Kindly let me know what these negative coordinated of coorX, coorY and coorZ means in this .csv file. when i open patient’s data in 3D slicer, I can view x,y,z coordinates in positive values
Can you describe where you got the csv file and what you expect the values to mean?
This comes up quite often for new users. Slicer uses RAS internally to display the point coordinates, but writes them as LPS to disk (fcsv or json files) for compatibility with other software. RAS to LPS involves negation of the values of first two coordinates. In recent slicers, you can export a table of of these coordinates either LPS or RAS, using the export Table option.
LPS Exported coordinates
RAS Exported coords
1 Like
thanks for reply. But how to find “export coordinate system”. what about CoorZ values sir? Can I see images showing LPS coordinates and not RAS?
I am try to scan LUNA16 images and they have provided annotated .csv file to look for cancer location which i shared.
thank you
LUNA16 sample data set providers have chosen ambiguous names in their coordinate system axes (coordX, coordY, and coordZ), but it seems that the coordinates are actually in LPS coordinate system.
Therefore, you can load these points by renaming the columns to label, r, a, s, and load them into Slicer as a table:
Then in Markups module create a new point list and import the table:
This makes all points to show up, which may be impractical (and very slow, unless you hide the point labels and/or disable interaction with the points).
Instead of dumping all points into a point list, you may want to display a sphere at the specified position. See an example code snippet for that in the script repository.