Scripts to project 3D and 4D maps to streamline points and perform math operations in space of streamline points

[grahamlittlephd]

Quick description

Scripts for projecting and analyzing 3D and 4D data on streamline points. Useful for analyzing different image modalities in the space of streamlines. For example, a correlation could be calculated from rsfMRI timeseries interpolated at streamline endpoints.

scil_tractogram_project_map_to_streamlines.py - takes a tractogram and map as input and interpolates the data from the map to every point for each streamline.

scil_tractogram_dpp_math.py - computes various mathematical operations for all points for each streamline or at each point independently.

Simple Example usage:
Projects fa data to each streamline point
scil_tractogram_project_map_to_streamlines.py in.trk fa.trk --in_maps fa.nii.gz --out_ddp_name fa

_Calculates mean fa for each streamline
scil_tractogram_dpp_math.py mean fa.trk fa_mean_per_streamline.trk --mode dps --in_dpp_name fa --out_name fa_mean

_Could then color streamlines using current functionality
scil_tractogram_assign_custom_color.py fa_mean_per_streamline.trk fa_mean_per_streamline_colored.trk --use_dps fa_mean --min_cmap 0

Example output of mean fa (jet color map) calculated for each streamline for tractography across the caudalenticular gray matter bridges:

Here is toy example and data for testing purposes:
toy_example_usage_project_map_to_two_streamlines.zip

Type of change

Check the relevant options.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

...

Checklist

• My code follows the style guidelines of this project (run autopep8)
• I added relevant citations to scripts, modules and functions docstrings and descriptions
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I moved all functions from the script file (except the argparser and main) to scilpy modules
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[pep8speaks]

Hello @grahamlittlephd, Thank you for updating !

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2024-02-19 17:58:10 UTC

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[EmmaRenauld]

Thanks! I will cite your scripts in my upcoming PR.

Let's already give it a good name fitting with the whole renaming fashion.
scil_project_map_to_streamlines.py --> scil_tractogram_project_map_to_streamlines.
(Mine will be scil_project_streamlines_to_map --> scil_tractogram_project_streamlines_to_map)

(Question for you Graham. Would it be a better English to say project_streamlines_onto_map??)

[EmmaRenauld]

Thanks!

I tested both scripts. Everything seems to work correctly! I still added quite a few comments, but it's just to improve clarity.

[EmmaRenauld]

Yes it's fine, but ok. I will manage it in another PR after. Let's simplify this one.

[arnaudbore]

GTG