Track tracingbutton in the
Add surface points. Selecting this option will add an additional point at the closest part of the brain surface to the first point, so that the track starts there.
Trace tracks. You can change:
Fit degree- what order spline fit to use (the default is 3, cubic)
Spline smoothing- how closely or not to fit the points (lower numbers fit more closely, for a less smooth interpolation)
Spline points- this doesn't affect the interpolation, but determines how many points are sampled from the interpolation (used for the summary)
Summarise- defaults to on, this will save a csv file, showing the brain area for each part of the interpolated track (determined by
Add surface pointIf the brain surface is damaged, you may not be able to trace perfectly from the surface. Selecting this option will add an additional point at the closest part of the brain surface to the first point, so that the track starts there.
.csvfile will be saved, showing the brain region for every spline point along the track.
Saveto save your points to be reloaded at a later date, and if you loaded your data in atlas space, you can also export the track to brainrender. The file will be saved as e.g.
track_0.npy. If you're using the brainrender GUI, use the
Load cellsbutton to load the track. Alternatively, using the Python API, you can visualise the track as follows: