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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