## page was renamed from DiffusionMeeting10 5 2007 ## page was renamed from DiffusionMeetingNotes = Notes from informal meeting about diffusion = On 10 May 2007 == Acquisition issues == === Need for optimization for fibre tracking === Issues are: * Number of averages vs number of directions * Isotropic vs defined diffusion angles - relating to anatomy * Cardiac gating; expected differences; whether this can be easily applied using Siemens setup. Is currently working for Oxford with Siemens patches - these may not be available to us === CBU acquisitions === * Default is 63 angles, 2 averages, 14 minutes * Alternative 30 directions 3 or 4 averages Need to investigate which is preferable for fibre tracking === WBIC === For fibre tracking: * 8 minutes, 2mm isotropic, 63 directions - ? one average (as it were) For traumatic brain injury patients (Virginia Newcombe): * 12 direction, 5 B values (allowing more accurate estimation of diffusion coefficent) * Physicists involved are Guy Williams + Adrian Carpenter == Analysis == CBU currently using FSL - see DiffusionFdtNotes BrainVisa set up, but display not working due to OpenGL problems. Needs local (desktop) install WBIC using dtiquery - http://graphics.stanford.edu/projects/dti/dti-query/ good display routines, fibre tracking - algorithm? Have also used FSL - particularly for fibre track cross subject analysis using TBSS program (see below). == Open questions == How to do quantitative cross-subject analysis or fibre track anatomy in relationship to neuropsychology? Investigation of TBSS? Using FSL fibre tracking for statistical analysis across subjects of connectivity between areas == Plan == Hope to set up more knowledge sharing between WBIC and CBU / CSL. Maybe Wiki pages for WBIC on diffusion experience and software. First step at understanding cross-subject analyses? Suggest journal club on TBSS main paper. S.M. Smith, H. Johansen-Berg, M. Jenkinson, D. Rueckert, T.E. Nichols, K.L. Miller, M.D. Robson, D.K. Jones, J.C. Klein, A.J. Bartsch, and T.E.J. Behrens. Acquisition and voxelwise analysis of multi-subject diffusion data with Tract-Based Spatial Statistics. Nature Protocols, 2(3):499-503, 2007. Technical report: http://www.fmrib.ox.ac.uk/analysis/research/tbss/tr05ss1.pdf MatthewBrett