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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.
XavierFinal 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>
