Hi - from the report log it looks like it run OK - however, indeed the forward and backwards estimates are quite different from each other, which isn't a good sign. I can't tell from the text file which steps might have not worked well - you need to look carefully through the web-page report with various stages summarised with image outputs. Cheers. On 7 Oct 2014, at 17:31, Xavier Aymerich <[log in to unmask]> wrote: > Hello, > > I have a problem generating report files using Siena. > > Html report file appears incomplete (see attached file) and final PBVC value is always a 2.0%. Text file include the same error with final PBVC value. > > I have found this problem using FSL 5.0.7. Using earlier versions of FSL it generates correct report files and a final PBVC value different to 2.0%. > > I am running the following command using Siena: > > siena file1.nii.gz file2.nii.gz -B "-f 0.3" > > Anyone could help me? > > Thanks in advance. > > Xavier > > > > > Final brain edge movement image > > atrophy 0 "growth" > > > > Estimated PBVC: 2.0 > > SIENA Methods > > Two-timepoint percentage brain volume change was estimated with SIENA [Smith 2001, Smith 2002], part of FSL [Smith 2004]. SIENA starts by extracting brain and skull images from the two-timepoint whole-head input data [Smith 2002b]. The two brain images are then aligned to each other [Jenkinson 2001, Jenkinson 2002] (using the skull images to constrain the registration scaling); both brain images are resampled into the space halfway between the two. Next, tissue-type segmentation is carried out [Zhang 2001] in order to find brain/non-brain edge points, and then perpendicular edge displacement (between the two timepoints) is estimated at these edge points. Finally, the mean edge displacement is converted into a (global) estimate of percentage brain volume change between the two timepoints. > > [Smith 2001] S.M. Smith, N. De Stefano, M. Jenkinson, and P.M. Matthews. > Normalised accurate measurement of longitudinal brain change. > Journal of Computer Assisted Tomography, 25(3):466-475, May/June 2001. > > [Smith 2002] S.M. Smith, Y. Zhang, M. Jenkinson, J. Chen, P.M. Matthews, A. Federico, and N. De Stefano. > Accurate, robust and automated longitudinal and cross-sectional brain change analysis. > NeuroImage, 17(1):479-489, 2002. > > [Smith 2004] S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. > Advances in functional and structural MR image analysis and implementation as FSL. > NeuroImage, 23(S1):208-219, 2004. > > [Smith 2002b] S.M. Smith. > Fast robust automated brain extraction. > Human Brain Mapping, 17(3):143-155, November 2002. > > [Jenkinson 2001] M. Jenkinson and S.M. Smith. > A global optimisation method for robust affine registration of brain images. > Medical Image Analysis, 5(2):143-156, June 2001. > > [Jenkinson 2002] M. Jenkinson, P.R. Bannister, J.M. Brady, and S.M. Smith. > Improved optimisation for the robust and accurate linear registration and motion correction of brain images. > NeuroImage, 17(2):825-841, 2002. > > [Zhang 2001] Y. Zhang, M. Brady, and S. Smith. > Segmentation of brain MR images through a hidden Markov random field model and the expectation maximization algorithm. > IEEE Trans. on Medical Imaging, 20(1):45-57, 2001. <report.siena> > --------------------------------------------------------------------------- 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