Hi,
The output of b0calc by default is a fraction of the main field strength (if --b0 is left at 1). So to get it in Tesla just multiply by your scanner's field strength. You can then convert into rad/s using the gyromagnetic ratio.
That being said, it is very difficult to get a good result from b0calc unless you have been very careful to get an accurate air/bone segmentation. This is hugely challenging from MRI alone as they are both dark on MRI but have different magnetic properties. So the input image to b0calc needs to have a value of 1 for all tissue, including non-brain tissue and bone, but not air. Using the struct_brain from BET will definitely not be useful as it removes all the non-brain tissues but these are absolutely crucial for determining the magnetic field inside the head (which is what b0calc is trying to do).
So I hope this helps and I hope you have some way of distinguishing bone from air (most easily with CT).
All the best,
Mark
On 25 Feb 2013, at 11:45, Louis Shue <[log in to unmask]> wrote:
> Hi,
>
> I am trying to figure out how to estimate a fieldmap for EPI correction using b0calc function.
>
> For starters I did some tests using data from the FSL course (http://www.fmrib.ox.ac.uk/fslcourse/). In particular I am using sample data from fsl_course_data/reg/feat_example because this directory contains some structural image and some scans necessary to form a fieldmap using conventional method (fsl_prepare_fieldmap).
>
> 1. bet images_006_grefieldmap521Hzpx3mm1001 fmap_mag_brain -f 0.5 -g 0
> 2. fsl_prepare_fieldmap SIEMENS images_007_grefieldmap521Hzpx3mm2001 fmap_mag_brain fmap_rads 2.46
>
> Secondly I ran b0calc on the extracted brain from struct image for data in the same directory.
>
> 1. bet struct struct_brain -f 0.5 -g 0
> 2. b0calc -i struct_brain -o struct_brain_fmap -v
>
> Right now there is a few problems. Notwithstanding the fact that struct_brain is of a much higher resolution than fmap_mag_brain (and hence the respective fieldmaps), the two resulting fieldmaps seem quite very different qualitatively (visually)!? Also, the dynamic range of struct_brain_fmap is very small. Are these the "expected" results?Or did I miss out any additional optional parameters for the b0calc stage??
>
> Any help is very much appreciated.
>
> Louis.
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