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Hi Merry, I think for the Siemens scanners the diffusion directions are programmed in the magnet coordinate system, which is defined as LAI: From Siemens' IDEA Manual: "The fixed coordinate system of the scanner hardware is the physical coordinate system. Standing in front of the scanner and look over the patient table into the magnet, then the x-axis points from left to right; y-axis points from down to up; z-axis points from rear to front (towards you)". That is why if you multiply the z component of the bvecs by -1 you get the right dtifit. -Pablo On Mon, 28 Jul 2008 14:40:49 -0400, Merry Mani <[log in to unmask]> wrote: >Dear FSL experts > > I have some DTI datasets that was acquired on a Siemens syngo >scanner sometime back. The data was acquired in the RAS format and >the bvecs for the scanner are prescribed in the LPS format. So, I >made the data into LAS format by using fslswapdim input -x y z >output; fslorient -swaporient output. I also multiplied the y >component of my original bvecs by -1 to make it correspond to LAS. >But, now my dtifit (V1) is wrong. > >But, if I use a bvec that would correspond to LPI format ( by >multiplying the z component of the original bvecs with -1) with data >in LAS, I get correct dtifit. Is that possible? In one of the >previous postings, it was said that the bvectors relate to the image >co-ordinates. What exactly did that mean? > >Also, I'm getting the exact same results as above (V1 and FA) when my >bvectors are in RAS and my data is in LAS. I'd assume that bvectors >and -bvectors should act the same for V1 calculations, is that right? > >Thanks, >-Merry