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I wasn't clear about the sequence we are using. GE names it "2Dfast", but it only acquires one line of k-space per echo. Acquiring multiple lines in a single echo is problematic because k-space is traversed in alternate directions as you go down the phase-encode axis. This complicates the phase calculation. A standard gradient echo sequence is fast enough. John On Nov 20, 2007 12:01 PM, David Lythgoe <[log in to unmask]> wrote: > On 20/11/07 17:06, "Carlos Faraco" <[log in to unmask]> wrote: > > > Alright, a few more things. I apologize if some of my questions may be > > rudimentary, but I just recently started to become familiar with > fieldmaps > > and also do not have a physics/programming background. > > > > So the suggestion has been to use the real and imaginary images and > > calculate the phase from them using atan2, or whatever other method > there > > may be. How is this different from using the phase image produced by the > > scanner? > > > > How is atan2 used? What would y and x be? I am looking at the syntax but > do > > not understand it too well. > > y is the imaginary component of the signal, and x is the real part. Part > of > the reason I acquire real & imaginary is that the complex maths > calculations > I did required them rather than magnitude & phase, so I acquire them > rather > than calculate them. I'll send you an abstract. > > > > > Dave, the reason you set saveinter = 1, is not necessarilly for the > purpose > > of saving the individual coil images, but just to get the combined coil > > image in the appropriate units, correct? > > I didn't know there was a way of getting the correct phase, so I needed > all > the individual coil images in order to calculate the the phase difference > between the SE & ASE myself. > > > > > If I use the real and imaginary images, do I still have to perform the > > processes described in the article? > > I assume if you use the method you mentioned of turning asset on, then > setting the asset factor to 1 you won't have to, just calculate the phase > difference. > > > > > John, what is your rationale for using the fast GRE and is there > anything > > you do with it differently than with standard GRE? I originally thought > the > > fast GRE acquired multiple lines of k-space per echo, however Dave > informed > > me this is incorrect. Thanks for you suggestion on the masking, that > makes > > sense. Do you just create this mask using FSL? > > I think this is a matter of terminology. GE fast sequences acquire a line > of > k-space at a time, whereas EPI acquires all lines of k-space in one shot > (or > more). With GE sequences the fieldmap will be in (almost) undistorted > space > similar to the structural (SPGR on GE). If you use EPI to create the > fieldmap, it will be distorted too. > As for the masking, applying bet to the magnitude image does a fair job. > > > > > Lastly, any more suggestions as to things I should be doing are greatly > > appreciated. Again, I am fairly new to fieldmaps and am sort of figuring > > this out on my own. > > > > Thanks! > -- John Ollinger University of Wisconsin Waisman Center, T233 1500 Highland Ave Madison, WI 53711 http://brainimaging.waisman.wisc.edu/~jjo/