nf-pediatric: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unreleased]

`Added`

New testing file for anatomical preprocessing and surface reconstruction of infant data.
New module for formatting of Desikan-Killiany atlas (for infant).
Output of tissue-specific fodf maps in BIDS output.
Anatomical preprocessing pipeline for infant data using M-CRIB-S and Infant FS.
Coregistration of T2w and T1w if both available for the infant profile.
New docker image for infant anatomical segmentation and surface reconstruction (M-CRIB-S and Infant FS)
Required --dti_shells and --fodf_shells parameters.

`Fixed`

Structural segmentation pipeline for infant data. (#3)
Correctly set fastsurfer version in docker container.

`Changed`

Bump nf-core version to 3.1.2.
Refactored -profile freesurfer to -profile segmentation.
Config files have been moved from the modules.config into themed config files for easier maintainability.
Fastsurfer and freesurfer outputs are now in their own dedicated output folder.

`Removed`

Custom atlas name parameter until the use of custom atlas is enabled.
White matter mask and labels files as required inputs since they can now be computed for all ages.

[Unreleased] - [2024-12-23]

`Added`

Update minimal nextflow version to 24.10.0.
Add subject and global-level QC using the MultiQC module.
If -profile freesurfer is used, do not run T1 preprocessing.
Optional DWI preprocessing using parameters.
New docker containers for fastsurfer, atlases, and QC.
Transform computation in segmentation/fastsurfer.

[Unreleased] - [2024-11-21]

`Added`

Complete test suites for the pipeline using stub-runs.
Complete port of Infant-DWI modules and workflows into the nf-core template.