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Hi Robert, I'm afraid I don't know a particular FAQ for this. There is some material in the FSL course, slides 117 and following of: http://www.fmrib.ox.ac.uk/fslcourse/lectures/flirt_fugue/flirt_fugue_slides.pdf You're on the right lines about voxel and world space differing. Essentially, voxel-space is just a way of numbering the voxels, it's fairly meaningless in terms of spatial location. World-space coordinates aim to be spatially meaningful. They aren't just translated from voxel-space though, i.e. there is not just an offset along each axis, as you seem to assume. Firstly, world-space takes into account the voxel dimensions, which is especially important if they are not isotropic (i.e. the voxels are cuboids rather than cubes), as well as the origin/translations. The voxel-world mapping can also include rotations, e.g. for an oblique acquisition the voxels won't be aligned with the desired anatomical axes. It can even include skews of the axes, in a general 12 degree-of-freedom affine transformation (this is what the 12 parameter matrix on slide 117 of the above allows for). Registration, using e.g. FLIRT, creates a correspondence between the world space of your image and the world space of e.g. the MNI template. (often, images are resampled/interpolated so that their voxel spaces correspond too). More info on how MNI space is defined can be found here: http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach I think that's all I have time for, I hope it's of use. Ged. Robert Terwilliger wrote: > Dear FSL, > > I am trying to determine a conversion (linear > translation) from fslview's coordinate system to > MNI152 coordinate space. > > My experience is that fslview, along with other > viewers I have used, sets the origin (0,0,0) as > follows: > > x = 0: leftmost location in the x direction (rightmost > radiologically), > y = 0: most posterior location, > z = 0: most inferior location. > > In an attempt to associate a specific coordinate with > the nearest anatomical structure, either in > command-line programs or in websites I've found, it > appears that (0,0,0) is somehow near the center (or > perhaps THE center) of the brain itself. > > It appears that there are two coordinate systems: a > voxel-based coordinate system and a so-called world > coordinate system, that latter having the MNI brain > centered at the origin. > > 1) Is there an FAQ or archived email discussion about > this? > 2) If not, what are the offsets along each axis to > convert from one system to the other..? > 3) Does FSL already have a command line tool that > automates this translation? > > Many thanks and regards, > > Robert Terwilliger > Laboratory of Neuro-Cognitive Development > University of Pittsburgh >