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Hi On 1 Nov 2011, at 14:23, Michael Harms wrote: > Hi Matthew, > Maybe I'm not planning on using fslcc in the manner for which it was > intended, but doesn't that mean that the resulting correlations will be > dependent on somewhat arbitrary things such as the number of 0 voxels? > i.e., the size of a brain mask that was previously applied? That's right - it's just a simple dumb correlation tool - I guess you could script fslmaths and fslstats to do more complex stuff. Cheers. > > Also, to avoid anyone getting confused, I'm sure you meant to include a > sqrt factor in your denominator, right? :) > > thanks, > -MH > > On Tue, 2011-11-01 at 13:53 +0000, Matthew Webster wrote: >> Hello Michael, >> No voxels are explicitly excluded from the calculation. The >> two input images are ( depending on command line options ) >> demeaned and then all timepoints and voxels are looped >> across to generate >> >> (image1_timepoint1*image2_timepoint2)/(sumsquares(image1_timepoint1).sumsquares(image1_timepoint2)) >> >> Hope this helps >> >> Matthew >>> >>>> Hello, >>>> I want to compute to the correlation (across voxels) of two images, and >>>> my understanding is that's what 'fslcc' is for. But, it isn't obvious >>>> to me what determines which specific voxels go into that calculation. >>>> If a voxel is zero in EITHER input volume, is that voxel then excluded >>>> from the calculation? (in which case I can control the voxels that >>>> contribute to the calculation by thresholding my input appropriately >>>> beforehand?) >>>> >>>> thanks, >>>> -MH >>>> >>>> >>> >>> > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------