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Kent, most logging of the cost functions appears to work at >=4 so perhaps try comparing registrations with -verbose 4 and see if you get enough info. Sorry I can't be more helpful. Perhaps when Mark Jenkinson sees this he'll have a better suggestion. On 9 Jan 2008, at 15:05, Dave Flitney wrote: > Kent, > > Looking at the sources: in find_cost_minima it will output "COST > minima" if verbose level is >= 3. Haven't had a chance to test it > but hopefully that'll do the trick? > > On 9 Jan 2008, at 14:45, Kent Conover wrote: > >> Hi Everybody, >> >> Thanks to some advice that I received from Heather Urry, I have >> had some success unwarping >> my EPI volumes. My question is, is there a way to statistically >> assess the effectiveness of FUGUE? >> I imagine that one could compare the mutual information scores for >> the registrations of >> distorted and corrected volumes to the subjects high resolution >> anatomical. However, FLIRT >> apparently does not report the final values of the cost function. >> I would appreciate any >> suggestions. >> >> Regards, >> >> -Kent >> >> PS. Here is Heather's advice on how to the transform the field map >> produced by the Siemens Magnetom Trio gre_field_mapping protocol >> for use by FUGUE: >> >> Hi Kent, >> >> For what it's worth, when I reconstruct our Siemens Magnetom Trio >> DICOM >> fieldmap images using MRIcron, I get 2 magnitude images and one >> phase map. >> The phase map is scaled with slope of 2 and an intercept of -4096. To >> convert that to radians per sec, I use the following command: >> >> fslmaths fieldmapping64s006a201.nii.gz -mul 3.14159 -div 4096 - >> div .00246 >> fieldmap.nii.gz >> >> fieldmapping64s006a201.nii.gz is the name of the phase map. >> >> Multiplying the phase map by 3.14159 and dividing by 4096 converts >> the >> image to -pi to pi. Dividing again by .00246 converts to >> radians/sec. .00246 is the TE difference, in seconds. In my case, >> TE1 = >> 2.84 ms and TE2 = 5.3 ms, thus TE diff = 2.46 ms, or .00246 s. >> >> fieldmap.nii.gz is the properly scaled fieldmap that is output by >> this >> command. It's the one that I use for B0 unwarping in FEAT. >> >> Hope this is helpful! Ignore if this isn't what you were looking >> for. :) >> >> Cheers, >> >> Heather >> >> >> >> > > -- > Cheers, Dave > > Dave Flitney, IT Manager > Oxford Centre for Functional MRI of the Brain > E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717 > URL: http://www.fmrib.ox.ac.uk/~flitney > > -- Cheers, Dave Dave Flitney, IT Manager Oxford Centre for Functional MRI of the Brain E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717 URL: http://www.fmrib.ox.ac.uk/~flitney