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Update fibertube_tracking.rst
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VincentBeaud authored Nov 19, 2024
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34 changes: 17 additions & 17 deletions docs/source/documentation/fibertube_tracking.rst
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Expand Up @@ -234,9 +234,9 @@ option. Let us do:

scil_fibertube_tracking.py fibertubes.trk tracking.trk --blur_radius 0.1 --step_size 0.1 --nb_fibertubes 3 --out_config tracking_config.json --processes 4 -v -f

This should take a minute or two. The loading bar of each thread will
only update every 100 streamlines. It may look like it's frozen, but
rest assured. it's still going!
This should take a minute or two and will produce 15 streamlines. The loading
bar of each thread will only update every 100 streamlines. It may look
like it's frozen, but rest assured. it's still going!

Reconstruction analysis
~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -308,24 +308,24 @@ giving us the following output in ``reconstruction_metrics.json``:
::

{
"vc_ratio": 0.0,
"ic_ratio": 0.0,
"nc_ratio": 1.0,
"res_vc_ratio": 0.06666666666666667,
"res_ic_ratio": 0.0,
"res_nc_ratio": 0.9333333333333333,
"mae_min": 0.014523808944519356,
"mae_max": 9.25675274988759,
"mae_mean": 1.3040961801420252,
"mae_med": 0.026874907457201936
"vc_ratio": 0.0,
"ic_ratio": 0.0,
"nc_ratio": 1.0,
"res_vc_ratio": 0.3333333333333333,
"res_ic_ratio": 0.3333333333333333,
"res_nc_ratio": 0.3333333333333333,
"mae_min": 0.004093314514974615,
"mae_max": 10.028780087103556,
"mae_mean": 3.055598084631571,
"mae_med": 0.9429987731800447
}

This data tells us that about none of our streamlines managed to stay
This data tells us that none of our 15 streamlines managed to stay
within the fibertube in which they were seeded (``"vc_ratio": 0.0``).
However, 6% of streamlines ended closer than one ``blur_radius`` away from
the end of their respective fibertube (``"res_vc_ratio": 0.06``).
However, 1/3 of streamlines ended closer than one ``blur_radius`` away from
the end of their respective fibertube (``"res_vc_ratio": 0.3333333333333333``).
Lastly, we notice that the streamline with the "worst" trajectory was on average
~9.26mm away from its fibertube (``"mae_max": 9.25675274988759``).
~10.03mm away from its fibertube (``"mae_max": 10.028780087103556``).

This is not very good, but it's to be expected with a --blur_radius and
--step_size of 0.1. If you have a few minutes, try again with 0.01!
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