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Hi Mark Thanks for those precision. For the Bruker data it is indeed easy since I have a phase difference map that is directly express in Hz. So I just multiply it by 6.28 and it seems to work well (after correction the result is reasonable) I also have data for Siemens (Trio or Verio both in vb17), where I also get a phase map. Looking at different post (and at the doc) I need to rescale the phase so that the values are between -pi and pi. I do not understand why the value should be between -pi and pi : the phase map seems to be already unwrapped. I gues so since looking at the data I do not see any strong transition in the phase value. So if the phase map is indeed unwrapped you can have phase values greater than pi ? what scaling do I need to do for Siemens phase map ? thanks for your help Romain Le 23/05/2012 11:06, Mark Jenkinson a écrit : > Dear Romain, > > You must have a magnitude image and an image that encodes the > field differences. We opt for using the units rad/s, which is easy to > convert from Hz (just multiply by 6.28) or Tesla (multiply by 42 MHz/T > to get Hz and then multiply by 6.28 to get rad/s). > > The latter information is derived from phase differences. > Depending on your scanner (and I have *no* experience with Bruker > I'm afraid), you may get one image (the difference) or two. These > may be phase values directly (though often scaled to span a large > integer range, like 0 to 4096 for 0 to pi radians) or may be in > real and imaginary parts. The tool fslcomplex has been written > to allow you to convert between the different forms. However, > once you have a phase difference you still need to divide by the > time difference between the images (normally the echo time > difference of the fieldmapping sequence if it is gradient-echo > based, but there are other alternatives too). Only after you've > divided by this time difference will you get units of rad/s rather > than just radians. > > I hope this helps. > All the best, > Mark > > On 16 May 2012, at 01:39, romain valabregue wrote: > >> Dear all >> >> I am trying to unwarp dti data from a mouse brain (with a Bruker 11.7 T) >> >> I get a little bit confused with the documentation >> http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html >> >> from what I understand I have a magnitude volume (that is easy) and a phase volume that is in Hz >> does anyone use Buker data and can confirm this ? >> >> >> So the only scaling I need is to multiply this phase volume by 6.28 and I do not need to enter the TE difference >> is that right ? >> >> I get value between -9000 and +4000 (or -3000 + 3000 if I restrict to the brain) >> does it seems reasonable ? >> >> thank you for your help >> >> Romain >>