Editor to measure volume

(Candice Nguyen) #1

Operating system: MAC
Slicer version: 4.11

I am using slicer to measure volume of the brain. I typically trace the area I want with draw effect and fill it. I do same thing slide by slide until the whole volume I am interested in is filled. I then use label statistic to get the volume. The program gives me volume and standard deviation. Can anyone please explain what the standard deviation means? I noticed with some measurements I got larger standard deviations than others. What can I do to improve my method and get a more accurate/precise measurements? Thanks

(Csaba Pinter) #2

First, I’d suggest that you use Segment Editor for segmentation, which has a Fill between slices tool that allows you to skip slices and then automatically fill the gaps in - this would fit your workflow and speed it up (and also the Editor module will be removed in 5.0).
Then you can use Segment Statistics to calculate the volume.

Standard deviation is about the voxel intensities not the volume. The volume is an exact measurement.

(Candice Nguyen) #3

So I am trying to use segment editor like you suggested, but as I filled a slide on axial, slides above and below were also filled. What happened if I do not want to include slides below and above?

Also, when I use fill between slides, there seem to be gaps. Will it affect my volume measurement? Thanks.

(Csaba Pinter) #4

You only fill one slice by default. Based on your screenshot your volume is not axis-aligned. You need to rotate the slice plane so that it aligns with your volume.

(Andras Lasso) #5

Yes, what you see is a feature: Slicer’s Segment Editor module allows editing on arbitrarily oriented views, which may intersect multiple slices.

Recent versions of Slicer show a warning button (with an exclamation mark) if any of the slice viewers are not aligned with the current segmentation axes. Click that button to snap each slice view to nearest segmentation axis.

If “Fill between slices” effect finds segments on consecutive slices then it considers them already 3D (already filled). So, you need to work with axis-aligned slice viewers and skip at least one slice between segmented slices.

Volume is reported for exactly what you see. If you see that segmentation is incomplete/inaccurate then you need to fix that before you compute volume.

(Candice Nguyen) #6

Where is the ruler option on slicer so I can measure diameter?

Thanks so much for all your helps

(Andras Lasso) #7

You can use the annotation toolbar to add a ruler - see details here: https://www.slicer.org/wiki/Documentation/Nightly/Modules/Annotations

(Candice Nguyen) #8

I am not sure why, but slicer is not showing me full view of these two slides and on the other view, I can’t roll between views like how we normally view CT scans. I randomly got it work one time and I could not get it worked again…Please help!!! Thanks…

(Andras Lasso) #9

Have you loaded your data set using DICOM module (using the DICOM browser that shows patient, study, series list)?

You may have several image series in a study and some of them may be single-slice, so make sure you choose a volumetric image. You can load all series in a study then go to Data module and click on eye icons to choose which one you would like to see.

(Candice Nguyen) #10

Yes I used DICOM. I pick patient then the views that have acquisition number to load. Normally it will just load images in three views sagital, coronal and axial. I am not sure what is wrong with this disc (I have not experienced this problem before), like you said some study may be single slice, but I got it to work on same disc, but I can’t get it to work again unfortunately.

(Andras Lasso) #11

Could you attach a screenshot of your DICOM browser? (erase patient name and ID if it is non-anonymized human patient data)

(Candice Nguyen) #12

Unfortunately it is non anonymized.

But I normally picked to open all views with acquisition number that is not 0. I need all three views to work.

(Andras Lasso) #13

From this screenshot it is not obvious if any of these are volumetric acquisitions. You can verify if there are multiple frames in a series by clicking “Metadata” button: if there is a slider near the top of the window then it confirms that the series contains multiple frames.

(Candice Nguyen) #14

Is this the slider?

It gotta have multiple frames because I got it to work and measured some volumes…closed it…then can not get it back to work again…

(Andras Lasso) #15

Did you select a single series when you got this slider? If yes, then it is a volume and if you click “Load” then you should see a volume (a full image in all three orthogonal slice viewers).

(Candice Nguyen) #16


I got it figure out at last…but now I am having another the problem as I tried to learn to use segment editor instead of editor.

  1. 46%20PM

How do I pull up segment_1 on segment stat to calculate volume?

With editor, all I have to do is use coronal on editor and pull coronal on stat to get volume. Segment editor and segment stat are more complicated.

  1. I used fill between slide and got this model but it does not look solid. What did I do wrong?


(Candice Nguyen) #17

  1. Why are there color outside the skull? I do not understand how fill in between works so I just want to make sure I get as accurate results as possible.


(Andras Lasso) #18

You need to use Segment Editor module (and not the legacy Editor module). Can you confirm that you are using Segment Editor?

(Candice Nguyen) #19

Below is what I used from the all modules tab:

(Candice Nguyen) #20