Merge pull request #1159 from ZhifangYe/master

ENH: Pre-cache DKT31 template in Docker image

Author: effigies

docker/scripts/get_templates.sh

@@ -8,6 +8,8 @@ OASIS_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/584
 OASIS_SHA256="d87300e91346c16f55baf6f54f5f990bc020b61e8d5df9bcc3abb0cc4b943113"
 NKI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/59cd90f46c613b02b3d79782"
 NKI_SHA256="4bba067f6675d15be96b205cb227e18a540673fd7e4577e13feedcef3a6f0ec5"
+OASIS_DKT31_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b16f17aeca4a80012bd7542"
+OASIS_DKT31_SHA256="623fa7141712b1a7263331dba16eb069a4443e9640f52556c89d461611478145"
 
 GET(){
     URL=$1; SHA256=$2;
@@ -32,4 +34,6 @@ echo "Getting OASIS template"
 GET "$OASIS_TEMPLATE" "$OASIS_SHA256"
 echo "Getting NKI template"
 GET "$NKI_TEMPLATE" "$NKI_SHA256"
+echo "Getting OASIS DKT31 template"
+GET "$OASIS_DKT31_TEMPLATE" "$OASIS_DKT31_SHA256"
 echo "Done!"

docs/environment.yml

@@ -28,4 +28,4 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.4.0
+    - niworkflows>=0.4.1

fmriprep/info.py

@@ -71,7 +71,7 @@
     'pybids>=0.5.1',
     'nitime',
     'nipype>=1.0.4',
-    'niworkflows>=0.4.0',
+    'niworkflows>=0.4.1',
     'statsmodels',
     'nipype',
     'seaborn',

fmriprep/interfaces/cifti.py

@@ -130,12 +130,10 @@ def _fetch_data(self):
             raise IOError("Freesurfer annotations for %s not found in %s" % (
                           self.inputs.surface_target, self.inputs.subjects_dir))
 
-        label_space = 'oasis_dkt31_mni152'
-        label_template = os.path.dirname(getters.get_dataset(label_space))
-        label_file = os.path.join(label_template,
-                                  'oasis_trt20_DKT31-MNI152NLin',
-                                  ('OASIS-TRT-20_jointfusion_DKT31_CMA_labels'
-                                   '_in_MNI152NLin2009cAsym_2mm_v2.nii.gz'))
+        label_space = 'tpl-OASISTRT20'
+        label_dir = getters.get_oasis_dkt31_mni152()
+        label_file = os.path.join(label_dir,
+                                  'tpl-OASISTRT20_variant-DKT31_space-MNI152NLin2009cAsym.nii.gz')
 
         download_link = getters.OSF_PROJECT_URL + getters.OSF_RESOURCES[label_space][0]
         return annotation_files, label_file, download_link

requirements.txt

@@ -1,2 +1,2 @@
-niworkflows>=0.4.0
+niworkflows>=0.4.1
 versioneer