# How to convert vtkPolyData to image coordinates?

**URL:** https://discourse.vtk.org/t/how-to-convert-vtkpolydata-to-image-coordinates/8108
**Category:** Support
**Tags:** python
**Created:** [March 22, 2022, 3:50pm UTC](https://discourse.vtk.org/t/how-to-convert-vtkpolydata-to-image-coordinates/8108 "2022-03-22T15:50:00Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![lbrandao](https://discourse.vtk.org/letter_avatar_proxy/v4/letter/l/9de0a6/32.png) [@lbrandao](https://discourse.vtk.org/u/lbrandao)
#### Post date: [March 22, 2022, 3:50pm UTC](https://discourse.vtk.org/t/how-to-convert-vtkpolydata-to-image-coordinates/8108/1 "2022-03-22T15:50:00Z")

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Dear All,

I have a vtkPolyData file (extension.vtk) with 12 points:

 ![image](https://discourse.vtk.org/uploads/default/original/2X/7/7bb7cb23d7caa37dce603225fdc5d46f265b9320.png)

These points are the annotation of a 3D image data (more exactly, a multi-slice DICOM image - one folder with 14 slices/frames .dcm).

I need to convert each of the previous points to image coordinates. I.e. given a point (e.g. -177.747, -136.373, 21.174) I need to find the correspondent (i, j, k) image coordinates (where k is the slice index).

This is what I tried:

```auto
# load 3D volume
volume_reader = sitk.ImageSeriesReader()
dicom_names = volume_reader.GetGDCMSeriesFileNames(multi_slice_volume_path)
volume_reader.SetFileNames(dicom_names)
image = volume_reader.Execute()

# load vtk points
reader = vtk.vtkPolyDataReader()
reader.SetFileName(lmks_vtk_file_path)
reader.Update()
vtkdata = reader.GetOutput()
vtk_points = numpy_support.vtk_to_numpy(vtkdata.GetPoints().GetData()) 

# convert vtk points to image coordinates
image_points = np.zeros((vtk_points.shape))

for i, coord in enumerate(vtk_points):
   coord = (float(coord[0]), float(coord[1]), float(coord[2]))
   image_points[i] = np.array(image.TransformPhysicalPointToIndex(coord)).astype(int)

```

But the image coordinates that I get are not correct.

```auto
[[-33. 190. 24.]
 [-52. 194. 23.]
 [-45. 178. 21.]
 [-35. 143. 26.]
 [-42. 166. 29.]
 [-72. 168. 26.]
 [-60. 147. 24.]
 [-25. 161. 24.]
 [-35. 181. 27.]
 [-66. 180. 25.]
 [-53. 161. 23.]
 [-29. 179. 23.]]

```

I get negative i coordinates (points outside the image boundaries) and the k coordinates are not within the expected range 0-13 (since I have a total of 14 slices).

I did further research but I couln’t find the solution. The closest clue was this post [https://discourse.vtk.org/t/mapping-between-coordinate-position-x-y-z-and-voxel-index/5357/4](https://discourse.vtk.org/t/mapping-between-coordinate-position-x-y-z-and-voxel-index/5357/4) by @dgobbi

Any help will be most appreciated. Thanks.

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<div class="post-metadata">

### Author: ![dave3d](https://discourse.vtk.org/user_avatar/discourse.vtk.org/dave3d/32/1157_2.png) [@dave3d](https://discourse.vtk.org/u/dave3d)
#### Post date: [March 22, 2022, 6:32pm UTC](https://discourse.vtk.org/t/how-to-convert-vtkpolydata-to-image-coordinates/8108/2 "2022-03-22T18:32:36Z")

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I would guess it has to do with LPS vs RAS coordinate systems. I’d suggest loading the data into Slicer and see if they align. Slicer does a good job of handling all the coordinate system intricacies.