Compute specificity maps¶

This tutorial covers ANS/RNS computation after reconstruction.

Install¶

For normal use, install the released package from PyPI:

python -m pip install hemispec-toolkit

For source development, use python -m pip install -e . from a local checkout.

For a complete packaged smoke test, run hemispec quickstart --out-dir hemispec_quickstart; it generates toy paired inputs and runs this compute path.

Required paired inputs¶

Each subject needs an actual target gray-matter map and a reconstructed counterpart in the same shape, affine, and orientation.

Current command¶

hemispec compute \
  --actual-glob "derivatives/*_GM_masked.nii.gz" \
  --predicted-glob "outputs/recon/*_PRED_LR_full.nii.gz" \
  --out-dir outputs/specificity \
  --save-subject-maps

This writes group-level ANS/RNS maps and, with --save-subject-maps, subject-level maps for validation and ROI extraction.

ROI export¶

ROI feature export is available through compute options. The atlas path is a placeholder until the public HemiSpec atlas assets are added or an external atlas installation is documented:

hemispec compute \
  --actual-glob "derivatives/*_GM_masked.nii.gz" \
  --predicted-glob "outputs/recon/*_PRED_LR_full.nii.gz" \
  --out-dir outputs/specificity \
  --roi-atlas <atlas-path> \
  --roi-out-csv outputs/roi_features.csv

There is not yet a standalone roi command.

Outputs¶

Subject-level ANS maps.
Subject-level RNS maps.
Optional ROI-level feature tables.
Group-level voxelwise summaries when enabled.

Checks before computation¶

HemiSpec should validate shape, affine, finite values, hemisphere labels, and valid masks before writing outputs.