Hello Lyidia,
The combination of intensity threshold and cluster size was used to segment the vessels from the noisy background of the angio data. The value of these multiple thresholds was determined empirically, choosing settings that cover both extremes (left wing, right wing). If I remember correctly, the thresholds 0.2 .. 0.8 are intensity values normalized by the maximum intensity in each angio data set.
To deal with the different voxel resolutions, I used 3dfractionize (which Bob wrote for that occasion). I recommend you use it too.
