Improve error messages in ReduceASLFiles

aslprep/interfaces/utility.py

@@ -40,7 +40,11 @@ class ReduceASLFiles(SimpleInterface):
     def _run_interface(self, runtime):
         aslcontext = pd.read_table(self.inputs.aslcontext)
         asl_img = nb.load(self.inputs.asl_file)
-        assert asl_img.shape[3] == aslcontext.shape[0]
+        if asl_img.shape[3] != aslcontext.shape[0]:
+            raise ValueError(
+                f"Number of volumes in {self.inputs.asl_file} ({asl_img.shape[3]}) doesn't equal "
+                f"number of rows in {self.inputs.aslcontext} ({aslcontext.shape[0]})."
+            )
 
         if self.inputs.processing_target == "control":
             files_to_keep = ["control", "label", "m0scan"]
@@ -49,9 +53,14 @@ def _run_interface(self, runtime):
         else:
             files_to_keep = ["cbf", "m0scan"]
 
+        n_volumes = aslcontext.shape[0]
         asl_idx = aslcontext.loc[aslcontext["volume_type"].isin(files_to_keep)].index.values
         asl_idx = asl_idx.astype(int)
-        self._results["metadata"] = reduce_metadata_lists(self.inputs.metadata, asl_idx)
+        self._results["metadata"] = reduce_metadata_lists(
+            metadata=self.inputs.metadata,
+            n_volumes=n_volumes,
+            keep_idx=asl_idx,
+        )
 
         asl_img = image.index_img(asl_img, asl_idx)
 

aslprep/tests/test_cli.py

@@ -273,7 +273,6 @@ def test_test_001(data_dir, output_dir, working_dir):
         "T1w",
         "MNI152NLin2009cAsym",
         "--scorescrub",
-        "--use-syn-sdc",
         "--force-no-ge",
         "--fs-no-reconall",
         f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",

aslprep/utils/asl.py

@@ -164,7 +164,7 @@ def get_bolus_duration(metadata: "dict[str, Any]", is_casl: bool) -> float:
         return metadata["BolusCutOffDelayTime"]
 
 
-def reduce_metadata_lists(metadata, metadata_idx):
+def reduce_metadata_lists(metadata, n_volumes, keep_idx):
     """Reduce any volume-wise metadata fields to only contain values for selected volumes."""
     # A hardcoded list of fields that may have one value for each volume.
     VOLUME_WISE_FIELDS = [
@@ -182,7 +182,12 @@ def reduce_metadata_lists(metadata, metadata_idx):
 
         value = metadata[field]
         if isinstance(value, list):
+            if len(value) != n_volumes:
+                raise ValueError(
+                    f"Number of elements in list-type metadata field {field} ({len(value)}) "
+                    f"doesn't equal the number of volumes in the ASL file ({n_volumes})."
+                )
             # Reduce to only the selected volumes
-            metadata[field] = [value[i] for i in metadata_idx]
+            metadata[field] = [value[i] for i in keep_idx]
 
     return metadata

aslprep/workflows/base.py

@@ -7,6 +7,7 @@
 from copy import deepcopy
 
 import bids
+import nibabel as nb
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.utils.connections import listify
@@ -562,6 +563,9 @@ def init_single_subject_wf(subject_id: str):
                 )
                 syn_preprocessing_wf.inputs.inputnode.in_epis = sources
                 syn_preprocessing_wf.inputs.inputnode.in_meta = source_meta
+                # Use all volumes of each run.
+                run_lengths = [nb.load(f).shape[3] for f in subject_data["asl"]]
+                syn_preprocessing_wf.inputs.inputnode.t_masks = [[True] * rl for rl in run_lengths]
 
                 workflow.connect([
                     (anat_fit_wf, syn_preprocessing_wf, [

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     "psutil >= 5.4",
     "pybids ~= 0.16.4",
     "requests",
-    "sdcflows",
+    "sdcflows ~= 2.6.0",
     "sentry-sdk >= 0.6.9",
     "smriprep ~= 0.13.1",
     "templateflow >= 23.0.0",