Operating system:windows 10
Slicer version:4.10.1
Expected behavior:no units
Actual behavior:unrealistic units
I am using a file composed of a stack of tiff images from uMRI that I merged using FIJI. When I open this file in slicer it works well. when I use the ruler I get a measurement that is not accurate. I know the size of each pixel, for instance 39x39x39 in microns. Is there a way to add this information?
Thanks
I don’t think you can add it to the tiff, but if you save in nrrd or nifti format then the spacing can be preserved.
You can edit spacing information manually in Volumes module / Volume Information section. I agree with @pieper that you should choose an image format that can store at least the most basic image geometry information (origin, spacing, axis directions).
Thanks that worked! I have been saving as NRRD just loading the original as a tiff. of course any segments I made no longer fit the original and won’t give me accurate measurements, is there any way to scale them?
You can scale the image and segmentation by applying the same linear transform using Transforms module (scaling factors are the 3 first values in the diagonal of the 4x4 transformation matrix).
Or you can export them as labelmap volume nodes and edit the spacing in the volumes module like you did for the background. Then you can re-import them as segmentation. (Import export controls are at the bottom of the Segmentations module).
Do you know a way to make the linear transform reduce by 3 decimal places? right now I can only get two in the boxes.
When I import the exported labelmap nodes I can’t select them as an active volume to change their image spacing.
You can press Ctrl++ to increase the number of displayed digits.