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dmri predict

Syntax

dmri predict FOLDER [options]
dmri predict --list-models [--repo-id REPOSITORY] [--revision REVISION]

FOLDER must contain data.nii.gz, nodif_brain_mask.nii.gz, bvals, and bvecs.

Checkpoint

  • --model NAME: model subfolder in the repository. Default: msb3s_2_4_6_128.
  • --repo-id OWNER/REPOSITORY: Hugging Face model repository. Default: manugloeck/dmri-pretrained.
  • --revision REVISION: Hub branch, tag, or commit.
  • --cache-dir PATH: Hugging Face cache location.
  • --local-files-only: do not contact the Hub.
  • --local-checkpoint PATH: local portable model bundle; bypasses the Hub.
  • --list-models: list repository model subfolders and exit.

Sampling

  • --quality {very-fast,fast,balanced,high}: named sampling settings. Default: balanced. Each name selects a conf/predict/quality/ group, so the numbers behind it are visible in the tree and recorded in the run's .hydra output.
  • --num-steps INTEGER: ODE steps per theta sample.
  • --mask-samples INTEGER: posterior mask samples.
  • --theta-samples INTEGER: posterior parameter samples.
  • --corrector {auto,none}: parameter correction policy.
  • --precision {fp32,bf16,fp16}: network-forward precision. CPU fp16 falls back to fp32.
  • --seed INTEGER: random seed. Default: 1.

Model selection

  • --model-mode {per-sample,best,fixed}: sampled model per theta draw, one selected model per voxel, or one fixed model.
  • --fixed-model {B1S,B2S,B3S}: fixed Ball3Stick-family model; implies fixed mode.

In per-sample mode, mask samples must be at least theta samples.

Hardware

  • --batch-size INTEGER: fixed voxels per batch; skips automatic sizing.
  • --memory-fraction FLOAT: fraction of device memory JAX may preallocate.

CPU prediction prints a warning because even a few thousand voxels can take a long time. Use a supported GPU accelerator when possible.

Output and interaction

  • --output-subdir NAME: directory inside FOLDER. Default: dmri_output.
  • --overwrite: replace an existing output directory.
  • --no-viewer: do not write view_results.html.
  • --non-interactive: do not prompt for missing choices.
  • --verbose: include detailed evaluation logs.

Interactive selection is used only when stdin and stdout are terminals. Use arrow keys or j/k, Enter, or number keys.

Checkpoint and configuration

  • --checkpoint-which {latest,best,STEP}: which checkpoint to load. Default: best. Use latest or a numeric step for bundles that provide those checkpoints.
  • --set KEY=VALUE: set any configuration key directly. Repeatable, and applied last so it overrides both --quality and the other flags.

--set is the escape hatch for anything without a dedicated flag:

dmri predict FOLDER --quality fast \
  --set evaluation.sampling.theta.params.t_max=60 \
  --set evaluation.export.theta.export_stds=true

Prediction composes conf/predict.yaml, which inherits the whole evaluation tree and layers the prediction presets on top. See Configuration.

See the prediction guide for workflow and output details.