Get image data from reformatted CT volume slice

DAVID_GARCIA_MATO · February 13, 2019, 11:45pm

Hello,

I need to get image data (meaning pixel/voxel values) from a reformatted CT volume slice.

I have developed a simple scripted module to load a CT volume and used the “Reformat” module in Slicer to reformat a CT slice to contain 3 predefined fiducials. Now, I would like to obtain the image data from that reformatted slice, meaning pixel/voxel values.

Is there a simple way to get that information?

I would really appreciate your help,

Thank you very much in advance,

Best,

David

muratmaga · February 14, 2019, 7:04am

arrayFromVolume is what you need I think. https://slicer.readthedocs.io/en/latest/developer_guide/slicer.html#slicer.util.arrayFromVolume

in the example below, a is the integer array of pixel values for the MRHead.

import SampleData

sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRHead()
a = arrayFromVolume(masterVolumeNode )

DAVID_GARCIA_MATO · February 18, 2019, 4:37pm

Hi,

I have just tried that, but “arrayFromVolume” method gives me the whole volume (3D matrix). How can I get just the pixel values of my reformatted slice?

Thanks!

David

cpinter · February 18, 2019, 5:53pm

What comes to mind are the transforms that take you from RAS to slice view XY or back, see these functions for example

github.com

Slicer/Slicer/blob/master/Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractEffect.h#L340-L366


/// Convert RAS position to XY in-slice position
static QPoint rasToXy(double ras[3], qMRMLSliceWidget* sliceWidget);
/// Convert RAS position to XY in-slice position, python accessor method
Q_INVOKABLE static QPoint rasToXy(QVector3D ras, qMRMLSliceWidget* sliceWidget);
/// Convert XYZ slice view position to RAS position:
/// x,y uses slice (canvas) coordinate system and actually has a 3rd z component (index into the
/// slice you're looking at), hence xyToRAS is really performing xyzToRAS. RAS is patient world
/// coordinate system. Note the 1 is because the transform uses homogeneous coordinates.
static void xyzToRas(double inputXyz[3], double outputRas[3], qMRMLSliceWidget* sliceWidget);
/// Convert XYZ slice view position to RAS position, python accessor method
Q_INVOKABLE static QVector3D xyzToRas(QVector3D inputXyz, qMRMLSliceWidget* sliceWidget);
/// Convert XY in-slice position to RAS position
static void xyToRas(QPoint xy, double outputRas[3], qMRMLSliceWidget* sliceWidget);
/// Convert XY in-slice position to RAS position
static void xyToRas(double xy[2], double outputRas[3], qMRMLSliceWidget* sliceWidget);
/// Convert XY in-slice position to RAS position, python accessor method
Q_INVOKABLE static QVector3D xyToRas(QPoint xy, qMRMLSliceWidget* sliceWidget);
/// Convert XYZ slice view position to image IJK position, \sa xyzToRas
static void xyzToIjk(double inputXyz[3], int outputIjk[3], qMRMLSliceWidget* sliceWidget, vtkOrientedImageData* image);
/// Convert XYZ slice view position to image IJK position, python accessor method, \sa xyzToRas

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This example might also be useful from the Threshold effect that takes the image from a slice view:

github.com

Slicer/Slicer/blob/master/Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorThresholdEffect.py#L382-L405


def setupPreviewDisplay(self):
  # Clear previous pipelines before setting up the new ones
  self.clearPreviewDisplay()


  layoutManager = slicer.app.layoutManager()
  if layoutManager is None:
    return


  # Add a pipeline for each 2D slice view
  for sliceViewName in layoutManager.sliceViewNames():
    sliceWidget = layoutManager.sliceWidget(sliceViewName)
    if not self.scriptedEffect.segmentationDisplayableInView(sliceWidget.mrmlSliceNode()):
      continue
    renderer = self.scriptedEffect.renderer(sliceWidget)
    if renderer is None:
      logging.error("setupPreviewDisplay: Failed to get renderer!")
      continue


    # Create pipeline
    pipeline = PreviewPipeline()

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I’m not sure if there is anything specific to using the Reformat module that these ideas don’t take into account, but I hope this helps!

DAVID_GARCIA_MATO · February 18, 2019, 6:19pm

Thanks @cpinter!! I think that’s what I needed!

David

lassoan · February 20, 2019, 2:08pm

There is also a short example showing how to get resliced image as a volume node and access it as a numpy array:

https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Get_reformatted_image_from_a_slice_viewer_as_numpy_array

DAVID_GARCIA_MATO · February 21, 2019, 1:40am

Quite useful! Thank you Andras!

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Get image data from reformatted CT volume slice

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