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[ENH] make SLF subdivisions default#140

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arokem merged 5 commits into
tractometry:mainfrom
36000:slf_subs
Jan 12, 2026
Merged

[ENH] make SLF subdivisions default#140
arokem merged 5 commits into
tractometry:mainfrom
36000:slf_subs

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@36000

@36000 36000 commented Jan 8, 2026

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Copilot AI review requested due to automatic review settings January 8, 2026 20:25

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Pull request overview

This PR makes SLF (Superior Longitudinal Fasciculus) subdivisions the default bundle configuration by removing the unified "Left/Right Superior Longitudinal" bundles from default_bd() and replacing them with three left-hemisphere SLF subdivisions (L_SLF1, L_SLF2, L_SLF3) in a new slf_bd() function. The change also adds new SLF template files and updates tests and examples to use "Inferior Longitudinal" bundles instead of the removed "Superior Longitudinal" bundles.

Key changes:

  • Removed unified "Left/Right Superior Longitudinal" bundles from default_bd()
  • Added slf_bd() function defining SLF subdivisions (currently left hemisphere only)
  • Added SLF template fetching infrastructure with 10 new template files
  • Updated default bundle configuration to include slf_bd() bundles
  • Updated tests and examples to use ILF bundles instead of removed SLF bundles

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file
File Description
AFQ/api/bundle_dict.py Removed unified SLF bundles from default_bd() and added new slf_bd() function for SLF subdivisions
AFQ/tasks/data.py Modified default bundle configuration to include slf_bd() bundles
AFQ/data/fetch.py Added SLF template fetching infrastructure with file lists, remote IDs, and MD5 hashes
AFQ/tests/test_api.py Updated test bundle selections from Superior Longitudinal to Inferior Longitudinal bundles
examples/tutorial_examples/plot_006_bids_layout.py Updated example bundle selections from Superior Longitudinal to Inferior Longitudinal bundles

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Comment thread AFQ/api/bundle_dict.py Outdated
Comment thread AFQ/api/bundle_dict.py
Comment thread AFQ/api/bundle_dict.py Outdated
@36000

36000 commented Jan 10, 2026

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@arokem this is ready for review/merge

@36000 36000 added this to the pyAFQ 3.0 milestone Jan 10, 2026

@arokem arokem left a comment

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Looks good! My only thought is that we might want to add something to the pyAFQ 2.0 example that shows how you would find just one SLF, which means retaining the option of using the old definition of the one whole bundle. WDYT?

Comment thread AFQ/api/bundle_dict.py Outdated
@arokem
arokem merged commit ce7fdf5 into tractometry:main Jan 12, 2026
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3 participants