Try 3.10.

.circleci/config.yml

@@ -4,7 +4,7 @@ orbs:
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennlinc/aslprep_build:0.0.4
+    - image: pennlinc/aslprep_build:0.0.5
   working_directory: /src/aslprep
 
 runinstall: &runinstall

.readthedocs.yaml

@@ -5,7 +5,7 @@ build:
   apt_packages:
     - graphviz
   tools:
-    python: "3.9"
+    python: "3.10"
 
 sphinx:
   configuration: docs/conf.py

Dockerfile

@@ -1,4 +1,4 @@
-FROM pennlinc/aslprep_build:0.0.4
+FROM pennlinc/aslprep_build:0.0.5
 
 # Install aslprep
 COPY . /src/aslprep

aslprep/workflows/asl/base.py

@@ -265,7 +265,8 @@ def init_asl_preproc_wf(
                 "midthickness",
                 "pial",
                 "sphere_reg_fsLR",
-                "thickness",
+                "midthickness_fsLR",
+                "cortex_mask",
                 "anat_ribbon",
                 # Fieldmap registration
                 "fmap",
@@ -487,6 +488,7 @@ def init_asl_preproc_wf(
                 ("std_t1w", "inputnode.target_ref_file"),
                 ("std_mask", "inputnode.target_mask"),
                 ("anat2std_xfm", "inputnode.anat2std_xfm"),
+                ("std_resolution", "inputnode.resolution"),
                 ("fmap_ref", "inputnode.fmap_ref"),
                 ("fmap_coeff", "inputnode.fmap_coeff"),
                 ("fmap_id", "inputnode.fmap_id"),
@@ -501,7 +503,6 @@ def init_asl_preproc_wf(
                 ("outputnode.motion_xfm", "inputnode.motion_xfm"),
             ]),
             (inputnode, ds_asl_std_wf, [
-                ("std_t1w", "inputnode.ref_file"),
                 ("anat2std_xfm", "inputnode.anat2std_xfm"),
                 ("std_space", "inputnode.space"),
                 ("std_resolution", "inputnode.resolution"),
@@ -630,8 +631,9 @@ def init_asl_preproc_wf(
                 ("white", "inputnode.white"),
                 ("pial", "inputnode.pial"),
                 ("midthickness", "inputnode.midthickness"),
-                ("thickness", "inputnode.thickness"),
+                ("midthickness_fsLR", "inputnode.midthickness_fsLR"),
                 ("sphere_reg_fsLR", "inputnode.sphere_reg_fsLR"),
+                ("cortex_mask", "inputnode.cortex_mask"),
                 ("anat_ribbon", "inputnode.anat_ribbon"),
             ]),
             (asl_anat_wf, asl_fsLR_resampling_wf, [("outputnode.asl_file", "inputnode.asl_file")]),

aslprep/workflows/asl/outputs.py

@@ -9,12 +9,13 @@
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 from niworkflows.interfaces.utility import KeySelect
 from niworkflows.utils.images import dseg_label
-from smriprep.workflows.outputs import _bids_relative
 
 from aslprep import config
 from aslprep.interfaces import DerivativesDataSink
 from aslprep.utils.spaces import SpatialReferences
 
+# from smriprep.workflows.outputs import _bids_relative  # fixed in new release, which reqs 3.10
+
 BASE_INPUT_FIELDS = {
     "asl": {
         "desc": "preproc",
@@ -71,6 +72,20 @@
 }
 
 
+def _bids_relative(in_files, bids_root):
+    from pathlib import Path
+
+    if not isinstance(in_files, (list, tuple)):
+        in_files = [in_files]
+    ret = []
+    for file in in_files:
+        try:
+            ret.append(str(Path(file).relative_to(bids_root)))
+        except ValueError:
+            ret.append(file)
+    return in_files
+
+
 def init_asl_fit_reports_wf(
     *,
     sdc_correction: bool,