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Initial implementation of antsRegistration_affine_SyN.sh#282

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gdevenyi:antsRegistration_affine_SyN
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Initial implementation of antsRegistration_affine_SyN.sh#282
gdevenyi wants to merge 3 commits into
nf-neuro:mainfrom
gdevenyi:antsRegistration_affine_SyN

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@gdevenyi

@gdevenyi gdevenyi commented Jan 8, 2026 •
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Describe your changes

Implement the CoBrALab variant of antsRegistrationSyN.sh with optimized pyramids.

List test packages used by your module

Checklist before requesting a review

  • Create the tool:
    • Edit ./modules/nf-neuro/<category>/<tool>/main.nf
    • Edit ./modules/nf-neuro/<category>/<tool>/meta.yml
    • Edit ./modules/nf-neuro/<category>/<tool>/environment.yml
  • Generate the tests:
    • Edit ./modules/nf-neuro/<category>/<tool>/tests/main.nf.test
    • Run the tests to generate the main.nf.test.snap snapshots
  • Ensure the syntax is correct :
    • Run prettier and editorconfig-checker to fix common syntax issues
    • Run nf-core modules lint and fix all errors
    • Ensure your variables have good, clear names

@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch from 390c9c1 to a90da89 Compare January 8, 2026 16:19
@AlexVCaron

AlexVCaron commented Jan 13, 2026

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Minimal work is required so the module fits with the nf-core framework. Modules names can only be composed of capital alphanumerical characters and must follow the category/module filenaming convention. So here, it would be (with category) REGISTRATION/COBRALABANTS, using the current file hierarchy.

Once done, most linting and testing should work out the box. But nf-test expects some naming/formatting, that sadly isn't targetted when nf-core conventions are not abided to.

@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch 2 times, most recently from 2878c25 to ae312c2 Compare January 15, 2026 18:45
@gdevenyi

gdevenyi commented Jan 22, 2026

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@AlexVCaron I can't sort out how to run the test properly inside the devcontainer, what's the appropriate command?

@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch from ae312c2 to b91bb4a Compare January 22, 2026 15:52
@AlexVCaron

AlexVCaron commented Jan 22, 2026 •
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I run the test suite for any component from the root of the repo via : nf-test test <path-to-component-base-directory> --update-snapshot --clean-snapshot

In this case, the path is modules/nf-neuro/registration/cobralab_ants

For the lint, it is done via the nf-core command, from the root of the repo again, but without the full path, just the component name : nf-core modules lint registration/cobralab_ants

Tell me of any problems, I can pull your PR and help debug !

@gdevenyi

gdevenyi commented Jan 22, 2026

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Right. OK. It seems like the devcontainer doesn't have the antsRegistration_affine_SyN.sh that I got merged into the main repo...

@AlexVCaron

AlexVCaron commented Jan 23, 2026

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I'll get into that this w-e. It should've been included in the build, I'll investigate

@AlexVCaron

AlexVCaron commented Jan 26, 2026

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As stated on scilus/containers-scilus#42, scilus/scilus:dev is the container including the dependency for now.

@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch 2 times, most recently from 0932c5d to a7e2ecb Compare February 5, 2026 04:43
@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch 2 times, most recently from 4db49ca to b09a2af Compare May 29, 2026 19:26
@arnaudbore

arnaudbore commented Jun 1, 2026

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@gdevenyi container is updated, we still have some issues with our servers I'll let you know asap when ready.

@gdevenyi

gdevenyi commented Jun 1, 2026

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@gdevenyi container is updated, we still have some issues with our servers I'll let you know asap when ready.

No problem my local testbed works.

@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch from b09a2af to e9318a2 Compare June 2, 2026 16:04
@gdevenyi gdevenyi force-pushed the antsRegistration_affine_SyN branch from e9318a2 to 191152d Compare June 4, 2026 15:23
gdevenyi added 2 commits June 4, 2026 11:24
@gdevenyi
Add moving mask support to cobralab_ants registration
568e62e 
Split single mask input into separate fixed_mask and moving_mask inputs,
matching the pattern from PR nf-neuro#367 for the ants registration module.
antsRegistration_affine_SyN.sh supports --fixed-mask and --moving-mask
as independent flags.
@gdevenyi
feat(cobralab_ants): add reproducibility mode, RNG seed, and single_t…
2fad756 
…hread support

- Forward --reproducibility and --random-seed CLI flags to
  antsRegistration_affine_SyN.sh (CoBrALab PR nf-neuro#7)
- Export ANTS_RANDOM_SEED env var (default 1234) for ancillary ANTs tools
- Replace hardcoded thread counts with task.ext.single_thread-aware
  expressions for ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS and OMP_NUM_THREADS
- Remove OPENBLAS_NUM_THREADS (set globally in test config)
- Add reproducibility, ants_rng_seed, single_thread args to meta.yml

Mirrors the pattern already applied to registration/ants (nf-neuro PR nf-neuro#342).
@gdevenyi

gdevenyi commented Jun 6, 2026

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Depends on scilus/containers-scilus#45, also need to update the container reference once its released

@arnaudbore

arnaudbore commented Jun 6, 2026

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Depends on scilus/containers-scilus#45, also need to update the container reference once its released

Merged and scilus/scilus:dev is updated

@gdevenyi

gdevenyi commented Jun 8, 2026

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This all works, I guess the only thing now is this should be pinned to an official scilus container version instead of dev

@gagnonanthony

gagnonanthony commented Jun 8, 2026

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I'm not sure there will be a release with a new version soon, right @arnaudbore ? In the meantime, you could pin it to the image SHA.

@gdevenyi

gdevenyi commented Jun 9, 2026

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In the meantime, you could pin it to the image SHA.

Sure.

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4 participants

@gdevenyi @AlexVCaron @arnaudbore @gagnonanthony