Implementation of antsRegistration_affine_SyN.sh for registration by gdevenyi · Pull Request #282 · nf-neuro/modules

gdevenyi · 2026-01-08T16:08:16Z

Describe your changes

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

List test packages used by your module

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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

AlexVCaron · 2026-01-13T21:45:15Z

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 · 2026-01-22T15:27:33Z

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

AlexVCaron · 2026-01-22T16:00:17Z

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 · 2026-01-22T16:23:52Z

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

AlexVCaron · 2026-01-23T23:50:24Z

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

AlexVCaron · 2026-01-26T17:08:15Z

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

arnaudbore · 2026-06-01T15:45:39Z

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

gdevenyi · 2026-06-01T16:56:16Z

@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.

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 · 2026-06-06T02:13:00Z

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

arnaudbore · 2026-06-06T04:03:45Z

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

Merged and scilus/scilus:dev is updated

gdevenyi · 2026-06-08T16:04:46Z

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

gagnonanthony · 2026-06-08T17:47:53Z

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 · 2026-06-09T14:51:14Z

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

Sure.

…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 · 2026-06-11T17:04:36Z

The masking implementation here depends on #369, if that's changed this should be as well

Copilot

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Adds a new registration/cobralab_ants Nextflow module to nf-neuro, including module metadata and an nf-test suite covering default, “quick”, “no warp”, and stub modes.

Changes:

Introduces the REGISTRATION_COBRALABANTS process implementation and module metadata.
Adds nf-test coverage and snapshots for multiple registration configurations.
Adds test tagging and per-test Nextflow config overrides.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
modules/nf-neuro/registration/cobralab_ants/main.nf	Adds the `REGISTRATION_COBRALABANTS` process implementation, including optional QC generation and stub behavior.
modules/nf-neuro/registration/cobralab_ants/meta.yml	Documents module inputs/outputs/tools and parameters used by the process.
modules/nf-neuro/registration/cobralab_ants/environment.yml	Adds module conda environment placeholder for linting/metadata consistency.
modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test	Adds `nf-test` cases for default, quick, no-warp, and stub runs.
modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test.snap	Adds snapshots asserting expected emitted outputs/hashes for each test.
modules/nf-neuro/registration/cobralab_ants/tests/nextflow.config	Test config enabling reproducibility + single-thread mode.
modules/nf-neuro/registration/cobralab_ants/tests/nextflow_quick.config	Test config enabling fast mode + QC + single-thread mode.
modules/nf-neuro/registration/cobralab_ants/tests/nextflow_no_warp.config	Test config enabling fast + linear-only (no nonlinear warp) + single-thread mode.
modules/nf-neuro/registration/cobralab_ants/tests/tags.yml	Adds tags mapping to allow selective test execution by module path.

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gdevenyi · 2026-07-14T17:48:47Z

+        for image in fixed_image warped; do
+            mrconvert *\${image}.nii.gz *\${image}_viz.nii.gz -stride -1,2,3
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_coronal.png \
+                --slices \$coronal_dim --axis coronal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_sagittal.png \
+                --slices \$sagittal_dim --axis sagittal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_axial.png \
+                --slices \$axial_dim --axis axial \$viz_params


Addressed in 587282e — the QC viz calls now use a concrete output filename instead of a glob on both input and output positions.

gdevenyi · 2026-07-14T17:48:47Z

+    input:
+        tuple val(meta), path(fixed_image), path(moving_image), path(fixed_mask), path(moving_mask) //** optional, input = [] **//


Invalid for this codebase — the //** optional, input = [] **// convention is how nf-neuro modules pass optional tuple file inputs (the test harness emits [], []). The declaration is identical to the canonical registration/ants module, which CI validates; meta.yml's mandatory: false remains the source of truth.

gdevenyi · 2026-07-14T17:48:47Z

+    moving_id=\$(basename $moving_image .nii.gz)
+    moving_id=\${moving_id#${meta.id}_*}


Addressed in 587282e — the .nii.gz assumption was resolved by adopting the extension-agnostic basename parsing from the registration/ants reference module, so both .nii and .nii.gz inputs are handled.

gdevenyi · 2026-07-14T17:48:47Z

+
+    ### ** QC ** ###
+    if $run_qc; then
+        mv $fixed_image fixed_image.nii.gz


Addressed in 587282e (see reply above) — extension-agnostic basename parsing now handles both .nii and .nii.gz.

gdevenyi · 2026-07-14T17:48:47Z

+        fixed_id=\$(basename $fixed_image .nii.gz)
+        fixed_id=\${fixed_id#${meta.id}_*}


Addressed in 587282e (see reply above) — extension-agnostic basename parsing now handles both .nii and .nii.gz.

gdevenyi · 2026-07-14T17:48:47Z

+process {
+    withName: "REGISTRATION_COBRALABANTS" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.reproducibility = true
+        ext.single_thread = true


Invalid — this publishDir expression is the established convention across every registration module test config in the repo (ants, anattodwi, convert, easyreg, synthmorph). Each config is scoped to a single process via withName, so there is no collision in practice.

gdevenyi · 2026-07-14T17:48:47Z

+          type: list
+          description: |
+            Tuple, Transformation files to warp images in fixed space, in the correct order
+            for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_warp, forward_affine ] ].


Invalid here — this wording is word-for-word identical to the canonical registration/ants module's forward_image_transform/backward_image_transform descriptions. A cobralab-only edit would diverge from the reference; this should be a separate repo-wide fix across ants/anattodwi/cobralab_ants.

gdevenyi · 2026-07-14T17:48:47Z

+          description: |
+            Tuple, transformation files to warp images in moving space, in the correct order
+            for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].


Invalid here — wording is identical to the canonical registration/ants module; should be a separate repo-wide fix rather than a cobralab-only change.

arnaudbore · 2026-06-23T03:36:35Z

@gdevenyi scilus/scilus:2.3.0 is ready 👍

gdevenyi · 2026-06-25T02:28:33Z

Cool. Still pending confirmation of the masking implementation in #369

Align cobralab_ants with the registration subworkflow masking rework (PR nf-neuro#369): gate fixed/moving mask forwarding behind masking_strategy (none/apriori/internal/both), add fixed_warped output (reference warped to moving space via antsApplyTransforms), and update tests accordingly.

Copilot

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

gdevenyi · 2026-07-14T17:48:12Z

+    moving_id=\$(basename $moving_image .nii.gz)
+    moving_id=\${moving_id#${meta.id}_*}


Addressed in 587282e — ID parsing is now extension-agnostic (handles both .nii and .nii.gz) and strips by ${prefix} instead of ${meta.id}, matching the registration/ants reference module.

gdevenyi · 2026-07-14T17:48:47Z

+        fixed_id=\$(basename $fixed_image .nii.gz)
+        fixed_id=\${fixed_id#${meta.id}_*}


Addressed in 587282e — fixed_id is now parsed extension-agnostically and stripped by ${prefix}, consistent with the moving_id parsing and the registration/ants reference module.

gdevenyi · 2026-07-14T17:48:47Z

+            mrconvert *\${image}.nii.gz *\${image}_viz.nii.gz -stride -1,2,3
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_coronal.png \
+                --slices \$coronal_dim --axis coronal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_sagittal.png \
+                --slices \$sagittal_dim --axis sagittal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_axial.png \
+                --slices \$axial_dim --axis axial \$viz_params


Addressed in 587282e — the QC mrconvert/scil_viz_volume_screenshot calls now use a concrete output filename (${image}_viz.nii.gz) instead of a glob, matching the registration/ants reference module.

…ames Address Copilot review: parse moving/fixed IDs extension-agnostically (.nii and .nii.gz) and strip by ${prefix} instead of ${meta.id}; use a concrete viz output filename instead of a glob. Matches the registration/ants reference module.

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

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

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

gdevenyi force-pushed the antsRegistration_affine_SyN branch 2 times, most recently from 0932c5d to a7e2ecb Compare February 5, 2026 04:43

gdevenyi force-pushed the antsRegistration_affine_SyN branch 2 times, most recently from 4db49ca to b09a2af Compare May 29, 2026 19:26

gdevenyi force-pushed the antsRegistration_affine_SyN branch from b09a2af to e9318a2 Compare June 2, 2026 16:04

Implementation of antsRegistration_affine_SyN.sh for registration

191152d

gdevenyi force-pushed the antsRegistration_affine_SyN branch from e9318a2 to 191152d Compare June 4, 2026 15:23

gdevenyi force-pushed the antsRegistration_affine_SyN branch 2 times, most recently from 3ec0077 to cb0a599 Compare June 11, 2026 17:03

gdevenyi marked this pull request as ready for review June 11, 2026 17:04

gdevenyi requested a review from a team June 11, 2026 17:04

Copilot AI review requested due to automatic review settings June 11, 2026 17:04

pull-request-management Bot requested review from AlexVCaron and Manonedde June 11, 2026 17:04

Copilot AI reviewed Jun 11, 2026

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gdevenyi changed the title ~~Initial implementation of antsRegistration_affine_SyN.sh~~ Implementation of antsRegistration_affine_SyN.sh for registration Jun 11, 2026

gdevenyi mentioned this pull request Jun 18, 2026

News Story: DNP is a good open-source citizen DouglasNeuroInformatics/Website#50

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Update cobralab_ants to container with reproducibility version

235e030

gdevenyi force-pushed the antsRegistration_affine_SyN branch from cb0a599 to 235e030 Compare June 25, 2026 15:24

gdevenyi marked this pull request as draft June 25, 2026 15:24

gdevenyi mentioned this pull request Jul 13, 2026

[ENH] Fix registration + use mask apply in tractoflow #369

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gdevenyi requested a review from Copilot July 14, 2026 17:11

Copilot started reviewing on behalf of gdevenyi July 14, 2026 17:11 View session

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		input:
		tuple val(meta), path(fixed_image), path(moving_image), path(fixed_mask), path(moving_mask) // optional, input = [] //

		moving_id=\$(basename $moving_image .nii.gz)
		moving_id=\${moving_id#${meta.id}_*}

		fixed_id=\$(basename $fixed_image .nii.gz)
		fixed_id=\${fixed_id#${meta.id}_*}

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