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Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot? |
faq |
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When visualizing anatomical MRIs and source reconstructed data with ft_sourceplot, it may happen that the image is plotted upside-down. This has to do with the way in which anatomical volumes are plotted in FieldTrip. For more information, see the frequently asked question What is the plotting convention for anatomical MRIs?.
{% include image src="/assets/img/faq/anat_upsidedownplotting/upside_down_sourceplot.png" width="400" %}
In itself this is not a problem, as explained here.
If for aesthetic reasons you do want the figure to be plotted upside-up, you can use the ft_volumereslice function to reslice the MRI, i.e. to interpolate the anatomy onto a new 3D grid that is aligned with the axes of the coordinate system. If you use the resliced MRI as input to ft_sourceinterpolate, the source reconstructed result will also show up as expected.
{% include image src="/assets/img/faq/anat_upsidedownplotting/correct_sourceplot.png" width="400" %}