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You might want to try looking at the fugue utility in FSL ( http://www.fmrib.ox.ac.uk/fsl/fugue/index.html). I've read on the mailing list of ways that you can substitute a magnitude image. Best, Michael On Mon, Jun 1, 2009 at 10:02 AM, Winston Chiong <[log in to unmask]>wrote: > Dear list users, > > We've been testing subjects on a task on which we're expecting a lot of > orbitofrontal and anterior temporal activation, and I had been anticipating > using the FieldMap utility to correct for susceptibility artifact. > Unfortunately, I've just learned that the GRE field mapping sequence that > we've been acquiring has been saving the phase data only, without the > magnitude data. (We're using a Siemens 3T TIM Trio scanner, acquiring a GRE > field map with TEs of 5.19 and 7.65ms, echo spacing of 0.8 and 118 echoes.) > Whereas, it looks like the FieldMap toolbox expects to have one phase and > one magnitude image. > > According to our Siemens rep, there's no way to reconstruct the magnitude > data from the phase volume that we have; however, he seemed to think that > the unwarping should be possible with the phase images only. Does anyone on > the list know of tools that can be used to do this in place of FieldMap, or > of a way to use the data that I've got to generate the data that FieldMap > expects? (Browsing through the list archives, it looks like SPM wants the > magnitude data in order to assess the SNR at each voxel--can I use any of my > other structural or functional images to generate this?) > > > Thanks, > Winston > > -- Research Associate Gazzaley Lab Department of Neurology University of California, San Francisco