# Get a flipped and rotated segmentation label image using python script

**URL:** <https://discourse.slicer.org/t/get-a-flipped-and-rotated-segmentation-label-image-using-python-script/13756>\
**Category:** Support\
**Tags:** segmentation, python\
**Created:** [September 29, 2020, 6:36pm UTC](https://discourse.slicer.org/t/get-a-flipped-and-rotated-segmentation-label-image-using-python-script/13756 "2020-09-29T18:36:56Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![N\_Hunter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/n_hunter/32/6823_2.png) [@N\_Hunter](https://discourse.slicer.org/u/N_Hunter)\
**Post date:** [September 29, 2020, 6:36pm UTC](https://discourse.slicer.org/t/get-a-flipped-and-rotated-segmentation-label-image-using-python-script/13756/1 "2020-09-29T18:36:56Z")

</div>

Hi, there, I recently use python script to export segmentations to labelmap and save it on the disk, to save some clicks. But instead, I get a rotated and flipped labelmap, like below:

![9](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/8/c85afe3ea5f1c1515d4e09dd0dc128709e74654b.png)

This should be a “4”, but instead, it was flipped and rotated “4”. I’ve tried both to save labelmap in nii.gz and nrrd format, all gives me the same result.

Here is my code:

```auto
def extract_label(mrml_fp):
   # load mrml file
   slicer.util.loadScene(mrml_fp)

    # access manually annotated label
   segs = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')

   # master volume
   volume_node = slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')

   if len(segs) != 1:
       raise "the number of segmentation node shoule be 1"

   annoted_segment_node = segs[0]
   annoted_seg = annoted_segment_node.GetSegmentation()

   # iterate through all the segments
   num_segments = annoted_seg.GetNumberOfSegments()

   for idx in range(num_segments):

      # create new segmentation node
      new_segement_node = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
      new_segement_node.CreateDefaultDisplayNodes()
   new_segement_node.SetReferenceImageGeometryParameterFromVolumeNode(volume_node[0])

      # add segment to new segmentation node
      segment = annoted_seg.GetNthSegment(idx)
      segment_name = segment.GetName()
      new_segement_node.GetSegmentation().AddSegment(segment)

      # export segmentation node to labelmap
      labelmap_volume_node = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
      slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(new_segement_node, labelmap_volume_node, volume_node[0])

      # save labelmap to disk
      dest_folder = os.path.dirname(mrml_fp)
      slicer.util.saveNode(labelmap_volume_node, os.path.join(dest_folder, "{}.nrrd".format(segment_name)))

      # remove created segmentation node
      slicer.mrmlScene.RemoveNode(labelmap_volume_node)
      slicer.mrmlScene.RemoveNode(new_segement_node)

   # clear scene
   slicer.mrmlScene.Clear(0)

```

Could you please tell me where I went wrong?