Beginner question: liver volumetry

Hello !
I’m a resident in surgery, interested in liver volumetry prior to hepatectomy.
In the team which I work with, we use an expensive software made by Fujifilm, called Synapse.
It has 2 features that I need in 3D slicer, and I can’t find a tutorial.

First : I want to extract the whole liver
For that, I found a plugin called RVX that is pretty fast and accurate to make “liver in” and “liver out”
See picture there :

But, my problem is when I go to another tab of 3Dslicer, i lose the informations of “liver in” and “liver out” that was made by the plugin. See the tab “segmentation” here :

How can I export the data to the whole software ?

Second question : I want to do volume measurements, not 3D reconstruction :
So how to know the total volume of “liver in”, in mililiters / cm3 ?

And third question, that is the hardest : I want to do hepatectomies :
How to trace lines on my CT scan (or on the 3D reconstruction), that can simulates a surgery (i.e right/left hepatectomy), and to know the volume of the resected lesion ?

On fujifilm synapse, I trace lines on different slices of the ct scan, then the software reconstruct the section between the different lines. Is it possible to do the same ?

Thanks a lot !


I haven’t gone through it myself but the tutorial here looks really good:

You can also check other SegmentEditor tutorials for general use of the resulting segmentations and you may be able to use those tools to emulate surgery. However SlicerLiver is much more specialized for this task. Also check SegmentStatistics for info on getting the volume metrics.

Hey !
Thanks for the answer !

Just tried “liver” plugin and I still do have a problem.

I arrived on this screen by using the sample data :

I still have a problem with volumetry.
I would like to know the volume of liver on either side of my resection line.

I can’t find a way to do it… If some one have an idea ?

Thanks a lot;


Looks like you are very close. Maybe @RafaelPalomar can suggest the next step?

Go to Segment Statistics.
Select the scalar volume (source images) and segmentation volume, then hit Apply. It will generate a table with volume and density measurements.

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Some news here !
Just succeed, but only one time…
I have another problem !!
First of all : I use the total liver volume by first exporting it from RVX plugin, to a .stl file.
Then, I import the stl file in “segment editor” of 3Dslicer (it is the only way I found to make the plugin communicate with the rest of the software).

Then, as @finetjul wisely told me, I used one of the scissors tool. I suceed one time !
But when I wanted to try another time with another CT scan, 3D slicer doesn’t answer anymore, or I need to wait > 15minutes

It says that I have to convert to binary labelmap data, then load for a lot and a lot of time until I force to quit the software.

Does someone have an idea ? Maybe exporting in another format than STL ?

AND second question :
When I succeed, I used the surface cut tool.
Sometimes it does this :

but sometimes, and I don’t know why, it does this :

Does anyone have an idea for these two problems ? I’m almost there !

Thanks a lot


Regarding the first question, your overall volume seems too big and does not fit your computer memory. You might want to reduce the size of your volume first (“Crop volume” module)

Regarding the second question, you do not seem to have the latest version of the SurfaceCut tool.

@ThomasHusson, with Slicer-Liver you can do liver volumetry computations. I see in your screenshot that you were very close (the resection volumetry group widget is what you need)

1 ) Create a volumetry output table (in your screenshot you had none created).
2) Your reference volume node looks correct, as well as your segmentation node.
3) Our volumetry calculations are based on seed points that you can mix (for instance if you want to combine different liver segments with a resection. Your case looks more simple you would need to create a new markups list and place a seed inside the resected liver segmentation.

Please, let us know if this works for you or if you need further assistance.

I’m sure @RuoyanMeng and @dalbenzioG will react if I’m missing anyhing

Hi @ThomasHusson
As @RafaelPalomar said you are very close! I created a simple instruction based on your screenshot, you can try to do the following steps above on your current actions. Let me know if you have further questions :smile:

Way better than my explaination. Thanks @RuoyanMeng!

Hey, update needed here!
I finally managed to do it on many patient files.

I used totalsegmentator, which I found better because it doesn’t take the IVC or portal trunk for the liver. I had a surestimation of the total liver volume using RVX.
Also, totalsegmentator doesn’t need time to ‘convert’ the data, which was a problem because it took a lot of time with RVX.

I drew the hepatectomy using the Draw tool and the Fill between Slices tool.

I’m going to record a video for a tutorial that I’ll post here, in French with English subtitles.

Thank you very much for all your answers, I wouldn’t be able to do it without you!

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I have a problem using “Fill between slices” : see topic here : Fill between slices issue : need help!

If anybody here have an idea, I (again) need your help!
Thank you very much +++

@ThomasHusson, I’m curious. Was it anything that didn’t work for you using the instructions @RuoyanMeng provided?

Hi there. I found a solution using the intersect tool.
Regarding the R-vesselX plugin, I didn’t use it because I couldn’t figure out how to trace a line directly on the CT scan as I did using the cut option.
Even placing ROI directly, I haven’t found how! Should I place it on each side of a line?

Using 3D reconstruction rather than directly on the CT scan is a problem because 3D reconstruction would be needed to easily trace a line (e.g. following a vein).
I found it much more difficult to manipulate the fiducials on the 3D reconstruction if the vascular reconstruction wasn’t done first.

If the line could be traced directly on the CT scan, like the cut tool does in SegmentEditor, that would solve my problems!
Maybe using points with ROI as @RuoyanMeng said? I haven’t found how …

Thank you very much

This is a great question!! I am an expert at contouring Liver Volumes in my Institution. In fact, i am the only expert. 18 years. Liver and spleen volumes from MRI. With acute accuracy. But i really would like to explore what 3D slicer has to offer. If i did master this software, it would be the tip of the iceberg for my clinical customers.
John Roeger UHN. Toronto Canada

@roeg, for the Slicer-Liver extension we have been working with CT imaging, but if you can get good liver segmentations on MRI, the extension would operate the same way. Let us know about your experience if you end up trying the extension and ask any questions you may encounter.

Thank you for the reply. My work is ongoing…( have lots of cases) but will be looking more and more into your product. I have a lot of new software as well… I also excel at clinical coverage, so very busy schedule. Looking forward
John Roeger
3D Technical Specialist
INR/VIR Clinical Technologist/Specialist