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Outputs

HemiSpec outputs should be predictable enough for downstream statistics, machine learning, and manuscript reporting.

Standard workflow layout

hemispec workflow and the GUI write a compact user-facing layout. The default final outputs are four voxel maps per subject plus optional tables and validation reports:

<out-dir>/
  voxel_maps/
    <subject>_ANS.L.nii.gz
    <subject>_ANS.R.nii.gz
    <subject>_RNS.L.nii.gz
    <subject>_RNS.R.nii.gz
  tables/
    subject_metric_summary.csv
    roi_features_bilateral.csv          # when ROI export is enabled and an atlas is available
    roi_features_bilateral_wide.csv     # when ROI export is enabled and an atlas is available
  validation/
    hemi_classify/                      # only when --run-classifier is enabled
    trt/                                # only when --run-trt is enabled

DGN reconstructions and one-direction metrics are intermediate implementation details. They are removed by default because the stitched actual/reconstructed recon maps are redundant for most users. To debug or run standalone validation on the merged bilateral maps, use --keep-intermediate in CLI or the matching GUI checkbox:

<out-dir>/
  intermediate/
    recon/
      L_to_R/
      R_to_L/
    direction_metrics/
      L_to_R/
      R_to_L/
    combined_maps/
      <subject>_ANS.nii.gz
      <subject>_RNS.nii.gz

Lower-level commands keep their own historical contracts. For example, hemispec compute --save-subject-maps still writes subject_maps/<subject>_ANS.nii.gz and subject_maps/<subject>_RNS.nii.gz under its chosen output directory.

Required metadata roadmap

Each run should eventually record:

  • HemiSpec version.
  • Model bundle version.
  • Input paths or dataset identifiers.
  • Main parameters.
  • Output paths.
  • Warnings and validation failures.

This full manifest contract is planned; it should not be described as complete until implemented.