Merge cohort entity into space entity in derivatives

.circleci/bcp_anat_outputs.txt

@@ -44,14 +44,14 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-preproc_T1w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-preproc_T1w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-WM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-aparcaseg_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-aseg_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-ribbon_mask.json

.circleci/bcp_anat_t2only_outputs.txt

@@ -48,14 +48,14 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-preproc_T2w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-preproc_T2w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-WM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_desc-aparcaseg_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_desc-aseg_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_desc-ribbon_mask.json

.circleci/bcp_full_outputs.txt

@@ -44,14 +44,14 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_white.surf.gii
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-brain_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-brain_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-preproc_T1w.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_desc-preproc_T1w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant+1_label-WM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-aparcaseg_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-aseg_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-ribbon_mask.json
@@ -82,10 +82,10 @@ sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-boldref_to-auto
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_boldref.json
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_boldref.nii.gz
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-preproc_bold.json
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-preproc_bold.nii.gz
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant+1_boldref.json
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant+1_boldref.nii.gz
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant+1_desc-brain_mask.json
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant+1_desc-brain_mask.nii.gz
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant+1_desc-preproc_bold.json
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant+1_desc-preproc_bold.nii.gz
 sub-01_ses-1mo.html

docs/outputs.md

@@ -240,8 +240,8 @@ these will be indicated with `[specifiers]`
 ```
   sub-<subject_label>/[ses-<session_label>/]
     func/
-      sub-<subject_label>_[specifiers]_space-<space_label>_desc-brain_mask.nii.gz
-      sub-<subject_label>_[specifiers]_space-<space_label>_desc-preproc_bold.nii.gz
+      sub-<subject_label>_[specifiers]_space-<space_label>+<cohort>_desc-brain_mask.nii.gz
+      sub-<subject_label>_[specifiers]_space-<space_label>+<cohort>_desc-preproc_bold.nii.gz
 ```
 
 :::{note}
@@ -311,6 +311,8 @@ Fieldmap registration outputs are part of the *minimal* processing level.
 
 Volumetric output spaces labels (`<space_label>` above, and in the following) include
 `T1w` and `MNI152NLin2009cAsym` (default).
+For space labels that include a cohort, the cohort is included in the space label,
+for example `MNIInfant+1`.
 
 #### Surfaces, segmentations and parcellations from FreeSurfer
 

nibabies/utils/bids.py

@@ -360,3 +360,17 @@ def age_to_months(age: int | float, units: ty.Literal['weeks', 'months', 'years'
     elif units == 'years':
         age *= YEARS_TO_MONTH
     return round(age)
+
+
+def combine_space(space, cohort) -> str:
+    """Combine space and cohort into a single string.
+
+    If cohort is not defined, return the space as is.
+    """
+    if space.startswith('space-'):
+        space = space.split('-')[1]
+    if cohort:
+        if cohort.startswith('cohort-'):
+            cohort = cohort.split('-')[1]
+        return f'{space}+{cohort}'
+    return space

nibabies/utils/tests/full-derivatives.yml

@@ -102,15 +102,12 @@ dataset_description:
     mode: image
     desc: hmc
   - suffix: boldref
-    space: MNIInfant
-    cohort: 1
+    space: MNIInfant+1
   - suffix: mask
-    space: MNIInfant
-    cohort: 1
+    space: MNIInfant+1
     desc: brain
   - suffix: bold
-    space: MNIInfant
-    cohort: 1
+    space: MNIInfant+1
     desc: preproc
   - suffix: bold
     space: fsLR

nibabies/workflows/anatomical/apply.py

@@ -68,7 +68,6 @@ def init_infant_anat_apply_wf(
                 'std_t1w',
                 'anat2std_xfm',
                 'std_space',
-                'std_cohort',
                 'std_resolution',
             ]
         ),
@@ -94,12 +93,11 @@ def init_infant_anat_apply_wf(
                 ('anat_mask', 'inputnode.anat_mask'),
                 ('anat_dseg', 'inputnode.anat_dseg'),
                 ('anat_tpms', 'inputnode.anat_tpms'),
+                ('std_space', 'inputnode.space'),
             ]),
             (inputnode, ds_std_volumes_wf, [
                 ('std_t1w', 'inputnode.ref_file'),
                 ('anat2std_xfm', 'inputnode.anat2std_xfm'),
-                ('std_space', 'inputnode.space'),
-                ('std_cohort', 'inputnode.cohort'),
                 ('std_resolution', 'inputnode.resolution'),
             ]),
         ])  # fmt:skip

nibabies/workflows/anatomical/outputs.py

@@ -590,12 +590,22 @@ def init_anat_derivatives_wf(
         from niworkflows.interfaces.space import SpaceDataSource
         from smriprep.interfaces.templateflow import TemplateFlowSelect
 
+        from nibabies.utils.bids import combine_space
+
         spacesource = pe.Node(SpaceDataSource(), name='spacesource', run_without_submitting=True)
         spacesource.iterables = (
             'in_tuple',
             [(s.fullname, s.spec) for s in spaces.cached.get_standard(dim=(3,))],
         )
 
+        combine_space_entity = pe.Node(
+            niu.Function(function=combine_space),
+            name='combine_space_entity',
+            run_without_submitting=True,
+            input_names=['space', 'cohort'],
+            output_names=['space'],
+        )
+
         gen_tplid = pe.Node(
             niu.Function(function=_fmt_cohort),
             name='gen_tplid',
@@ -690,6 +700,10 @@ def init_anat_derivatives_wf(
             (inputnode, select_xfm, [
                 ('anat2std_xfm', 'anat2std_xfm'),
                 ('template', 'keys')]),
+            (spacesource, combine_space_entity, [
+                ('space', 'space'),
+                ('cohort', 'cohort'),
+            ]),
             (spacesource, gen_tplid, [('space', 'template'),
                                       ('cohort', 'cohort')]),
             (gen_tplid, select_xfm, [('out', 'key')]),
@@ -724,11 +738,12 @@ def init_anat_derivatives_wf(
             ]
             # Connect the space input of these datasinks
             + [
-                (
-                    spacesource,
-                    n,
-                    [('space', 'space'), ('cohort', 'cohort'), ('resolution', 'resolution')],
-                )
+                (combine_space_entity, n, [('space', 'space')])
+                for n in (ds_std_t1w, ds_std_mask, ds_std_dseg, ds_std_tpms)
+            ]
+            # Connect the resolution input of these datasinks
+            + [
+                (spacesource, n, [('resolution', 'resolution')])
                 for n in (ds_std_t1w, ds_std_mask, ds_std_dseg, ds_std_tpms)
             ]
         )

nibabies/workflows/base.py

@@ -575,7 +575,6 @@ def init_single_subject_wf(
                     ('outputnode.std_t1w', 'inputnode.std_t1w',),
                     ('outputnode.anat2std_xfm', 'inputnode.anat2std_xfm'),
                     ('outputnode.space', 'inputnode.std_space'),
-                    ('outputnode.cohort', 'inputnode.std_cohort'),
                     ('outputnode.resolution', 'inputnode.std_resolution'),
                 ]),
             ])  # fmt:skip
@@ -792,7 +791,6 @@ def init_single_subject_wf(
                     (template_iterator_wf, bold_wf, [
                         ('outputnode.space', 'inputnode.std_space'),
                         ('outputnode.resolution', 'inputnode.std_resolution'),
-                        ('outputnode.cohort', 'inputnode.std_cohort'),
                         ('outputnode.std_t1w', 'inputnode.std_t1w'),
                         ('outputnode.std_mask', 'inputnode.std_mask'),
                         ('outputnode.anat2std_xfm', 'inputnode.anat2std_xfm'),

nibabies/workflows/bold/base.py

@@ -144,8 +144,6 @@ def init_bold_wf(
         Value of space entity to be used in standard space output filenames
     std_resolution
         Value of resolution entity to be used in standard space output filenames
-    std_cohort
-        Value of cohort entity to be used in standard space output filenames
     anat2mni6_xfm
         Transform from anatomical space to MNI152NLin6Asym space
     mni6_mask
@@ -154,7 +152,7 @@ def init_bold_wf(
         Transform from MNI152NLin2009cAsym to anatomical space
 
     Note that ``anat2std_xfm``, ``std_space``, ``std_resolution``,
-    ``std_cohort``, ``std_t1w`` and ``std_mask`` are treated as single
+    ``std_t1w`` and ``std_mask`` are treated as single
     inputs. In order to resample to multiple target spaces, connect
     these fields to an iterable.
 
@@ -244,7 +242,6 @@ def init_bold_wf(
                 'std_mask',
                 'std_space',
                 'std_resolution',
-                'std_cohort',
                 # MNI152NLin6Asym warp, for CIFTI use
                 # 'anat2mni6_xfm',
                 # 'mni6_mask',
@@ -498,7 +495,6 @@ def init_bold_wf(
                 ('std_t1w', 'inputnode.template'),
                 ('std_space', 'inputnode.space'),
                 ('std_resolution', 'inputnode.resolution'),
-                ('std_cohort', 'inputnode.cohort'),
             ]),
             (bold_fit_wf, ds_bold_std_wf, [
                 ('outputnode.bold_mask', 'inputnode.bold_mask'),

nibabies/workflows/bold/outputs.py

@@ -728,7 +728,6 @@ def init_ds_volumes_wf(
                 'anat2std_xfm',
                 # Entities
                 'space',
-                'cohort',
                 'resolution',
                 # Transforms previously used to generate the outputs
                 'motion_xfm',
@@ -781,7 +780,6 @@ def init_ds_volumes_wf(
             ('source_files', 'source_file'),
             ('bold', 'in_file'),
             ('space', 'space'),
-            ('cohort', 'cohort'),
             ('resolution', 'resolution'),
         ]),
         (sources, ds_bold, [('out', 'Sources')]),
@@ -872,7 +870,6 @@ def init_ds_volumes_wf(
             (inputnode, datasink, [
                 ('source_files', 'source_file'),
                 ('space', 'space'),
-                ('cohort', 'cohort'),
                 ('resolution', 'resolution'),
             ])
             for datasink in datasinks

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "pybids >= 0.15.0",
     "requests",
     "sdcflows >= 2.14.0",
-    "smriprep >= 0.19.1",
+    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
     "tedana >= 23.0.2",
     "templateflow >= 25.0.3",
     "toml",