FIX: modify pybids args after their style changes

Author: josephmje

dmriprep/io.py

@@ -21,17 +21,26 @@ def get_bids_subject_input_files(subject_id, bids_input_directory):
     subjects = layout.get_subjects()
     assert subject_id in subjects, "subject {} is not in the bids folder".format(subject_id)
 
-    ap_file = layout.get(subject=subject_id, fmap="epi", modality="fmap", dir="AP")
+    ap_file = layout.get(subject=subject_id,
+                         datatype='fmap',
+                         suffix='epi',
+                         dir='AP',
+                         extensions=['.nii', '.nii.gz'])
     assert len(ap_file) == 1, 'found {} ap fieldmap files and we need just 1'.format(len(ap_file))
 
-    pa_file = layout.get(subject=subject_id, fmap="epi", modality="fmap", dir="PA")
+    pa_file = layout.get(subject=subject_id,
+                         datatype='fmap',
+                         suffix='epi',
+                         dir='PA',
+                         extensions=['.nii', '.nii.gz'])
+
     assert len(pa_file) == 1, 'found {} pa fieldmap files and we need just 1'.format(len(pa_file))
 
-    dwi_files = layout.get(subject=subject_id, modality="dwi")
+    dwi_files = layout.get(subject=subject_id, datatype='dwi', suffix='dwi')
     valid_dwi_files = []
 
     for d in dwi_files:
-        if d.filename.startswith(op.abspath(op.join(bids_input_directory, 'sub-' + subject_id))):
+        if d.path.startswith(op.abspath(op.join(bids_input_directory, 'sub-' + subject_id))):
             valid_dwi_files.append(d.filename)
 
     dwi_file = [d for d in valid_dwi_files if d.endswith('.nii.gz') and not "TRACE" in d]
@@ -52,8 +61,8 @@ def get_bids_subject_input_files(subject_id, bids_input_directory):
 
     outputs = dict(subject_id="sub-"+subject_id,
                    dwi_file=dwi_file[0],
-                   dwi_file_AP=ap_file[0].filename,
-                   dwi_file_PA=pa_file[0].filename,
+                   dwi_file_AP=ap_file[0].path,
+                   dwi_file_PA=pa_file[0].path,
                    bvec_file=bvec_file[0],
                    bval_file=bval_file[0],
                    subjects_dir=op.abspath(subjects_dir))