Dear Marcelo,
The range of values is quite large, though not unreasonable.
Given that it covers non-brain tissue as well, then I think that's why it is bigger than normal.
If you re-measure it only within the brain (e.g. using a mask) then it should probably reduce a bit.
I wouldn't think this was problematic just from this though.
As for getting two phase maps, you'll need to unwrap each and take the difference. This is different from what the fsl_prepare_fieldmap script is expecting (and different from what we normally see on Siemens scanners) so you'll need to do your own processing following the guidelines in the documentation, rather than using this script. Siemens uses a particular scaling of their own phase difference outputs, so unfortunately you can't create a phase difference map and easily feed it into the script either.
All the best,
Mark
On 20 Sep 2012, at 20:26, Marcelo Mattar <[log in to unmask]> wrote:
> Hi, Mark,
>
> This is all very helpful, thanks a lot.
>
> 1) I've been playing around with prelude and fugue, but I don't know if the fieldmap I'm getting "looks right". If anybody could take a look and tell me what you think, it would be very helpful. http://dl.dropbox.com/u/2951700/fieldmap.png
> In that image, the range of values is from -3000 to more than 6000.
>
> 2) I have also been trying to use the fsl_prepare_fieldmap GUI, since I have a Siemens Trio at my University. However, the output of my B0map scan includes 2 B0magnitude maps, and 2 B0phase maps. In order to use the fsl_prepare_fieldmap script, how can I make a suitable single Phase Map file, to be used as an input to the program?
>
> Thanks a lot!
>
> --Marcelo Mattar
>
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