Merge pull request #1273 from effigies/fix/new_templates

FIX: Accommodate new template formats

Author: effigies

fmriprep/__about__.py

@@ -98,7 +98,7 @@
     'pybids>=0.6.3',
     'nitime',
     'nipype>=1.1.1',
-    'niworkflows>=0.4.2',
+    'niworkflows>=0.4.3',
     'statsmodels',
     'seaborn',
     'indexed_gzip>=0.8.2',

fmriprep/workflows/anatomical.py

@@ -50,6 +50,10 @@
 )
 from ..utils.misc import fix_multi_T1w_source_name, add_suffix
 
+TEMPLATE_MAP = {
+    'MNI152NLin2009cAsym': 'mni_icbm152_nlin_asym_09c',
+    }
+
 
 #  pylint: disable=R0914
 def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
@@ -330,7 +334,7 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
     )
 
     if 'template' in output_spaces:
-        template_str = nid.TEMPLATE_MAP[template]
+        template_str = TEMPLATE_MAP[template]
         ref_img = op.join(nid.get_dataset(template_str), '1mm_T1.nii.gz')
 
         t1_2_mni.inputs.template = template_str

fmriprep/workflows/bold/resampling.py

@@ -29,6 +29,7 @@
     # See https://github.com/poldracklab/fmriprep/issues/768
     PatchedConcatenateLTA as ConcatenateLTA
 )
+from ..anatomical import TEMPLATE_MAP
 
 from .util import init_bold_reference_wf
 
@@ -259,7 +260,7 @@ def _aslist(in_value):
 
     gen_ref = pe.Node(GenerateSamplingReference(), name='gen_ref',
                       mem_gb=0.3)  # 256x256x256 * 64 / 8 ~ 150MB)
-    template_str = nid.TEMPLATE_MAP[template]
+    template_str = TEMPLATE_MAP[template]
     gen_ref.inputs.fixed_image = op.join(nid.get_dataset(template_str), '1mm_T1.nii.gz')
 
     mask_mni_tfm = pe.Node(

requirements.txt

@@ -1,2 +1,2 @@
-niworkflows>=0.4.2
+niworkflows>=0.4.3
 versioneer