Is there any sort of "batch" segment statistics?

Maxnach · March 7, 2021, 5:10pm

Hello everyone,

I performed semi-automated segmentation of muscles on many CT-scan of patients. The data base is organized this way : patients \ slice \ segmentation. For each patients, there is 2 or 3 slice at different time points (its only one slice for the measurements, not a volume). I would like to compute the mean area + mean density in a first step (and eventually apply a pyradiomics pipeline further on). Here is the structure of the data :

Is there anyway to compute a batch script (or maybe it already exists?) that would create a single table with patients name and corresponding “segment statistic output” ? I have more >100 and must admit I’m afraid I’ll have to do everything manually…

pieper · March 8, 2021, 4:22pm

I haven’t done this myself, but if you are able to do a little bit of python programming this is certainly doable. Have you gone through the tutorials enough that you are comfortable with doing some scripting? If so we can give you some specific suggestions for this task.

Maxnach · March 8, 2021, 4:28pm

Hello,

Thank you very much for your answer. The problem is I am a complete beginner in programming language…currently starting with R for PhD purposes but never done python or matlab…

I went through the tutorial but did not find any pre-set option/tools to get the segment statistic output in a table with patient’s name (as organized in the DICOM)…

pieper · March 8, 2021, 4:34pm

Is there anyone here who has done something similar and is able to step up with some code?

100 cases is on that borderline where you might just be more efficient to do it by hand, although you will benefit much more in the long term by learning the python scripting.

You might start by looking at the Case Iterator.

Maxnach · March 8, 2021, 5:40pm

Thank you for your quick feedback.

My main issue is that I already performed all segmentations and it seems that Case Iterator would have required me to start with it beforehand…

I already tried manually but this is a nightmare as I have ± 100 patients with 1 to 3 studies per patients (hence >200) and when I go to segment statistics, the lists of studies are not sorted by patients name but by slice names, which makes almost impossible to match each slice names with each .DICOM files :
Slicer segment

Help^^

lassoan · March 8, 2021, 8:01pm

You can find example scripts for processing a single case script repository and module tests). Once you have a code snippet that works for a single file, you can iterate through all the files in a folder.

Andinet_Enquobahrie · March 9, 2021, 8:24pm

Dear @Maxnach

Can you try something like the following (iterate through all the segmentation MRML modes in your slicer scene and generate the statistics…)? here is a code snippet to demonstrate this for mean intensity

for segmentationNode in slicer.util.getNodesByClass('vtkMRMLSegmentationNode'):
    segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
    segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.mean.enabled", str(True)) 
    segStatLogic.computeStatistics()
    stats = segStatLogic.getStatistics()
    for segmentId in stats['SegmentIDs']:
        mean = np.array(stats[segmentId,"ScalarVolumeSegmentStatisticsPlugin.mean"])
        print(mean)

Andinet

Maxnach · March 9, 2021, 8:51pm

Dear Andinet,

Many thanks for your suggestion, I’m a proper beginner and maybe I did it wrong, but here is the outcome in the python command prompt :

Also, maybe that could help, I read a bit since your mentionned MRML and it seems indeed that every segmentation has its MRML ref, however the labelling (numbers) does not make any sense to me :

The magical solution would be some script that measures the segment.stat from the MRML-ref segmentation/scalar volume and could “match” it with DICOM name/date… which I guess is what you did with this code snippet… but tried everything cannot launch it properly… any ideas where I could have go wrong ?

Many thanks in advance, I feel a solution is not far but my 0 background in coding is probably hiding it

Andinet_Enquobahrie · March 9, 2021, 10:06pm

Here is a little bit of a more complete code snippet

import SegmentStatistics
import numpy as np

segStatLogic = SegmentStatistics.SegmentStatisticsLogic()

#Scalar Volume MRML Node List ( You will need this to generate image intensity statistics )
scalarVolumeNode = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')

#WARNING: Assuming all segmentations were done on the same master volume, in this case the first one
segStatLogic.getParameterNode().SetParameter("ScalarVolume", scalarVolumeNode[0].GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.mean.enabled", str(True))

for segmentationNode in slicer.util.getNodesByClass('vtkMRMLSegmentationNode'):
    print(segmentationNode.GetID())
    segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
    segStatLogic.computeStatistics()
    stats = segStatLogic.getStatistics()
    for segmentId in stats['SegmentIDs']:
        mean = np.array(stats[segmentId,"ScalarVolumeSegmentStatisticsPlugin.mean"])
        print(mean)

Andinet

Maxnach · March 9, 2021, 10:16pm

Thank you so much, it seems it loader the segmentation, but there were an error at some point. Of note, each master volume has its own segmentation (actually each master volume = 1 slice of 1 patient at 1 time point)

import SegmentStatistics

import numpy as np

segStatLogic = SegmentStatistics.SegmentStatisticsLogic()

#Scalar Volume MRML Node List ( You will need this to generate image intensity statistics )

scalarVolumeNode = slicer.util.getNodesByClass(‘vtkMRMLScalarVolumeNode’)

#WARNING: Assuming all segmentations were done on the same master volume, in this case the first one

segStatLogic.getParameterNode().SetParameter(“ScalarVolume”, scalarVolumeNode[0].GetID())

segStatLogic.getParameterNode().SetParameter(“ScalarVolumeSegmentStatisticsPlugin.mean.enabled”, str(True))

for segmentationNode in slicer.util.getNodesByClass(‘vtkMRMLSegmentationNode’):

…

… print(segmentationNode.GetID())

…

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segStatLogic.getParameterNode().SetParameter(“Segmentation”, segmentationNode.GetID())

File “”, line 1

segStatLogic.getParameterNode().SetParameter(“Segmentation”, segmentationNode.GetID())

^