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HI - yes you should just use the finalPBVC. Cheers. On 12 Dec 2013, at 21:19, Amlish Munir <[log in to unmask]> wrote: > Hi folks, > > I have just started working with the Siena package to quantify atrophy. As a test, I've run siena on the same image, as well as a slightly modified image where I've removed some white matter. > > Same image for time point 1 and time point 2: > -------------------------------------------------------- > - Curiously, when Siena was run on the same image, the atrophy measurements for A to B and B to A are non-zero and the same sign (not correcting for direction) meaning A to B has growth and B to A has growth . While this results in a total atrophy of 0 ( AtoB + -1*(BtoA) ), I can't understand why a constant is being introduced when the images are the same. Does the algorithm introduce a constant offset and as a result we should only ever consider the final PBVC? > > /usr/local/fsl/bin/fast B_halfwayto_A_brain > B_halfwayto_A_brain.vol 2>&1 > finding brain edges > finding flow > AREA 242168 mm^2 > VOLC 1064.67 mm^3 > RATIO 0.00439641 mm > PBVC 0.170188 % > > /usr/local/fsl/bin/fast A_halfwayto_B_brain > A_halfwayto_B_brain.vol 2>&1 > finding brain edges > finding flow > AREA 242168 mm^2 > VOLC 1064.67 mm^3 > RATIO 0.00439641 mm > PBVC 0.170188 % > > finalPBVC 0 % > > > Same base image for time point 1 and 2 but some white matter from 2 is manually removed: > ---------------------------------------------------------------------------------------------------------------- > - Results seem sensible with atrophy being recorded appropriately around the constructed lesion but the lesion does bias the registration slightly leading to edge differences. > > Thanks for your help. > > Amlish --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet