From 3ac8d552e2b54939958b14b99b899dca86d81efc Mon Sep 17 00:00:00 2001 From: VincentBeaud Date: Thu, 14 Nov 2024 16:42:29 -0500 Subject: [PATCH] Update demo for high precision data bug --- docs/source/documentation/fibertube_tracking.rst | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/docs/source/documentation/fibertube_tracking.rst b/docs/source/documentation/fibertube_tracking.rst index 2f2f28a75..1d1ff6775 100644 --- a/docs/source/documentation/fibertube_tracking.rst +++ b/docs/source/documentation/fibertube_tracking.rst @@ -111,6 +111,20 @@ volume. This is accomplished using ``scil_tractogram_filter_collisions.py``. +**Caution**: Some tractograms, especially if old, were created with a very high +float precision. ``scil_tractogram_filter_collisions.py`` does not save its +output with such precision. This means that after filtering once and saving +the result, new collisions may be created from saving at a lower float +precision. It will require a second filtering to be truly collision-free. + +If you are using the ``--out_metrics`` parameter on high float precision +data, the script may even throw an error saying that not all collisions were +filtered prior to metrics computation. + +**Solution**: If you encounter such behaviour, we recommend you load and save +your tractogram to be filtered with modern tools such as MI-Brain or the +Nibabel python library. (Which scilpy scripts use) + :: scil_tractogram_filter_collisions.py centerlines_resampled.trk diameters.txt fibertubes.trk --save_colliding --out_metrics metrics.txt -v -f