Finalize BIDS Atlas compliance

[tsalo]

Closes #1540.

Changes proposed in this pull request

• Move built-in atlases (Glasser, Gordon, Tian, Myers-Labonte, MIDB) into base Docker image.
• Modify collect_atlases to support fully-BIDS-compliant atlases.

Documentation that should be reviewed

[codecov]

Codecov Report

❌ Patch coverage is 83.82353% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 82.87%. Comparing base (72555de) to head (c954c5a).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
xcp_d/interfaces/bids.py	80.39%	4 Missing and 6 partials ⚠️
xcp_d/utils/atlas.py	80.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1584      +/-   ##
==========================================
- Coverage   82.91%   82.87%   -0.05%     
==========================================
  Files          58       58              
  Lines        7886     7924      +38     
  Branches     1124     1130       +6     
==========================================
+ Hits         6539     6567      +28     
- Misses       1011     1015       +4     
- Partials      336      342       +6     

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[Copilot]

Pull request overview

This pull request implements BIDS Atlas v1.11.0 compliance for XCP-D, addressing issue #1540. The changes reorganize atlas file structure and naming conventions to align with the recently finalized BIDS Atlas specification.

Changes:

• Moved built-in atlases (Glasser, Gordon, Tian, Myers-Labonte, MIDB, HCP) from package data to base Docker image (version 0.0.24)
• Updated BIDS entity names: segmentation → atlas, space → template (tpl)
• Changed atlas TSV column name from label → name per BIDS v1.11.0
• Reorganized output structure: atlases/ → derivatives/atlases/tpl-<label>/
• Updated DatasetType from atlas → derivative in dataset_description.json
• Added new CopyAtlasDescription interface to copy atlas description files

Reviewed changes

Copilot reviewed 45 out of 55 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
xcp_d/interfaces/bids.py	Added CopyAtlasDescription interface; updated CopyAtlas to use tpl/atlas entities
xcp_d/workflows/parcellation.py	Added atlas_dataset_paths tracking; updated output directory to derivatives/atlases
xcp_d/workflows/bold/outputs.py	Changed entity from 'segmentation' to 'atlas' in DerivativesDataSink calls
xcp_d/workflows/anatomical/parcellation.py	Changed entity from 'segmentation' to 'atlas'
xcp_d/interfaces/connectivity.py	Updated to use 'name' column instead of 'label' from atlas TSV files
xcp_d/utils/atlas.py	Changed filter from 'space' to 'template'; updated TSV column validation
xcp_d/utils/bids.py	Changed DatasetType from 'atlas' to 'derivative'
xcp_d/data/_bids_config.json	Updated entity patterns and path patterns for new naming scheme
xcp_d/cli/*	Updated atlas output path to derivatives/atlases
xcp_d/tests/*	Updated test paths to new naming convention
docs/*.rst	Updated documentation to reflect BIDS v1.11.0 structure
Dockerfile	Bumped base image to 0.0.24 with built-in atlases
xcp_d/data/atlases/*	Removed all built-in atlas files (moved to Docker image)

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