scilpy

Getting started

Getting ready for tutorials
- Installation
- Download data

Documentation & Tutorials

1. Manipulating volumes
- Cropping volumes
2. Reconstructing the local model
3. Performing tractography
4. Tractogram manipulations
5. Bundle segmentation and analysis (tractometry, profilometry)
6. Connectivity
- Connectivity analyses
  - Examples
– From raw data to a complete project –
– Visualization –
- Create overlapping slice mosaics
- Adding data_per_point to tractograms for visualization
– Useful utilitary scripts –
- Using development containers with Visual Studio Code
- Instructions to write the tsv files “participants.tsv” for the script scil_stats_group_comparison
  - Header
  - Specific row
– Reproducing scilpy paper figures –

Modules and API reference

Modules
Scripts

scilpy

5. Bundle segmentation and analysis (tractometry, profilometry)
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5. Bundle segmentation and analysis (tractometry, profilometry)

This section covers bundle analysis methods in scilpy.

Tractogram Segmentation into bundles
Profilometry (statistics on bundles)
Tractometry (comparing bundles)
Creating a bundle template from a chosen population

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