Merge pull request #1643 from oesteban/fix/1641

FIX: FreeSurfer without adding some ``fs*`` to ``--output-spaces``

.circleci/config.yml

@@ -9,6 +9,15 @@ jobs:
       - image: docker:18.01.0-ce-git
     working_directory: /tmp/src/fmriprep
     steps:
+      - checkout
+      - run:
+          name: Check whether build should be skipped
+          command: |
+            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+              echo "Only docs build"
+              circleci step halt
+            fi
+
       - run:
           name: Install parallel gzip and python3
           command: |
@@ -21,7 +30,6 @@ jobs:
             - docker-v3-
           paths:
             - /tmp/cache/docker.tar.gz
-      - checkout
       - setup_remote_docker
       - run:
           name: Load Docker image layer cache
@@ -215,6 +223,10 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
+            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+              echo "Only docs build"
+              circleci step halt
+            fi
             if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?tests\]' )" != "" ]]; then
               echo "Skipping pytest job"
               circleci step halt
@@ -332,6 +344,10 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
+            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+              echo "Only docs build"
+              circleci step halt
+            fi
             if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds005\]' )" != "" ]]; then
               echo "Skipping ds000005 build"
               circleci step halt
@@ -482,6 +498,10 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
+            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+              echo "Only docs build"
+              circleci step halt
+            fi
             if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds054\]' )" != "" ]]; then
               echo "Skipping ds000054 build"
               circleci step halt
@@ -617,6 +637,10 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
+            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+              echo "Only docs build"
+              circleci step halt
+            fi
             if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds210\]' )" != "" ]]; then
               echo "Skipping ds000210 build"
               circleci step halt

docs/workflows.rst

@@ -490,10 +490,11 @@ Resampling BOLD runs onto standard spaces
     from collections import OrderedDict
     from fmriprep.workflows.bold import init_bold_std_trans_wf
     wf = init_bold_std_trans_wf(
-        standard_spaces=OrderedDict([('MNI152Lin', {}),
-                                     ('fsaverage', {'density': '10k'})]),
+        freesurfer=True,
         mem_gb=3,
         omp_nthreads=1,
+        standard_spaces=OrderedDict([('MNI152Lin', {}),
+                                     ('fsaverage', {'density': '10k'})]),
     )
 
 This sub-workflow concatenates the transforms calculated upstream (see

fmriprep/workflows/bold/base.py

@@ -411,7 +411,7 @@ def init_func_preproc_wf(
     summary = pe.Node(
         FunctionalSummary(
             slice_timing=run_stc,
-            registration='FreeSurfer' if freesurfer else 'FSL',
+            registration=('FSL', 'FreeSurfer')[freesurfer],
             registration_dof=bold2t1w_dof,
             pe_direction=metadata.get("PhaseEncodingDirection"),
             tr=metadata.get("RepetitionTime")),
@@ -739,12 +739,13 @@ def init_func_preproc_wf(
         # Apply transforms in 1 shot
         # Only use uncompressed output if AROMA is to be run
         bold_std_trans_wf = init_bold_std_trans_wf(
-            standard_spaces=std_spaces,
+            freesurfer=freesurfer,
             mem_gb=mem_gb['resampled'],
             omp_nthreads=omp_nthreads,
+            standard_spaces=std_spaces,
+            name='bold_std_trans_wf',
             use_compression=not low_mem,
             use_fieldwarp=fmaps is not None,
-            name='bold_std_trans_wf'
         )
         workflow.connect([
             (inputnode, bold_std_trans_wf, [

fmriprep/workflows/bold/resampling.py

@@ -169,9 +169,10 @@ def select_target(subject_id, space):
 
 
 def init_bold_std_trans_wf(
-    standard_spaces,
+    freesurfer,
     mem_gb,
     omp_nthreads,
+    standard_spaces,
     name='bold_std_trans_wf',
     use_compression=True,
     use_fieldwarp=False
@@ -187,25 +188,28 @@ def init_bold_std_trans_wf(
         from collections import OrderedDict
         from fmriprep.workflows.bold import init_bold_std_trans_wf
         wf = init_bold_std_trans_wf(
-            standard_spaces=OrderedDict([('MNI152Lin', {}),
-                                         ('fsaverage', {'density': '10k'})]),
+            freesurfer=True,
             mem_gb=3,
             omp_nthreads=1,
+            standard_spaces=OrderedDict([('MNI152Lin', {}),
+                                         ('fsaverage', {'density': '10k'})]),
         )
 
     **Parameters**
 
+        freesurfer : bool
+            Whether to generate FreeSurfer's aseg/aparc segmentations on BOLD space.
+        mem_gb : float
+            Size of BOLD file in GB
+        omp_nthreads : int
+            Maximum number of threads an individual process may use
         standard_spaces : OrderedDict
             Ordered dictionary where keys are TemplateFlow ID strings (e.g.,
             ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, or ``fsLR``),
             or paths pointing to custom templates organized in a TemplateFlow-like structure.
             Values of the dictionary aggregate modifiers (e.g., the value for the key ``MNI152Lin``
             could be ``{'resolution': 2}`` if one wants the resampling to be done on the 2mm
             resolution version of the selected template).
-        mem_gb : float
-            Size of BOLD file in GB
-        omp_nthreads : int
-            Maximum number of threads an individual process may use
         name : str
             Name of workflow (default: ``bold_std_trans_wf``)
         use_compression : bool
@@ -268,8 +272,6 @@ def init_bold_std_trans_wf(
 
     # Filter ``standard_spaces``
     vol_std_spaces = [k for k in standard_spaces.keys() if not k.startswith('fs')]
-    freesurfer = [k for k in standard_spaces.keys()
-                  if k.startswith('fs') and k != 'fsLR']
 
     workflow = Workflow(name=name)