Displaying results with streamlinesΒΆ

Fixels rendered as lines using the fixel plot tool of mrview are appropriate for viewing 2D slices (e.g. Fig. 6 in this paper); however to better appreciate all the fibre pathways affected and to visualise the full extent of the results in 3D, we developed a visualisation approach based on the whole-brain template-derived tractogram (as explained by Fig 4).

First use tckedit to reduce the whole-brain template tractogram to a sensible number of streamlines (2 million is too many for typical graphics cards to render smoothly). This step assumes you have the same folder structure and filenames from the FBA tutorials. From the template directory:

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 fwe_pvalue.tsf.

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.