Hi Chenxi,

Thanks for your question. The shift option specifies where the origin is in voxel space which does not depend on voxel dimensions, ie the voxel index is used to identify the location in the coordinate system. When this was written, the middle of each voxel was defined as the voxel index, so the middle of voxel (1,1,1) would be located at coordinate (1,1,1) and voxel (30,40,50) would be located at coordinate (30,40,50) etc. However, when we made this program compatible with other programs we noticed a small half-voxel shift in the location of the tracts because other programs defined the 'bottom' corner of the image volume to be located at (0,0,0). So for example the middle of voxel (1,1,1) was at (0.5,0.5,0.5) and voxel (30,40,50) was at (29.5,39.5,49.5), etc. So the shift parameter just converts between these two coordinates. This does not depend on your voxel dimensions in real space, ie when the coordinates are scaled to represent a real length in mm. So you should not have to change this parameter unless you feel that your tracts are shifted in some program, as the origins may not be standardized.

I hope that helps,

Russell