Fix anat-to-tpl xfm grabbed by kaitj · Pull Request #293 · childmindresearch/rbc

kaitj · 2026-04-09T18:58:01Z

Fixes #288

Summary

resolve_functional queried the inverse warp (from-MNI152NLin6Asym_to-T1w) for anat_to_template, but resample_bold_to_template expects the forward warp (from-T1w_to-MNI152NLin6Asym) since ANTs applies transforms in reverse list order
Same bug in orchestration/all.py where anat_outputs.inverse_xfm was passed as anat_to_template for the in-memory (non-resolved) code path
Renamed forward_xfm/inverse_xfm to direction-explicit names (anat_to_template_xfm, template_to_anat_xfm, etc.) across all NamedTuples, exports, and tests
Fixed incorrect BIDS labels in longitudinal exports (previously labeled as T1w<->longitudinal, actually longitudinal<->MNI152NLin6Asym)
Fixed test mock attribute names that silently diverged from the real NamedTuple fields (Mock() auto-creates any attribute)
Fixed stat overlay misalignment in CI report: _render_stat_overlay was computing slice indices independently for background and overlay, causing different axial slices to be selected (z-scored maps have a different non-zero extent than the template BOLD)

Test plan

Unit tests pass (729 passed)
Run resample_bold_to_template on real data with both forward and inverse warps to confirm the forward warp produces correct results
Verify CI report shows correctly aligned fALFF/ReHo overlays

github-actions · 2026-04-09T18:58:44Z

Coverage Report

File	Stmts	Miss	Cover	Missing
rbc
__init__.py	1	0	100%
context.py	25	8	68%	70, 75–77, 79–80, 93–94
metadata.py	56	0	100%
rbc/bids
__init__.py	9	0	100%
_schema.py	585	4	99%	776, 782, 790, 1101
anatomical.py	24	3	87%	44, 47–48
builder.py	72	7	90%	233–235, 362, 364–365, 386
functional.py	42	5	88%	46–49, 84
longitudinal.py	25	0	100%
metrics.py	23	1	95%	44
qc.py	17	0	100%
query.py	67	42	37%	103–107, 121–125, 127–128, 130–135, 137, 139, 153, 159–165, 198, 207, 209–216, 225, 257, 266–267
session.py	47	0	100%
rbc/cli
__init__.py	1	0	100%
all.py	49	2	95%	84, 109
anatomical.py	25	2	92%	47, 63
base.py	71	9	87%	56, 62, 123–125, 131–133, 156
functional.py	33	2	93%	67, 87
longitudinal.py	27	2	92%	46, 63
main.py	42	0	100%
metrics.py	42	2	95%	77, 95
qc.py	25	2	92%	45, 61
rbc/core
__init__.py	3	0	100%
common.py	26	12	53%	43–45, 62–70
fileops.py	27	4	85%	69–72
fsl2itk.py	42	0	100%
nifti.py	192	5	97%	236–237, 244–245, 524
niwrap.py	56	1	98%	58
rbc/core/anatomical
__init__.py	4	0	100%
registration.py	15	4	73%	59, 151, 166, 183
segmentation.py	24	8	66%	64, 74–76, 92, 114, 125, 141
rbc/core/functional
__init__.py	13	0	100%
coregistration.py	7	2	71%	44, 55
despiking.py	7	3	57%	32, 36–37
distortion.py	130	40	69%	269–271, 321, 324, 332–335, 341–346, 349, 352–353, 356, 365–369, 375–376, 387–388, 391, 397, 443–444, 447, 455, 461, 470–471, 474, 484, 491
erosion.py	32	1	96%	50
initialization.py	9	4	55%	35, 42–43, 63
masking.py	34	25	26%	53, 55–56, 58–59, 62–65, 69, 91, 134, 183, 197, 208, 223, 233, 249, 258, 271, 285, 296, 306, 319, 328
motion.py	57	37	35%	62, 64–67, 69, 71, 73, 76–77, 83–84, 86–87, 95–97, 99, 102, 105, 107, 124–125, 135–138, 159, 169, 171–172, 175, 177–179, 181, 183
nuisance.py	81	60	25%	78, 80–85, 87, 89–90, 93, 96–98, 100–102, 104–110, 112–116, 118, 163, 165, 167, 170–171, 173–175, 178, 181–182, 185–187, 190–193, 197, 203–205, 207, 235, 243, 269, 278, 307, 316, 322
regressors.py	89	6	93%	163, 193, 325–328
resampling.py	54	43	20%	37–42, 74–76, 78, 80–81, 85–87, 90, 93, 105, 107–108, 112, 114, 150–152, 154–155, 159, 161–162, 167–169, 173–174, 177, 180, 187, 199, 201–202, 207, 209
timing.py	16	11	31%	46–47, 49–53, 58, 60, 66–67
rbc/core/longitudinal
__init__.py	1	0	100%
transform.py	46	7	84%	106–107, 165–168, 170
rbc/core/metrics
__init__.py	3	0	100%
alff.py	90	1	98%	265
reho.py	66	0	100%
smoothing.py	7	3	57%	36, 42–43
standardization.py	27	11	59%	64, 66–68, 70, 72–75, 77–78
timeseries.py	57	1	98%	120
rbc/core/qc
__init__.py	6	0	100%
dvars.py	26	0	100%
motion.py	31	0	100%
registration.py	41	0	100%
xcp.py	41	0	100%
rbc/orchestration
__init__.py	32	2	93%	90, 93
all.py	41	9	78%	131–132, 137, 145, 153–154, 171, 173–174
anatomical.py	37	22	40%	49–52, 57–58, 60–63, 85–87, 89–90, 94, 101, 104, 109–110, 116, 118
functional.py	41	12	70%	124–126, 128–129, 133, 139, 142, 147–148, 157, 159
longitudinal.py	56	1	98%	150
metrics.py	46	30	34%	32–35, 38–40, 67, 75–76, 100–102, 104–106, 110, 118–121, 123–124, 130–132, 137, 145, 152, 154
qc.py	34	0	100%
rbc/workflows
__init__.py	10	0	100%
anatomical.py	47	19	59%	90–93, 97–102, 107, 177–180, 182–184, 188
functional.py	98	56	42%	113–114, 122, 127–128, 136, 207–208, 211–212, 215–216, 219, 222–225, 235–237, 247–248, 251, 254, 257–258, 266–267, 274–275, 282–283, 290–291, 294–296, 299–302, 314–315, 327, 329–332, 335–336, 345–346, 354, 361, 430, 436
metrics.py	39	17	56%	80–81, 86–87, 90–93, 96–99, 103–106, 108
qc.py	53	33	37%	87, 89–90, 93, 96, 99–104, 107, 116–118, 122–125, 127–131, 133–134, 136–138, 141, 158, 165, 167
rbc_resources
__init__.py	38	0	100%
TOTAL	3240	581	82%

Tests	Skipped	Failures	Errors	Time
730	0 💤	0 ❌	0 🔥	10.496s ⏱️

The self-hosted runner's network blocks raw.githubusercontent.com, causing setup-uv to fail when fetching the version manifest. Pinning the version skips the network lookup entirely.

The mocks used `long_to_anat_xfm`/`anat_to_long_xfm` but the actual NamedTuple fields are `long_to_template_xfm`/`template_to_long_xfm`. Mock() silently creates any attribute, so this mismatch was invisible.

_render_stat_overlay was calling _build_mosaic independently for the background and stat map. Since _axial_slices picks slices based on non-zero extent, the z-scored maps (which have zeros outside the mask and negative values) computed different slice indices than the template BOLD underlay, causing visible misalignment in the overlay. Now computes slice indices once from the background volume and reuses them for the stat map.

Fix anat-to-tpl xfm grabbed

de328e5

kaitj and others added 4 commits April 9, 2026 15:17

Rename xfm attrs to be more clear

d148fde

Fix integration assertion

ca5f1a6

Pin uv version in full test workflow to avoid manifest fetch

7aaca11

The self-hosted runner's network blocks raw.githubusercontent.com, causing setup-uv to fail when fetching the version manifest. Pinning the version skips the network lookup entirely.

Fix mock attribute names to match AnatomicalLongOutputs fields

3e9949b

The mocks used `long_to_anat_xfm`/`anat_to_long_xfm` but the actual NamedTuple fields are `long_to_template_xfm`/`template_to_long_xfm`. Mock() silently creates any attribute, so this mismatch was invisible.

nx10 marked this pull request as ready for review April 9, 2026 23:13

nx10 merged commit 9ea91af into main Apr 10, 2026
8 checks passed

nx10 deleted the maint/ants-transforms branch April 10, 2026 07:02

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Fix anat-to-tpl xfm grabbed#293

Fix anat-to-tpl xfm grabbed#293
nx10 merged 6 commits into
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maint/ants-transforms

kaitj commented Apr 9, 2026 •

edited by nx10

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kaitj commented Apr 9, 2026 •

edited by nx10

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