FIX: Re-add cohort identifier to template name (#416)

* FIX: Re-add cohort identifier to template name

* FIX: XFM io

* FIX: Query data with nipreps config

Also rename variables to play nice with pdb

* TST: Add test for derivatives ingestion

* PIN: niworkflows latest

* MAINT: Update ruff settings

* STY: ruff fixes

* TST: Ensure config is string

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib >= 2.2.0",
     "nibabel >= 4.0.1",
     "nipype >= 1.7.0",
-    "niworkflows >= 1.8.0",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy",
     "packaging",
     "pybids >= 0.11.1",
@@ -138,6 +138,8 @@ source = [
 
 [tool.ruff]
 line-length = 99
+
+[tool.ruff.lint]
 extend-select = [
   "F",
   "E",
@@ -162,10 +164,10 @@ extend-select = [
   "Q",
 ]
 
-[tool.ruff.flake8-quotes]
+[tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"
 
-[tool.ruff.extend-per-file-ignores]
+[tool.ruff.lint.extend-per-file-ignores]
 "*/test_*.py" = ["S101"]
 
 [tool.ruff.format]

smriprep/data/io_spec.json

@@ -50,8 +50,8 @@
       "forward": {
         "datatype": "anat",
         "extension": [
-          "h5",
-          "txt"
+          ".h5",
+          ".txt"
         ],
         "from": "T1w",
         "to": null,
@@ -61,8 +61,8 @@
       "reverse": {
         "datatype": "anat",
         "extension": [
-          "h5",
-          "txt"
+          ".h5",
+          ".txt"
         ],
         "from": null,
         "to": "T1w",

smriprep/utils/bids.py

@@ -25,6 +25,7 @@
 from pathlib import Path
 
 from bids.layout import BIDSLayout
+from niworkflows.data import load as nwf_load
 
 from ..data import load_resource
 
@@ -39,36 +40,38 @@ def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patt
         if patterns is None:
             patterns = _patterns
 
-    layout = BIDSLayout(derivatives_dir, config=['bids', 'derivatives'], validate=False)
+    deriv_config = nwf_load('nipreps.json')
+    layout = BIDSLayout(derivatives_dir, config=deriv_config, validate=False)
 
     derivs_cache = {}
-    for k, q in spec['baseline'].items():
-        q['subject'] = subject_id
-        item = layout.get(return_type='filename', **q)
+    for key, qry in spec['baseline'].items():
+        qry['subject'] = subject_id
+        item = layout.get(return_type='filename', **qry)
         if not item:
             continue
 
-        derivs_cache['t1w_%s' % k] = item[0] if len(item) == 1 else item
+        derivs_cache[f't1w_{key}'] = item[0] if len(item) == 1 else item
 
     transforms = derivs_cache.setdefault('transforms', {})
-    for space in std_spaces:
-        for k, q in spec['transforms'].items():
-            q = q.copy()
-            q['subject'] = subject_id
-            q['from'] = q['from'] or space
-            q['to'] = q['to'] or space
-            item = layout.get(return_type='filename', **q)
+    for _space in std_spaces:
+        space = _space.replace(':cohort-', '+')
+        for key, qry in spec['transforms'].items():
+            qry = qry.copy()
+            qry['subject'] = subject_id
+            qry['from'] = qry['from'] or space
+            qry['to'] = qry['to'] or space
+            item = layout.get(return_type='filename', **qry)
             if not item:
                 continue
-            transforms.setdefault(space, {})[k] = item[0] if len(item) == 1 else item
+            transforms.setdefault(_space, {})[key] = item[0] if len(item) == 1 else item
 
-    for k, q in spec['surfaces'].items():
-        q['subject'] = subject_id
-        item = layout.get(return_type='filename', **q)
+    for key, qry in spec['surfaces'].items():
+        qry['subject'] = subject_id
+        item = layout.get(return_type='filename', **qry)
         if not item or len(item) != 2:
             continue
 
-        derivs_cache[k] = sorted(item)
+        derivs_cache[key] = sorted(item)
 
     return derivs_cache
 

smriprep/utils/tests/__init__.py

@@ -0,0 +1,5 @@
+from niworkflows.data import Loader
+
+load_data = Loader(__package__)
+
+DERIV_SKELETON = load_data('derivatives.yml')

smriprep/utils/tests/derivatives.yml

@@ -0,0 +1,101 @@
+dataset_description:
+  Name: smriprep-outputs
+  BIDSVersion: 1.9.0
+  DatasetType: derivative
+'01':
+  anat:
+  - suffix: mask
+    desc: brain
+  - suffix: T1w
+    desc: preproc
+  - suffix: dseg
+  - suffix: probseg
+    label: CSF
+  - suffix: probseg
+    label: GM
+  - suffix: probseg
+    label: WM
+  - suffix: xfm
+    from: MNI152NLin2009cAsym
+    to: T1w
+    mode: image
+    extension: .h5
+  - suffix: xfm
+    from: T1w
+    to: MNI152NLin2009cAsym
+    mode: image
+    extension: .h5
+  - suffix: xfm
+    from: T1w
+    to: MNIPediatricAsym+3
+    mode: image
+    extension: .h5
+  - suffix: xfm
+    from: MNIPediatricAsym+3
+    to: T1w
+    mode: image
+    extension: .h5
+  - suffix: white
+    hemi: L
+    extension: .surf.gii
+  - suffix: white
+    hemi: R
+    extension: .surf.gii
+  - suffix: pial
+    hemi: L
+    extension: .surf.gii
+  - suffix: pial
+    hemi: R
+    extension: .surf.gii
+  - suffix: midthickness
+    hemi: L
+    extension: .surf.gii
+  - suffix: midthickness
+    hemi: R
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    space: fsLR
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    space: fsLR
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    space: fsLR
+    desc: msmsulc
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    space: fsLR
+    desc: msmsulc
+    extension: .surf.gii
+  - suffix: thickness
+    hemi: L
+    extension: .shape.gii
+  - suffix: thickness
+    hemi: R
+    extension: .shape.gii
+  - suffix: sulc
+    hemi: L
+    extension: .shape.gii
+  - suffix: sulc
+    hemi: R
+    extension: .shape.gii

smriprep/utils/tests/test_bids.py

@@ -0,0 +1,30 @@
+from niworkflows.utils.testing import generate_bids_skeleton
+
+from ..bids import collect_derivatives
+from . import DERIV_SKELETON
+
+
+def test_collect_derivatives(tmp_path):
+    deriv_dir = tmp_path / 'derivatives'
+    generate_bids_skeleton(deriv_dir, str(DERIV_SKELETON))
+    output_spaces = ['MNI152NLin2009cAsym', 'MNIPediatricAsym:cohort-3']
+    collected = collect_derivatives(deriv_dir, '01', output_spaces)
+    for suffix in ('preproc', 'mask', 'dseg'):
+        assert collected[f't1w_{suffix}']
+    assert len(collected['t1w_tpms']) == 3
+    xfms = collected['transforms']
+    for space in output_spaces:
+        assert xfms[space]['reverse']
+        assert xfms[space]['forward']
+    for surface in (
+        'white',
+        'pial',
+        'midthickness',
+        'sphere',
+        'thickness',
+        'sulc',
+        'sphere_reg',
+        'sphere_reg_fsLR',
+        'sphere_reg_msm',
+    ):
+        assert len(collected[surface]) == 2

smriprep/workflows/fit/registration.py

@@ -185,6 +185,12 @@ def init_register_template_wf(
         mem_gb=2,
     )
 
+    fmt_cohort = pe.Node(
+        niu.Function(function=_fmt_cohort, output_names=['template', 'spec']),
+        name='fmt_cohort',
+        run_without_submitting=True,
+    )
+
     # fmt:off
     workflow.connect([
         (inputnode, split_desc, [('template', 'template')]),
@@ -202,8 +208,12 @@ def init_register_template_wf(
         ]),
         (trunc_mov, registration, [
             ('output_image', 'moving_image')]),
-        (split_desc, outputnode, [
+        (split_desc, fmt_cohort, [
             ('name', 'template'),
+            ('spec', 'spec'),
+        ]),
+        (fmt_cohort, outputnode, [
+            ('template', 'template'),
             ('spec', 'template_spec'),
         ]),
         (registration, outputnode, [
@@ -225,3 +235,10 @@ def _make_outputnode(workflow, out_fields, joinsource):
         workflow.connect([(pout, out, [(f, f) for f in out_fields])])
         return pout
     return pe.Node(niu.IdentityInterface(fields=out_fields), name='outputnode')
+
+
+def _fmt_cohort(template, spec):
+    cohort = spec.pop('cohort', None)
+    if cohort is not None:
+        template = f'{template}:cohort-{cohort}'
+    return template, spec