when I overlay an image containing integers (labels/rois) the value equal to one is not displayed. See screenshot. Other values 2 - 6 are. 0 obviously not.
Bug?
I can’t reproduce the problem with the voxels with value 1 not displaying on my system… Can you tell me a bit more about your OS, graphics card and driver, the specifics of the image you’re trying to overlay (e.g. mrinfo R_kmean.nii.gz)?
I can however reproduce the issue with the zero values not displaying. I agree that’s probably a bug, I’ll see if I can fix that.
Ok, that’s interesting… I tried with a image with 32-bit unsigned int datatype, and that seemed to overlay fine. I’m not sure what’s going on, but given that it works correctly with an 8-bit datatype, there’s a good chance this will be related to the OpenGL drivers and how they handle 32-bit int textures: there’s a possibility that the driver internally converts these to 16-bit ints, even though the OpenGL 3.3 standard mandates that they should be available. Stranger things have happened…
From that point of view alone, I’d be interested to know what OS, graphics card, and drivers you’re using, if only so others with similar issues can understand what the issue might be. You can find a lot of this information just by running:
Other question that I have: is it possible to use a custom colour map (or LUT). E.g. freesurfer.lut to view labelconvert output?
These are kind of two separate questions:
Adding colours to parcellation images: I chose to provide the label2colour command to explicitly calculate such, rather than trying to provide an interface to such within mrview.
Custom colour maps: Already listed as a feature request. I’d certainly like to have something like viridis implemented. This is however not a trivial code change, so is likely predicated on @jdtournier or myself getting to it…