# Extracting 2D axial slice from 3D volume using current slice view
**URL:** https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390
**Category:** Support
**Created:** [August 27, 2023, 8:01pm UTC](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390 "2023-08-27T20:01:18Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@calici](https://discourse.slicer.org/u/calici)
#### Post date: [August 27, 2023, 8:01pm UTC](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390/1 "2023-08-27T20:01:18Z")
Hi!
Currently I am working on developing a custom extension.
One of the functionalities that I want to implement is a user can scroll in axial view and select the axial slice as the slice-of-interest. Then I want to use this slice a 2D nrrd/mha file in my algorithm.
I looked at the similar topics and implemented suggested ways. The problem is that my original volume has size (512, 512 ,225) but extracted slice has size (932, 548, 1). I want it to be (512, 512, 1). How can I extract with correct shape?
Below you may find the code I used and images [1].
Thank you!
```auto
sliceNodeID = "vtkMRMLSliceNodeRed"
# Get image data from slice view
sliceNode = slicer.mrmlScene.GetNodeByID(sliceNodeID)
appLogic = slicer.app.applicationLogic()
sliceLogic = appLogic.GetSliceLogic(sliceNode)
sliceLayerLogic = sliceLogic.GetBackgroundLayer()
reslice = sliceLayerLogic.GetReslice()
reslicedImage = vtk.vtkImageData()
reslicedImage.DeepCopy(reslice.GetOutput())
# Create new volume node using resliced image
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
volumeNode.SetIJKToRASMatrix(sliceNode.GetXYToRAS())
volumeNode.SetAndObserveImageData(reslicedImage)
volumeNode.CreateDefaultDisplayNodes()
volumeNode.CreateDefaultStorageNode()
slicer.util.exportNode(volumeNode, )
```
1. _Soler, L., A. Hostettler, V. Agnus, A. Charnoz, J. Fasquel, J. Moreau, A. Osswald, M. Bouhadjar, and J. Marescaux. “ **3D image reconstruction for comparison of algorithm database: A patient specific anatomical and medical image database.** ” IRCAD, Strasbourg, France, Tech. Rep (2010)_
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### Author:  [@pieper](https://discourse.slicer.org/u/pieper)
#### Post date: [August 27, 2023, 9:27pm UTC](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390/2 "2023-08-27T21:27:44Z")
Assuming the data was axial (like this CT) you can just access the volume node as an array and get `array[k]` where k is the slice offset transformed to IJK space. I f you look in the script repository you can find all the pieces pretty easily.
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### Author:  [@calici](https://discourse.slicer.org/u/calici)
#### Post date: [August 28, 2023, 1:42am UTC](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390/3 "2023-08-28T01:42:41Z")
Hi Steve,
Thank you very much for your answer!
Previously I got slice offset but could not find a way to obtain the slice itself by using that value. With your hint I got the idea.
I am not sure if it is an elegant solution but I am leaving my code as a reference:
```auto
# Get image data from current axial (red) slice view
sliceNodeID = "vtkMRMLSliceNodeRed"
sliceNode = slicer.mrmlScene.GetNodeByID(sliceNodeID)
appLogic = slicer.app.applicationLogic()
sliceLogic = appLogic.GetSliceLogic(sliceNode)
sourceVolumeNode = sliceLogic.GetBackgroundLayer().GetVolumeNode()
# Get current axial slice in RAS:
sliceOffset = sliceLogic.GetSliceOffset()
# Convert RAS to IJK:
volumeRasToIjk = vtk.vtkMatrix4x4()
sourceVolumeNode.GetRASToIJKMatrix(volumeRasToIjk)
point_VolumeRas = [0, 0, sliceOffset, 1]
point_Ijk = [0, 0, 0, 1]
volumeRasToIjk.MultiplyPoint(point_VolumeRas, point_Ijk)
point_Ijk = [int(round(c)) for c in point_Ijk[0:3] ]
# Get slice of interest as a volume:
imageArray = slicer.util.arrayFromVolume(sourceVolumeNode)
sliceOfInterest = imageArray[point_Ijk[-1], :, :]
volumeOfInterestNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLScalarVolumeNode')
slicer.util.updateVolumeFromArray(volumeOfInterestNode, sliceOfInterest)
# Copy image origin, spacing and direction:
ijkToRas = vtk.vtkMatrix4x4()
sourceVolumeNode.GetIJKToRASMatrix(ijkToRas)
volumeOfInterestNode.SetIJKToRASMatrix(ijkToRas)
# Export:
slicer.util.saveNode(volumeOfInterestNode, r"C:\extracted_slice.nrrd")
```
Best regards!
---
### Author:  [@calici](https://discourse.slicer.org/u/calici)
#### Post date: [August 31, 2023, 3:54am UTC](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390/4 "2023-08-31T03:54:06Z")
New edit
Much shorter version if anyone is interested:
```auto
sliceNodeID = "vtkMRMLSliceNodeRed"
sliceNode = slicer.mrmlScene.GetNodeByID(sliceNodeID)
appLogic = slicer.app.applicationLogic()
sliceLogic = appLogic.GetSliceLogic(sliceNode)
sliceOffset = sliceLogic.GetSliceOffset()
k = sliceLogic.GetSliceIndexFromOffset(sliceOffset) - 1 # -1 since 1-based
```