Merge branch 'master' of https://github.com/poldracklab/fmriprep into remove_init_vol_aroma

Author: jdkent

.circleci/config.yml

@@ -483,10 +483,10 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds054-anat-v6-{{ .Branch }}-{{ epoch }}
-            - ds054-anat-v6-{{ .Branch }}
-            - ds054-anat-v6-master
-            - ds054-anat-v6-
+            - ds054-anat-v7-{{ .Branch }}-{{ epoch }}
+            - ds054-anat-v7-{{ .Branch }}
+            - ds054-anat-v7-master
+            - ds054-anat-v7-
       - run:
           name: Setting up test
           command: |
@@ -520,7 +520,7 @@ jobs:
                 --fs-no-reconall --debug --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds054-anat-v6-{{ .Branch }}-{{ epoch }}
+         key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
          paths:
             - /tmp/ds054/work
             - /tmp/ds054/derivatives
@@ -601,8 +601,8 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds210-anat-v3-{{ epoch }}
-            - ds210-anat-v3-
+            - ds210-anat-v4-{{ epoch }}
+            - ds210-anat-v4-
       - run:
           name: Setting up test
           command: |
@@ -636,7 +636,7 @@ jobs:
                 --fs-no-reconall --debug --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds210-anat-v3-{{ epoch }}
+         key: ds210-anat-v4-{{ epoch }}
          paths:
             - /tmp/ds210/work
             - /tmp/ds210/derivatives

.gitignore

@@ -66,6 +66,16 @@ target/
 #Ipython Notebook
 .ipynb_checkpoints
 
+# pycharm project settings
+.idea
+
+# vscode project settings
+.vscode
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
 auth/
 secrets.py
 local_settings.py

fmriprep/workflows/bold/confounds.py

@@ -607,7 +607,8 @@ def _getbtthresh(medianval):
         # connect nodes to ICA-AROMA
         (smooth, ica_aroma, [('smoothed_file', 'in_file')]),
         (bold_mni_trans_wf, ica_aroma, [
-            ('outputnode.bold_mask_mni', 'report_mask')]),
+            ('outputnode.bold_mask_mni', 'report_mask'),
+            ('outputnode.bold_mask_mni', 'mask')]),
         (melodic, ica_aroma, [('out_dir', 'melodic_dir')]),
         # generate tsvs from ICA-AROMA
         (ica_aroma, ica_aroma_confound_extraction, [('out_dir', 'in_directory')]),