nitk Neuroimaging Toolkit (nitk), and usage examples.

Nitk provides:

1. A template of a typical data science project following Cookiecutter Data Science

• nitk aims to provides functionalities not (yet) available in nilearn or scikit learn. Alway prefers nilearn functionnality if available.
• scripts provides example usage.

Provide utils functions and commands organized by software.

    nitk/
    ├── bids
    │   ├── Related to BIDS
    ├── cat12vbm
    │   └── Related to CAT12 VBM pipeline
    ├── fs
    │   └── Freesufer
    ├── image
    │   └─── Image, referential, mask, resampling, preprocessing
    │        * (list of) Niftii image(s).
    |        * array data structure (n_subjects, n_channels, image_axis0, image_axis1, ...)
    ├── mesh
    │   └── Related to meshes (giftii)
    │        
    └── spmsegment
        └── Related to spm sgementation

Data organisation

Environement Creation for the first time

pixi init
pixi add pandas scikit-learn seaborn openpyxl ipykernel  nilearn fsleyes  shap
pixi shell

Cloning this environement

pixi install

Provides

• niml: library with basics utils functions
• scripts_tables: machine learning scripts using tables (csv/xlsx files)