Error: Invalid coordinateSystemFlag value

szhang · August 12, 2020, 3:58am

Hello
In Error log, there comes an error showing “VTK: Invalid coordinateSystemFlag value:0”, how to fix this, by coordinate system conversion?
It looks like coordinateSystemFlag = 0 for RAS system which is used by Slicer, then why is it problematic?

Thank you!

lassoan · August 12, 2020, 6:45pm

Thanks for reporting this. Invalid coordinateSystemFlag value is reported when you run a CLI module that does not specify coordinateSystem="lps". As long as you specify lps or ras as coordinate system, you can ignore this warning (and I’ll push a fix today to prevent displaying warning in this case).

szhang · August 12, 2020, 7:21pm

Thank you, great to know!
May I learn how to specify coordinate system in the module? doesn’t it depend on the configuration associated with the data being imported? or since mostly we import DICOM, by default it is set like this?

int coordinateSystem = vtkMRMLStorageNode::CoordinateSystemLPS

lassoan · August 12, 2020, 7:23pm

See an example how to specify coordinate system for input points here:

github.com

Slicer/Slicer/blob/ebc74c7ca99c28a395ebc099a14b002fb28decf1/Modules/CLI/ACPCTransform/ACPCTransform.xml#L15


<index>1</index>
<description><![CDATA[<p>Calculate a transformation that aligns brain images to standard orientation based on anatomical landmarks.</p><p>The ACPC line extends between two points, one at the anterior commissure and one at the posterior commissure. The resulting transform will bring the line connecting the two points horizontal to the AP axis.</p><p>The midline is a series of points (at least 3) defining the division between the hemispheres of the brain (the mid sagittal plane). The resulting transform will result in the output volume having the mid sagittal plane lined up with the AS plane.</p><p>Use the Filtering module <b>Resample Scalar/Vector/DWI Volume</b> to apply the transformation to a volume.</p>]]></description>
<version>1.0</version>
<documentation-url>http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ACPCTransform</documentation-url>
<license>slicer3</license>
<contributor>Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)</contributor>
<acknowledgements><![CDATA[This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.]]></acknowledgements>
<parameters>
  <label>Transform panel</label>
  <description><![CDATA[Calculate a transform from midline and ACPC fiducial lists.]]></description>
  <point multiple="true" coordinateSystem="ras">
    <name>ACPC</name>
    <label>ACPC Line</label>
    <longflag>--acpc</longflag>
    <description><![CDATA[ACPC line, a list of two fiducial points, one at the anterior commissure and one at the posterior commissure.]]></description>
    <default>0,0,0</default>
  </point>
  <point multiple="true" coordinateSystem="ras">
    <name>Midline</name>
    <label>Midline</label>
    <longflag>--midline</longflag>

Topic		Replies	Views
BGFDG_vtkMRMLModelNodeH.vtp does not contain coordinate system information. Assuming LPS Development	4	197	August 23, 2021
Changes to VTK polydata between 4.10 and 4.11 Support vtk	1	540	April 27, 2021
Incorrect overlay of vti and stl from the same dicom series Support segmentation	4	1227	May 20, 2019
VMTK extract centerline fails with VMTK using VTK9 Development vmtk , vmtk-centerline	3	1234	July 12, 2021
Point data error when visualize the difference between two volumetric meshes Development python	8	240	January 13, 2023

Error: Invalid coordinateSystemFlag value

Related Topics