Hi Flemming, are you sure the mask is a cube? I am not familiar with the tutorial files, but I would check this first. In chimera, the Volume Viewer window will show the map/mask dimensions in voxels to the right of the volume name. You could also check the graphic in the “import volume” job you ran in cryosparc, which indicates volume dimensions.
I am not familiar with ChimeraX, but in chimera I would run “vop resample #vol1 ongrid #vol2” where vol2 is the reference. Then save the new volume and ensure its dimensions are a cube with one of the two methods above. You could molmap a PDB to generate vol1 which is a subset region of vol2, or you could use the segmentation tool in chimera or the volume eraser to slice up the original map since you don’t have a PDB. The segmentation tool will shrink the volume such that you must resample ongrid to the reference (starting map).
Regarding your question about the threshold, this is a map contour level you must choose which essentially sets the size of the mask. Open the original map alongside the map you are using as the starting point for your mask. Adjust the threshold of this map to engulf the region of the reference you are interested in. Then set a dilation radius, which adds more volume beyond the threshold level.