sdc: SyN-SDC pipeline package (packages/sdc) for the browser and Node #464

Context

Chain preprocessing, restricted SyN registration and the field-map fit in one package that the app and the command line both import.

• Q51 (fixed): the outputs keep the b0 volumes.
• Q52 (fixed): the default mask is MindGrab (model mindgrab) of the mean b0. The user can upload a mask instead.

Size: L (one large PR, or split it in the PR plan).

Decisions (20 October 2026): this issue follows the sdc plan (PR #499, section 9).

Scope

• packages/sdc: EPI reference from the b0 volumes, MindGrab masks (or an uploaded mask), anat clip and DenoiseImage, epi2anat affine, Laplacians, the prior warp through the T1w-to-MNI affine of Q59 (with a "no prior" option), restricted SyN, field-map fit (sdc: Rust crate for displacement-to-field-map conversion and B-spline approximation #463), one resampling of the DWI series.
• Read the PE direction and TotalReadoutTime from the sidecar or the sidebar. Else compute TotalReadoutTime from EffectiveEchoSpacing, as get_trt does. Do not use EstimatedTotalReadoutTime or sdcflows' fallback. Refuse without both (Q62). Never guess the polarity.
• Add the sdc/prior/ files to models/sdc.manifest.json (Q60).
• Outputs (plan section 5): *_desc-sdc_dwi.nii.gz (b0 volumes kept, Jacobian factor), bval and bvec passed through, *_desc-preproc_fieldmap.nii.gz in Hz, *_desc-coeff_fieldmap.nii.gz, *_from-orig_to-sdc_mode-image_xfm.nii.gz, *_desc-brain_mask.nii.gz, JSON sidecars.
• Inject runtimes (browser workers or Node drivers), as packages/brain2print does.

Acceptance criteria

• A Node test runs the full pipeline on the full-brain ds005134 sub-01 on the 2 mm grid (Q67, Q68) and meets the gate of Q66 against sdc/reference/: d ≤ max(spread, 0.05 Hz) and d < 0.5 Hz. It runs in a native workflow job (pull requests that change the SDC code, nightly, manual) with a require variable.
• A Node test runs the pipeline on the slab with the full T1w (Q64) and reports its difference from the native slab runs (report only).
• Refusal tests: a missing PE direction, a missing TotalReadoutTime and a missing T1w give clear errors.
• The output names and sidecars follow BIDS derivatives. A test loads the outputs with the input path of n4 and of noddi (NIfTI + bval + bvec), and both accept them.
• Cancellation through an AbortSignal stops the workers.
• A changeset describes the change (pnpm changeset).

References

• brain2print package
• Design
• Repository rules (AGENTS.md)

Dependencies

• sdc: ANTs WebAssembly entry points for SyN-SDC (restricted SyN, Laplacian, DenoiseImage, BSpline apply) #462: sdc: ANTs WebAssembly entry points for SyN-SDC (restricted SyN, Laplacian, DenoiseImage, BSpline apply)
• sdc: Rust crate for displacement-to-field-map conversion and B-spline approximation #463: sdc: Rust crate for displacement-to-field-map conversion and B-spline approximation
• shared: BIDS folder reader for diffusion inputs (dwi, fmap IntendedFor, anat T1w) #410: shared: BIDS folder reader for diffusion inputs (dwi, fmap IntendedFor, anat T1w)
• shared: one module for BIDS-derivative names and sidecars of the DWI apps #413: shared: one module for BIDS-derivative names and sidecars of the DWI apps