MultiVolume Explorer and Segment Editor Error

loading
mri
import
multivolume
segment-editor

#1

Hi all - I am trying to load a cine-MRI (link to data is below). I was able to import it through the DICOM import, but the results look off.

Furthermore, when I go to “volume rendering,” there is no volume generated, but when I go to the “volume” module, it shows a volume is present.

Also, I am not able to use the segment editor module for some reason. It is not reading the correct pixel values. I attached a screenshot of an attempt to use thresholding in the “Segment Editor” module, but the results do not make sense. The parts that it thresholds appear to be random.

Any help would be appreciated - thanks in advance.

LINK: https://drive.google.com/drive/folders/1Av3KorE_H6tt77zmDwat37fWqx24bN_6?usp=sharing


How to Import cine-MRI Images
(Andrey Fedorov) #2

The DICOM dataset loaded as a MultiVolume node (4d dataset), which means you cannot use Slicer functionality that work with 3d data.

You can extract individual temporal frames from the miltivolume, and apply those operations. You can also check “Enable copying” which will give you a 3d volume with a copy of the currently selected frame. You can then use Volume rendering to render that frame, and if you toggle “Play” you will see Volume rendering of the temporal changes (as shown in this movie: https://www.slicer.org/w/images/0/04/BeatingHeart.mov).


#3

Thank you! I will try this out.

Is that “Beating Heart” data set shown in the video available to the public for downloading?


(Andras Lasso) #4

In recent nightly builds, you can load 4D image as volume Sequence (if you install Sequences extension). Sequence browser module provides a 3D proxy node that you can use for segmentation, volume rendering, etc. You can create a corresponding sequence node for 4D segmentation; or segment a single 3D volume and use Sequence Registration extension to automatically extend it to all other time points.


(Andras Lasso) #5

If you install Sequences extension, then you’ll find two 4D cardiac CTs in Sample Data module that you can load by a single click.


(Andrey Fedorov) #6

Yes, you can download the dataset in the Tutorials section of the module documentation page: https://www.slicer.org/wiki/Documentation/Nightly/Modules/MultiVolumeExplorer


#7

Is there any information available such as the patient’s age? Furthermore, are there any good databases that 3D Slicer has access to that features patients with different cardiomyopathies?

Thank you!


(Steve Pieper) #8

There isn’t a lot of public cardiac data, but here’s one source:

http://www.cardiacatlas.org/studies/sunnybrook-cardiac-data/

If anyone knows of other datasets for research please post.


(Andrey Fedorov) #9

If you refer to the dataset linked from the documentation page, there is no further information available about the patient scanned.


(elham) #10

I have the same question. When I open shortaxis Cardiac MR Image, I can just see an image like what Aginn share here.
Can I open these image through sequence? How can I do that?
I think the problem is that slicer show DIOCOM image in sagital/coronal/axial coordinates but I need a shortaxis/longaxis coordinate.


(Andras Lasso) #11

Do you have a single-slice time sequence (2D+t) or a volume sequence (3D+t)?