Fiducials in Slicer-4.11. / 4.10 "R" and "A" flipped coordinates?

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1

Dear all,

I use Slicer to create Fiducials/annotate landmarks in nifti images for a project. I have multiple computers to work on. After annotating them on computer 1 with Slicer 4.11. I open them on computer 2 with Slicer 4.10 and the points are displayed flipped. When I check the coordinates under the module Markups, they are still the same as in the fcsv file, but I noticed, that in Slicer 4.10. the A coordinates are positive when they are negative in the fcsv file and negative when they are positive in the fcsv in R and A direction.

my point in fcsv file:

Markups fiducial file version = 4.11
CoordinateSystem = LPS
columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
1,-0.0034653465346536905,-10.54306930693069,-19.5,0,0,0,1,1,1,0,chiasma,vtkMRMLScalarVolumeNode2

So they same fcsv file looks like this in both Slicers:

  • Slicer 4.11: R= +0.003 A= +10.5 S= -19.5
  • Slicer 4.10. markup R= -0.003 A= -10.5 S= -19.5

Is there something I do wrong? How can I create files that are the same across versions in Slicer?

2

In case someone else will ever have this issue. Slicer 4.10. fcsv files look like this:

Markups fiducial file version = 4.10
CoordinateSystem = 0

If I read them into Slicer 4.11. the points are were I would expect them. If I load a fcsv file created with 4.11. into 4.10. it will not take into account LPS System (?) and one has to adjust/flip the files before. The LPS Coordinate System is the one expected by ANTs/ITK so it actually saves you some time if you want to apply transfroms to the fcsv files.

3

Here is what I came up with to handle the situation. Upon reading, the coordinates are converted to LPS, unless they are already LPS:

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4

@CST Is there a specific reason for using a very old Slicer version? You are missing out on hundreds of fixes and new features if you use a Slicer version that was released several years ago.

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