# Create and overlay a segmentation on a volume

**URL:** <https://discourse.slicer.org/t/create-and-overlay-a-segmentation-on-a-volume/19994>\
**Category:** Development\
**Created:** [October 4, 2021, 5:49pm UTC](https://discourse.slicer.org/t/create-and-overlay-a-segmentation-on-a-volume/19994 "2021-10-04T17:49:40Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![S\_Arbabi](https://avatars.discourse-cdn.com/v4/letter/s/dfb087/32.png) [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Post date:** [October 4, 2021, 5:49pm UTC](https://discourse.slicer.org/t/create-and-overlay-a-segmentation-on-a-volume/19994/1 "2021-10-04T17:49:40Z")

</div>

I want to apply a threshold value on an image and overlay this threshold result as a segmentation (or labelmap) on the image.  
Based on a sample in script repository I tried to do it this way:

```auto
    threshold = 500
    
    #getting volume node and its image as array
    volumeNode = slicer.util.getNode("volume")
    volumeNode_array = slicer.util.arrayFromVolume(volumeNode)

    #creating new segmentation node and segment and set its reference image geometry to volume node
    segmentationNode = slicer.vtkMRMLSegmentationNode()
    slicer.mrmlScene.AddNode(segmentationNode)
    segmentationNode.CreateDefaultDisplayNodes()
    segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(volumeNode)
    segmentationNode.GetSegmentation().AddEmptySegment()
    segmentId = segmentationNode.GetSegmentation().GetSegmentIdBySegmentName('Segment_1')

    #get the array of segmentation, update its values and refresh the segmentatin
    segmentArray = slicer.util.arrayFromSegmentBinaryLabelmap(segmentationNode, segmentId, volumeNode)
    segmentArray[:] = 0
    segmentArray[volumeNode_array > threshold] = 1
    slicer.util.updateSegmentBinaryLabelmapFromArray(segmentArray, segmentationNode, segmentId, volumeNode)

```

this returns this error:

```auto
    segmentArray = slicer.util.arrayFromSegmentBinaryLabelmap(segmentationNode, segmentId, volumeNode)
TypeError: arrayFromSegmentBinaryLabelmap() takes 2 positional arguments but 3 were given

```

I see in the documentation though this function can take 3 arguments, the last one is reference volume:

```auto
referenceVolumeNode: a volume node that determines geometry (origin, spacing, axis directions, extents) of the array.

```

It is also stated that:

```auto
If not specified then the volume that was used for setting the segmentation's geometry is used as for the reference volume.

```

since I’m setting the reference image geometry upper in code, if I don’t pass the referenceVolumeNode I will get this error:

```auto
    segmentArray[volumeNode_array > threshold] = 1
IndexError: boolean index did not match indexed array along dimension 0; dimension is 0 but corresponding boolean dimension is 135

```

I appreciate any ideas in this regard.

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 4, 2021, 6:19pm UTC](https://discourse.slicer.org/t/create-and-overlay-a-segmentation-on-a-volume/19994/2 "2021-10-04T18:19:34Z")

</div>

_Latest_ version of the Slicer documentation on ReadTheDocs (this is the one that is shown by default when you don’t specify a version) is for latest Slicer Preview Release. The [code snippet](https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#read-and-write-a-segment-as-a-numpy-array) works well for the latest Slicer Preview Release.

For older versions of the script repository, you would need to choose the corresponding version in the lower-left corner in ReadTheDocs, but since we migrated the script repository in Slicer-4.13, there are no earlier archived versions.

Therefore, you either need to update your Slicer or modify the code snippet to match the API of the Slicer version you are using. I would recommend updating your Slicer, as the new Slicer Stable Release will be out soon, which will have the same API as the latest Slicer Preview Release.