Merge pull request #1286 from nipreps/fix/1282-multiecho-list-bugs

ENH: Flatten multi-echo lists in circumstances that they fail

Author: oesteban

mriqc/utils/misc.py

@@ -24,6 +24,7 @@
 
 import json
 from collections import OrderedDict
+from collections.abc import Iterable
 from pathlib import Path
 
 import pandas as pd
@@ -237,6 +238,14 @@ def _flatten_dict(indict):
     return out_qc
 
 
+def _flatten_list(xs):
+    for x in xs:
+        if isinstance(x, Iterable) and not isinstance(x, (str, bytes)):
+            yield from _flatten_list(x)
+        else:
+            yield x
+
+
 def _datalad_get(input_list, nprocs=None):
     from mriqc import config
 
@@ -255,7 +264,7 @@ def _datalad_get(input_list, nprocs=None):
         25, 'DataLad dataset identified, attempting to `datalad get` unavailable files.'
     )
     return get(
-        input_list,
+        list(_flatten_list(input_list)),
         dataset=str(config.execution.bids_dir),
         jobs=nprocs
         if not None

mriqc/workflows/functional/base.py

@@ -43,6 +43,8 @@
 This workflow is orchestrated by :py:func:`fmri_qc_workflow`.
 """
 
+from collections.abc import Iterable
+
 import nibabel as nb
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
@@ -87,7 +89,11 @@ def fmri_qc_workflow(name='funcMRIQC'):
     full_files = []
     for bold_path in dataset:
         try:
-            bold_len = nb.load(bold_path).shape[3]
+            bold_len = nb.load(
+                bold_path[0]
+                if isinstance(bold_path, Iterable) and not isinstance(bold_path, (str, bytes))
+                else bold_path
+            ).shape[3]
         except nb.filebasedimages.ImageFileError:
             bold_len = config.workflow.min_len_bold
         except IndexError:  # shape has only 3 elements