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fedorov merged 2 commits into from
Nov 13, 2026
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Update description of highdicom match_geometry parameter #196

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Update description of deprecated tol parameter in highdicom's match_g…
CPBridge Nov 13, 2026
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style: pre-commit fixes
pre-commit-ci[bot] Nov 13, 2026
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12 changes: 6 additions & 6 deletions scripts/hf/card_template.md
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Expand Up @@ -109,10 +109,10 @@ spacing and gantry tilt are all common.

[highdicom](https://highdicom.readthedocs.io/) handles this, and returns a
`Volume` that keeps voxel spacing and the patient-space affine next to the
array. The examples below were tested with highdicom 0.28.2.
array. The examples below were tested with highdicom 0.29.0.

```bash
pip install "highdicom>=0.28.2" duckdb idc-index torch
pip install "highdicom>=0.29.0" duckdb idc-index torch
```

Start in the catalog. `volume_geometry_index` flags every CT, MR and PET series
Expand Down Expand Up @@ -232,11 +232,11 @@ A segmentation often covers fewer slices than its image, is rotated relative to
the source image, or stores the slices in the opposite order; `match_geometry`
pads, flips and rotates it (as required) onto the image grid. It raises
`RuntimeError` when the two grids are offset by a fraction of a voxel, and
rounding in stored positions alone can cause that: some `nsclc_radiomics`
segmentations sit 2e-5 voxels off their CT, just beyond the default tolerance,
and `match_geometry(ct, tol=1e-4)` accepts them. Loosen `tol` no further than
rounding in stored positions alone can occasionally cause that. In such cases,
`match_geometry(ct, position_tol=tol)` can be used to loosen the tolerance to
accept them, where by default `tol=1e-2`. Loosen `position_tol` no further than
you need: a large tolerance can hide a segmentation that is genuinely misaligned
with its image.
with its image and requires resampling.

`combine_segments=True` returns a label map, in which each voxel holds the
number of the segment it belongs to, or 0. NLSTSeg segments each lesion
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