SIENA is a package for both single-time-point (“cross-sectional”) and two-time-point (“longitudinal”) analysis of brain change, in particular, the estimation of atrophy (volumetric loss of brain tissue). SIENA has been used in many clinical studies.
Siena estimates percentage brain volume change (PBVC) betweem two input images, taken of the same subject, at different points in time. It calls a series of FSL programs to strip the non-brain tissue from the two images, register the two brains (under the constraint that the skulls are used to hold the scaling constant during the registration) and analyse the brain change between the two time points. It is also possible to project the voxelwise atrophy measures into standard space in a way that allows for multi-subject voxelwise statistical testing. An extension for ventricular analysis is provided in FSL5.
Sienax estimates total brain tissue volume, from a single image, normalised for skull size. It calls a series of FSL programs: It first strips non-brain tissue, and then uses the brain and skull images to estimate the scaling between the subject’s image and standard space. It then runs tissue segmentation to estimate the volume of brain tissue, and multiplies this by the estimated scaling factor, to reduce head-size-related variability between subjects.