardial surface using Segment Editor module. These tutorials should help you getting started: https://www.slicer.org/wiki/Documentation/Nightly/Training#Segmentation

1 Like