ENH: Add sphere registration to fit workflow, check for precomputed

.circleci/config.yml

@@ -12,6 +12,9 @@ _machine_defaults: &machine_defaults
 _python_defaults: &python_defaults
   docker:
     - image: cimg/python:3.10.9
+      auth:
+        username: $DOCKER_USER
+        password: $DOCKER_PAT
   working_directory: /tmp/src/smriprep
 
 _docker_auth: &docker_auth
@@ -43,6 +46,9 @@ _pull_from_registry: &pull_from_registry
 docs_deploy: &docs
   docker:
     - image: node:8.10.0
+      auth:
+        username: $DOCKER_USER
+        password: $DOCKER_PAT
   working_directory: /tmp/gh-pages
   steps:
     - run:

.circleci/ds005_outputs.txt

@@ -16,6 +16,7 @@ smriprep/sub-01/anat/sub-01_desc-brain_mask.json
 smriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
 smriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
 smriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
+smriprep/sub-01/anat/sub-01_desc-ribbon_mask.json
 smriprep/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
 smriprep/sub-01/anat/sub-01_dseg.nii.gz
 smriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
@@ -27,6 +28,7 @@ smriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
+smriprep/sub-01/anat/sub-01_hemi-L_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 smriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
 smriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
@@ -37,6 +39,7 @@ smriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
+smriprep/sub-01/anat/sub-01_hemi-R_sphere.surf.gii
 smriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 smriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
 smriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii

smriprep/data/io_spec.json

@@ -70,68 +70,91 @@
         "mode": "image"
       }
     },
-    "std_xfms": {
-      "anat2std_xfm": {
+    "surfaces": {
+      "white": {
         "datatype": "anat",
-        "extension": "h5",
-        "from": "T1w",
-        "to": [],
-        "suffix": "xfm",
-        "mode": "image"
+        "hemi": ["L", "R"],
+        "space": null,
+        "suffix": "white",
+        "extension": ".surf.gii"
       },
-      "std2anat_xfm": {
+      "pial": {
         "datatype": "anat",
-        "extension": "h5",
-        "from": [],
-        "to": "T1w",
-        "suffix": "xfm",
-        "mode": "image"
-      }
-    },
-    "surfaces": {
-      "t1w_aseg": {
+        "hemi": ["L", "R"],
+        "space": null,
+        "suffix": "pial",
+        "extension": ".surf.gii"
+      },
+      "midthickness": {
         "datatype": "anat",
-        "desc": "aseg",
-        "suffix": "dseg"
+        "hemi": ["L", "R"],
+        "space": null,
+        "suffix": "midthickness",
+        "extension": ".surf.gii"
       },
-      "t1w_aparc": {
+      "sphere": {
         "datatype": "anat",
-        "desc": "aparcaseg",
-        "suffix": "dseg"
+        "hemi": ["L", "R"],
+        "space": null,
+        "desc": null,
+        "suffix": "sphere",
+        "extension": ".surf.gii"
       },
-      "t1w2fsnative_xfm": {
+      "thickness": {
         "datatype": "anat",
-        "from": "T1w",
-        "to": "fsnative",
-        "extension": "txt",
-        "suffix": "xfm",
-        "mode": "image"
+        "hemi": ["L", "R"],
+        "space": null,
+        "suffix": "thickness",
+        "extension": ".shape.gii"
       },
-      "fsnative2t1w_xfm": {
+      "sulc": {
         "datatype": "anat",
-        "from": "fsnative",
-        "to": "T1w",
-        "extension": "txt",
-        "suffix": "xfm",
-        "mode": "image"
+        "hemi": ["L", "R"],
+        "space": null,
+        "suffix": "sulc",
+        "extension": ".shape.gii"
       },
-      "surfaces": {
+      "curv": {
         "datatype": "anat",
         "hemi": ["L", "R"],
-        "extension": "surf.gii",
-        "suffix": [ "inflated", "midthickness", "pial", "white"]
+        "space": null,
+        "suffix": "curv",
+        "extension": ".shape.gii"
       },
-      "morphometrics": {
+      "sphere_reg": {
         "datatype": "anat",
         "hemi": ["L", "R"],
-        "extension": "shape.gii",
-        "suffix": ["thickness", "sulc", "curv"]
+        "space": null,
+        "desc": "reg",
+        "suffix": "sphere",
+        "extension": ".surf.gii"
       },
+      "sphere_reg_fsLR": {
+        "datatype": "anat",
+        "hemi": ["L", "R"],
+        "space": "fsLR",
+        "desc": "reg",
+        "suffix": "sphere",
+        "extension": ".surf.gii"
+      },
+      "sphere_reg_msm": {
+        "datatype": "anat",
+        "hemi": ["L", "R"],
+        "space": "fsLR",
+        "desc": "msmsulc",
+        "suffix": "sphere",
+        "extension": ".surf.gii"
+      }
+    },
+    "masks": {
       "anat_ribbon": {
         "datatype": "anat",
         "desc": "ribbon",
         "suffix": "mask",
-        "extension": "nii.gz"
+        "extension": [
+          ".nii.gz",
+          ".nii"
+        ]
       }
     }
   },

smriprep/utils/bids.py

@@ -21,39 +21,13 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Utilities to handle BIDS inputs."""
-from collections import defaultdict
 from pathlib import Path
 from json import loads
 from pkg_resources import resource_filename as pkgrf
 from bids.layout import BIDSLayout
-from bids.layout.writing import build_path
 
 
-def get_outputnode_spec():
-    """
-    Generate outputnode's fields from I/O spec file.
-
-    Examples
-    --------
-    >>> get_outputnode_spec()  # doctest: +NORMALIZE_WHITESPACE
-    ['t1w_preproc', 't1w_mask', 't1w_dseg', 't1w_tpms',
-    'std_preproc', 'std_mask', 'std_dseg', 'std_tpms',
-    'anat2std_xfm', 'std2anat_xfm',
-    't1w_aseg', 't1w_aparc',
-    't1w2fsnative_xfm', 'fsnative2t1w_xfm',
-    'surfaces', 'morphometrics', 'anat_ribbon']
-
-    """
-    spec = loads(Path(pkgrf("smriprep", "data/io_spec.json")).read_text())["queries"]
-    fields = ["_".join((m, s)) for m in ("t1w", "std") for s in spec["baseline"].keys()]
-    fields += [s for s in spec["std_xfms"].keys()]
-    fields += [s for s in spec["surfaces"].keys()]
-    return fields
-
-
-def collect_derivatives(
-    derivatives_dir, subject_id, std_spaces, freesurfer, spec=None, patterns=None
-):
+def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patterns=None):
     """Gather existing derivatives and compose a cache."""
     if spec is None or patterns is None:
         _spec, _patterns = tuple(
@@ -65,27 +39,9 @@
         if patterns is None:
             patterns = _patterns
 
-    derivs_cache = defaultdict(list, {})
     layout = BIDSLayout(derivatives_dir, config=["bids", "derivatives"], validate=False)
-    derivatives_dir = Path(derivatives_dir)
-
-    def _check_item(item):
-        if not item:
-            return None
-
-        if isinstance(item, str):
-            item = [item]
-
-        result = []
-        for i in item:
-            if not (derivatives_dir / i).exists():
-                i = i.rstrip(".gz")
-                if not (derivatives_dir / i).exists():
-                    return None
-            result.append(str(derivatives_dir / i))
-
-        return result
 
+    derivs_cache = {}
     for k, q in spec["baseline"].items():
         q["subject"] = subject_id
         item = layout.get(return_type='filename', **q)
@@ -94,18 +50,6 @@
 
         derivs_cache["t1w_%s" % k] = item[0] if len(item) == 1 else item
 
-    for space in std_spaces:
-        for k, q in spec["std_xfms"].items():
-            q["subject"] = subject_id
-            q["from"] = q["from"] or space
-            q["to"] = q["to"] or space
-            item = layout.get(return_type='filename', **q)
-            if not item:
-                continue
-            derivs_cache[k] += item
-
-    derivs_cache = dict(derivs_cache)  # Back to a standard dictionary
-
     transforms = derivs_cache.setdefault('transforms', {})
     for space in std_spaces:
         for k, q in spec["transforms"].items():
@@ -118,18 +62,14 @@
                 continue
             transforms.setdefault(space, {})[k] = item[0] if len(item) == 1 else item
 
-    if freesurfer:
-        for k, q in spec["surfaces"].items():
-            q["subject"] = subject_id
-            item = _check_item(build_path(q, patterns))
-            if not item:
-                continue
+    for k, q in spec["surfaces"].items():
+        q["subject"] = subject_id
+        item = layout.get(return_type='filename', **q)
+        if not item or len(item) != 2:
+            continue
 
-            if len(item) == 1:
-                item = item[0]
-            derivs_cache[k] = item
+        derivs_cache[k] = sorted(item)
 
-    derivs_cache["template"] = std_spaces
     return derivs_cache