Fix functional stage failing to find anat derivatives in all pipeline

[nx10]

Summary

• The all orchestrator loaded only raw input data (filtering desc is null) and passed the same session DataFrame to both anatomical and functional stages
• After anatomical processing exported derivatives (desc-brain T1w, masks, transforms) to disk, the functional stage's resolve_functional could not find them because the DataFrame was never refreshed with the new files
• This caused FileNotFoundError: Expected BIDS file not found: ... suffix='T1w', entities={'desc': 'brain'} at the start of functional processing
• Fix: pass anatomical outputs in-memory to the functional stage via the new anat_inputs parameter, consistent with how metrics and QC already receive in-memory outputs from earlier stages

Related

• Investigate anat_to_template transform direction in resolve_functional #288: Investigate anat_to_template transform direction in resolve_functional
• Add integration test for rbc all pipeline stage handoff #289: Add integration test for rbc all pipeline stage handoff

Test plan

• Unit tests: process_session with/without anat_inputs, all.run() field mapping
• Run rbc all on a dataset with both anat and func data (previously crashed at functional start)
• Run standalone rbc func (unchanged path, uses DataFrame resolve as before)
• Integration tests for full pipeline handoff (Add integration test for rbc all pipeline stage handoff #289)

[github-actions]

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 🔥	10.303s ⏱️

[kaitj]

lgtm 🚀

Was going to mention something about a test for "all" in the e2e since we do it for all the individual ones (except maybe longitudinal atm?), but saw you had the other PR open.