[skip tests][skip docs][skip ds210][skip ds054] pass mask into ica-aroma and merge with upstream

Author: jdkent

.circleci/config.yml

@@ -165,8 +165,8 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - regression-v0-{{ epoch }}
-            - regression-v0-
+            - regression-v2-{{ epoch }}
+            - regression-v2-
       - run:
           name: Get truncated BOLD series
           command: |
@@ -193,7 +193,7 @@ jobs:
           paths:
             - data
       - save_cache:
-         key: regression-v0-{{ epoch }}
+         key: regression-v2-{{ epoch }}
          paths:
             - /tmp/data
 
@@ -227,10 +227,6 @@ jobs:
             fi
       - attach_workspace:
           at: /tmp
-      - restore_cache:
-          keys:
-            - regression-v0-{{ epoch }}
-            - regression-v0-
       - run:
           name: Check PyPi preconditions
           command: |
@@ -260,7 +256,13 @@ jobs:
               -e FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
               --entrypoint="py.test" poldracklab/fmriprep:latest \
               /root/src/fmriprep/ \
-              --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
+              -svx --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
+      - run:
+          name: Package new masks
+          no_output_timeout: 10m
+          working_directory: /tmp/data/reports
+          command: |
+            tar cfz fmriprep_bold_mask.tar.gz fmriprep_bold_mask/*/*.nii.gz
       - run:
           name: Test fmriprep-wrapper (Python 2)
           command: |
@@ -719,7 +721,9 @@ workflows:
       - get_data:
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -732,6 +736,8 @@ workflows:
           requires:
             - build
           filters:
+            branches:
+              ignore: /tests?\/.*/
             tags:
               only: /.*/
 
@@ -740,7 +746,9 @@ workflows:
             - build
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -760,7 +768,9 @@ workflows:
             - build
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -770,7 +780,9 @@ workflows:
             - build
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 
@@ -781,7 +793,9 @@ workflows:
           filters:
             branches:
               # only: /meepi.*/
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /tests?\/.*/
             tags:
               only: /.*/
 

fmriprep/__about__.py

@@ -98,7 +98,7 @@
     'pybids==0.6.5',
     'nitime',
     'nipype>=1.1.3',
-    'niworkflows>=0.4.3',
+    'niworkflows>=0.4.4',
     'statsmodels',
     'seaborn',
     'indexed_gzip>=0.8.2',

fmriprep/interfaces/cifti.py

@@ -130,10 +130,9 @@ def _fetch_data(self):
             raise IOError("Freesurfer annotations for %s not found in %s" % (
                           self.inputs.surface_target, self.inputs.subjects_dir))
 
-        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')
+        label_space = 'OASISTRT20'
+        label_file = str(getters.get_template(label_space) /
+                         '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

fmriprep/workflows/bold/confounds.py

@@ -581,7 +581,8 @@ 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')]),

fmriprep/workflows/bold/tests/test_util.py

@@ -1,10 +1,11 @@
 ''' Testing module for fmriprep.workflows.bold.util '''
 import pytest
 import os
+from pathlib import Path
 
 import numpy as np
 from nipype.pipeline import engine as pe
-from nipype.utils.filemanip import fname_presuffix
+from nipype.utils.filemanip import fname_presuffix, copyfile
 from nilearn.image import load_img
 
 from niworkflows.interfaces.masks import ROIsPlot
@@ -46,33 +47,49 @@ def symmetric_overlap(img1, img2):
         'ds000216/sub-03_task-rest_echo-4_bold.nii.gz',
         'ds000237/sub-03_task-MemorySpan_acq-multiband_run-01_bold.nii.gz',
         'ds000237/sub-06_task-MemorySpan_acq-multiband_run-01_bold.nii.gz',
-        )
-    ])
+        'ds001240/sub-26_task-localizerimagination_bold.nii.gz',
+        'ds001240/sub-26_task-localizerviewing_bold.nii.gz',
+        'ds001240/sub-26_task-molencoding_run-01_bold.nii.gz',
+        'ds001240/sub-26_task-molencoding_run-02_bold.nii.gz',
+        'ds001240/sub-26_task-molretrieval_run-01_bold.nii.gz',
+        'ds001240/sub-26_task-molretrieval_run-02_bold.nii.gz',
+        'ds001240/sub-26_task-rest_bold.nii.gz',
+        'ds001362/sub-01_task-taskname_run-01_bold.nii.gz',
+    )
+])
 def test_masking(input_fname, expected_fname):
     bold_reference_wf = init_bold_reference_wf(omp_nthreads=1, enhance_t2=True)
     bold_reference_wf.inputs.inputnode.bold_file = input_fname
 
     # Reconstruct base_fname from above
     dirname, basename = os.path.split(input_fname)
-    newpath = os.path.join(os.getenv('FMRIPREP_REGRESSION_REPORTS', '.'),
-                           os.path.basename(dirname))
+    dsname = os.path.basename(dirname)
+    reports_dir = Path(os.getenv('FMRIPREP_REGRESSION_REPORTS', ''))
+    newpath = reports_dir / dsname
     out_fname = fname_presuffix(basename, suffix='_masks.svg', use_ext=False,
-                                newpath=newpath)
-    os.makedirs(newpath, exist_ok=True)
+                                newpath=str(newpath))
+    newpath.mkdir(parents=True, exist_ok=True)
 
     mask_diff_plot = pe.Node(ROIsPlot(), name='mask_diff_plot')
     mask_diff_plot.inputs.in_mask = expected_fname
     mask_diff_plot.inputs.out_report = out_fname
 
+    outputnode = bold_reference_wf.get_node('outputnode')
     bold_reference_wf.connect([
-        (bold_reference_wf.get_node('outputnode'), mask_diff_plot, [
-            ('ref_image', 'in_file'),
-            ('bold_mask', 'in_rois'),
-            ])])
+        (outputnode, mask_diff_plot, [('ref_image', 'in_file'),
+                                      ('bold_mask', 'in_rois')])
+    ])
     res = bold_reference_wf.run(plugin='MultiProc')
 
     combine_masks = [node for node in res.nodes if node.name.endswith('combine_masks')][0]
     overlap = symmetric_overlap(expected_fname,
                                 combine_masks.result.outputs.out_file)
 
+    mask_dir = reports_dir / 'fmriprep_bold_mask' / dsname
+    mask_dir.mkdir(parents=True, exist_ok=True)
+    copyfile(combine_masks.result.outputs.out_file,
+             fname_presuffix(basename, suffix='_mask',
+                             use_ext=True, newpath=str(mask_dir)),
+             copy=True)
+
     assert overlap > 0.95, input_fname

requirements.txt

@@ -1,4 +1,4 @@
-niworkflows>=0.4.3
+niworkflows>=0.4.4
 grabbit==0.2.3
 pybids==0.6.5
 versioneer