Displaying results with streamlines
Fixels rendered directly as lines using the fixel plot tool of mrview are appropriate for viewing 2D slices; however, to better appreciate all the fibre pathways affected and to visualise the full extent of the results in 3D, it’s also possible to use a visualisation based on the whole-brain template-derived tractogram [Raffelt2017].
tckedit to reduce the whole-brain template tractogram to a sensible
number of streamlines (2 million is quite a lot for certain graphics cards to render
smoothly). This step assumes you have the same folder structure and filenames from the
FBA tutorials. From the
tckedit tracks_2_million_sift.tck -num 200000 tracks_200k_sift.tck
Map fixel values to streamline points, save them in a “track scalar file”. For example:
fixel2tsf stats_fdc/fwe_pvalue.mif tracks_200k_sift.tck fdc_fwe_pvalue.tsf
fixel2tsf stats_fdc/abs_effect_size.mif tracks_200k_sift.tck fdc_abs_effect_size.tsf
Visualise track scalar files using the tractogram tool in MRview. First load the
streamlines (tracks_200k_sift.tck). Then right click and select ‘colour by (track)
scalar file’. For example you might load the
abs_effect_size.tsf file. Then
to dynamically threshold (remove) streamline points by p-value select the “Thresholds”
dropdown and select “Separate Scalar file” to load
Note that you can also threshold and view all brain fixels by deselecting “crop to slice” in the fixel plot tool. However it can be harder to appreciate the specific pathways affected. The downside to viewing and colouring results by streamline, then viewing all streamlines (uncropped to slice), is that without transparency you only see the colours on the outside of the significant pathways, where normally the effect size/p-value is most severe in the ‘core’ of the fibre pathway.
Good examples of both fixel as well as streamline visualisations of FBA results can be found in [Mito2018a].