trksnapshot 0.1.1

Tractometry Visualization Tool

trksnapshot

Installatoin

pip install trksnapshot==0.1 (project page)

Description

trksnapshot is a CLI for creating bundle visualizations (created using FURY and DIPY). It supports

1. Visualizing 3D bundles in an interactive window with custom color options and camera view. These include per-bundle color and along-tract color using BUAN (for tractometry results).
2. Supports plotting bundle with glass brain and pial surfaces.
3. Rotate the camera however you like and save camera settings to produce consistent plots.
4. Save snapshot images for publication-ready figures!

All bundle visualizations in our recent work Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry were created with this script. Here's one of the figures:

Usage

[RECOMMENDED] To visualization bundle(s) with default pial surfaces (in MNI space)

python snapshot_bundle.py \
      -i /path_to_tractogram/bundle*.trk \
      -glass default_pial \
      -show

You may also provide your own pial surface files

python snapshot_bundle.py \
      -i /path_to_tractogram/bundle*.trk \
      -glass /path_to_surfaces/pial_left.nii /path_to_surfaces/pial_right.nii \
      -show

To visualization bundle(s) with default glass brain (must be in MNI space)

python snapshot_bundle.py \
      -i /path_to_tractogram/bundle*.trk \
      -glass default_glass \
      -show

To visualization bundle with pial surfaces with BUAN output

python snapshot_bundle.py \
      -i /path_to_tractogram/bundle.trk \
      -f /path_to_buan_results/pvals.npy \
      -ctitle pvalues -auto -cbar /path_to_output_folder/cbar.png \
      -glass /path_to_surfaces/pial_left.gii.gz /path_to_surfaces/pial_right.gii.gz
      -show \
      -o /path_to_output_folder/bundle.png

Citations

1. Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry
2. FURY: advanced scientific visualization