fix: minor bugs remaining, derivatives check on circle

Author: oesteban

.circleci/config.yml

@@ -414,7 +414,7 @@ jobs:
           name: Checking outputs of full fMRIPrep run
           command: |
             mkdir -p /tmp/ds005/test
-            find /tmp/ds005/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
+            find /tmp/ds005/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
             exit $?
       - run:
@@ -437,7 +437,7 @@ jobs:
           command: |
             mkdir -p /tmp/ds005/test
             sudo rm -rf /tmp/ds005/derivatives_partial/freesurfer
-            find /tmp/ds005/derivatives_partial -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
+            find /tmp/ds005/derivatives_partial \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds005_partial_outputs.txt /tmp/ds005/test/outputs.out
             exit $?
       - run:
@@ -562,7 +562,7 @@ jobs:
           name: Checking outputs of fMRIPrep
           command: |
             mkdir -p /tmp/ds054/test
-            find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
+            find /tmp/ds054/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
             exit $?
       - run:
@@ -700,7 +700,7 @@ jobs:
           name: Checking outputs of fMRIPrep
           command: |
             mkdir -p /tmp/ds210/test
-            find /tmp/ds210/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
+            find /tmp/ds210/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds210_outputs.txt /tmp/ds210/test/outputs.out
             exit $?
       - run:

fmriprep/config.py

@@ -547,6 +547,7 @@ def init_spaces(checkpoint=True):
 
     internal = workflow.internal_spaces
     if internal is not None and internal.strip():
-        spaces += [ref for s in internal.split(' ')
-                   for ref in Reference.from_string(s)]
+        for ref in internal.split(' '):
+            spaces.add(ref)
+
     workflow.spaces = spaces

fmriprep/workflows/bold/base.py

@@ -226,7 +226,7 @@ def init_func_preproc_wf(bold_file):
 
     # By default, force-bbr for t2s_coreg unless user specifies otherwise
     if config.workflow.t2s_coreg and config.workflow.use_bbr is None:
-        config.workflow.use_bbr.use_bbr = True
+        config.workflow.use_bbr = True
 
     # Build workflow
     workflow = Workflow(name=wf_name)