Hey @Warclu
Have you compared the output data?
It's hard to estimate the difference between the methods only by the visualization.
And even the visualization parameters in these two tools are not the same.
The color map and scale are not the same, and in these plots, you used the inflated brain in Brainstorm and the regular surface on Fieldtrip.
You may need for example to export the FT data and display it with brainstorm or visce versa.
Also, you said that you used different head models, so this may also affect your results. I recommend using the same methods/models on all steps, including the head model (not only the conductivities).
Fieldtrip has multiple variants of the BEM, while Brainstorm uses the OpenMeeg, and they may be different in the parameters.
I recommend using the same parameters in all the previous steps before comparing the inverse algorithms.