Merge pull request #1350 from fliem/fix-stc

[ENH] Respect SliceEncodingDirection metadata

Author: effigies

.zenodo.json

@@ -83,6 +83,11 @@
       "affiliation": "Department of Psychology, University of Oslo",
       "orcid": "0000-0002-8508-9088"
     },
+    {
+      "name": "Liem, Franz",
+      "affiliation": "University of Zurich",
+      "orcid": "0000-0003-0646-4810"
+    },
     {
       "name": "Poldrack, Russell A.",
       "affiliation": "Department of Psychology, Stanford University",

fmriprep/__about__.py

@@ -97,7 +97,7 @@
     'grabbit==0.2.3',
     'pybids==0.6.5',
     'nitime',
-    'nipype>=1.1.3',
+    'nipype>=1.1.4',
     'niworkflows==0.4.4',
     'statsmodels',
     'seaborn',

fmriprep/workflows/bold/stc.py

@@ -69,7 +69,8 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'):
     slice_timing_correction = pe.Node(
         afni.TShift(outputtype='NIFTI_GZ',
                     tr='{}s'.format(metadata["RepetitionTime"]),
-                    slice_timing=metadata['SliceTiming']),
+                    slice_timing=metadata['SliceTiming'],
+                    slice_encoding_direction=metadata.get('SliceEncodingDirection', 'k')),
         name='slice_timing_correction')
 
     copy_xform = pe.Node(CopyXForm(), name='copy_xform', mem_gb=0.1)