ilex-hub/syn_disco.bold.1

SynDisCo -- MASILab fieldmap-free EPI distortion correction (b0 + BOLD) -- SynBOLD-DisCo -- fMRI BOLD distortion correction (5-fold)

Description

SynDisCo is a JAX / Equinox port of MASILab's two distortion-correction nets -- Synb0-DisCo (dMRI b0) and SynBOLD-DisCo (fMRI BOLD) -- consolidated as a single multi-variant family class because the two upstream repos ship byte-identical model.py architectures and differ only by training corpus.

Each modality is a 5-fold ensemble of a 3D U-Net with 3 pooling stages, InstanceNorm3d + LeakyReLU(0.01) intra-block norm/activation, ConvTranspose3d throughout the decoder (not the more typical Conv+Upsample split), and bare 1x1 Conv3d/ConvTranspose3d at the bottleneck and head. Input is a 2-channel atlas-space (padded 80x96x80) volume stacking the distorted target (b0 or BOLD) with a co-registered T1w anatomical; output is a single-channel synthesised undistorted target ready to drive FSL TopUp for susceptibility distortion correction without reverse-PE acquisition or separate fieldmap.

v0 ships two bundles (one per modality), each holding the upstream's full 5-fold weights stacked on a leading fold axis. The forward applies eqx.filter_vmap across the folds and means the output -- byte-equivalent to the upstream pipeline's fslmaths -Tmean ensemble step.

Intended use

fMRI sibling of the b0 variant. Synthesise an undistorted BOLD from T1w + the distorted (mean) BOLD for TopUp recovery; same atlas-space input format and ensemble policy as the b0 variant. Use when an fMRI acquisition lacks a reverse-PE / fieldmap calibration scan but a T1w is available.

Usage

from ilex.models.syn_disco import SynDisCo
model = SynDisCo.from_pretrained('ilex-hub/syn_disco.bold.1')

Authors

Schilling K. G., Blaber J., Huo Y., Newton A., Hansen C., Nath V., Yao T., Newlin N. R., Cai L. Y., Yang Q., Landman B. A., et al. (MASILab, Vanderbilt University; Synb0-DisCo + SynBOLD-DisCo upstreams)

Citation

Schilling K. G., Blaber J., Huo Y., Newton A., Hansen C., Nath V., et al. (2020). Synthesized b0 for diffusion distortion correction (Synb0-DisCo). PLoS One 15(7), e0236418. doi:10.1371/journal.pone.0236418. Yao T., Newlin N. R., Cai L. Y., Yang Q., Williams O., Beason-Held L. L., Resnick S. M., Schilling K. G., Landman B. A. (2023). SynBOLD-DisCo -- Synthetic BOLD images for distortion correction of fMRI without additional calibration scans. Imaging Neuroscience 1, 1-13.

References

• Schilling K.G., Blaber J., Huo Y., Newton A., Hansen C., Nath V., Shafer A.T., Williams O., Resnick S.M., Rogers B., Anderson A.W., Landman B.A. (2020). Synthesized b0 for diffusion distortion correction (Synb0-DisCo). PLoS One 15(7):e0236418. doi:10.1371/journal.pone.0236418.
• Yao T., Newlin N.R., Cai L.Y., Yang Q., Williams O., Beason- Held L.L., Resnick S.M., Schilling K.G., Landman B.A. (2023). SynBOLD-DisCo -- Synthetic BOLD images for distortion correction of fMRI without additional calibration scans. Imaging Neuroscience 1, 1-13.
• Synb0-DisCo upstream code, weights, license - github.com/MASILab/Synb0-DISCO (MIT).
• SynBOLD-DisCo upstream code, weights, license - github.com/MASILab/SynBOLD-DisCo (MIT).

License

HF Hub license tag: mit

Effective terms: MIT (copyright (c) MASILab, Vanderbilt University) on both the upstream code and the pretrained weights of Synb0-DisCo (github.com/MASILab/Synb0-DISCO) and SynBOLD-DisCo (github.com/MASILab/SynBOLD-DisCo). The ilex JAX / Equinox port code is separately licensed under Apache-2.0 / GPL-3.0.

Upstream license reference: https://opensource.org/licenses/MIT

Copyright

Synb0-DisCo and SynBOLD-DisCo upstreams are copyright (c) MASILab, Vanderbilt University, MIT-licensed. The JAX / Equinox port code in this package is separately licensed under Apache-2.0 / GPL-3.0 per the wider ilex license boundary; the MIT terms on the upstream weights are preserved through the canonical bundle's _ilex.origin = 'pytorch' provenance.

Upstream source

Original weights / reference implementation: https://github.com/MASILab/Synb0-DISCO

Provenance

This artefact was produced by ilex's save/load pipeline. The architecture is implemented in ilex.models.syn_disco.SynDisCo and the weights have been converted from their upstream format. See the upstream source above for the canonical reference.