Merge remote-tracking branch 'upstream/master' into doc/pr_template_update

Author: effigies

.circleci/config.yml

@@ -156,6 +156,46 @@ jobs:
             - /tmp/data
             - /tmp/ds005/derivatives/freesurfer
 
+  get_regression_data:
+    machine:
+      # Ubuntu 14.04 with Docker 17.10.0-ce
+      image: circleci/classic:201711-01
+    working_directory: /home/circleci/data
+    steps:
+      - restore_cache:
+          keys:
+            - regression-v0-{{ epoch }}
+            - regression-v0-
+      - run:
+          name: Get truncated BOLD series
+          command: |
+            mkdir -p /tmp/data
+            if [[ ! -d /tmp/data/fmriprep_bold_truncated ]]; then
+              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
+                -O fmriprep_bold_truncated.tar.gz "https://osf.io/286yr/download"
+              tar xvzf fmriprep_bold_truncated.tar.gz -C /tmp/data/
+            else
+              echo "Truncated BOLD series were cached"
+            fi
+      - run:
+          name: Get pre-computed masks
+          command: |
+            if [[ ! -d /tmp/data/fmriprep_bold_mask ]]; then
+              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
+                -O fmriprep_bold_mask.tar.gz "https://osf.io/s4f7b/download"
+              tar xvzf fmriprep_bold_mask.tar.gz -C /tmp/data/
+            else
+              echo "Pre-computed masks were cached"
+            fi
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+            - data
+      - save_cache:
+         key: regression-v0-{{ epoch }}
+         paths:
+            - /tmp/data
+
   update_cache:
     machine:
       # Ubuntu 14.04 with Docker 17.10.0-ce
@@ -186,6 +226,10 @@ jobs:
             fi
       - attach_workspace:
           at: /tmp
+      - restore_cache:
+          keys:
+            - regression-v0-{{ epoch }}
+            - regression-v0-
       - run:
           name: Load Docker image layer cache
           no_output_timeout: 30m
@@ -202,6 +246,9 @@ jobs:
           no_output_timeout: 2h
           command: |
             docker run -ti --rm=false \
+              -v /tmp/data:/tmp/data \
+              -e FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
+              -e FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
               --entrypoint="py.test" poldracklab/fmriprep:latest \
               /root/src/fmriprep/ --doctest-modules --ignore=docs --ignore=setup.py
       - run:
@@ -665,6 +712,11 @@ workflows:
             tags:
               only: /.*/
 
+      - get_regression_data:
+          filters:
+            branches:
+              ignore: /docs?\/.*/
+
       - build_docs:
           requires:
             - build
@@ -684,6 +736,7 @@ workflows:
       - test_pytest:
           requires:
             - build
+            - get_regression_data
           filters:
             branches:
               ignore: /docs?\/.*/

.github/config.yml

@@ -0,0 +1,35 @@
+# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  Thanks for opening this pull request!
+  We have detected this is the first time for you to contribute
+  to *fMRIPrep*.
+  Please check out our [contributing guidelines](https://github.com/poldracklab/fmriprep/blob/master/CONTRIBUTING.md).
+  
+  We invite you to list yourself as a *fMRIPrep* contributor, so if your name
+  is not already mentioned, please modify the
+  [``.zenodo.json``](https://github.com/poldracklab/fmriprep/blob/master/.zenodo.json)
+  file with your data right above Russ' entry. Example:
+
+  ```
+
+  {
+     "name": "Contributor, New FMRIPrep",
+     "affiliation": "Department of fMRI prep'ing, Open Science Made-Up University",
+     "orcid": "<your id>"
+  },
+
+  {
+     "name": "Poldrack, Russell A.",
+     "affiliation": "Department of Psychology, Stanford University",
+     "orcid": "0000-0001-6755-0259"
+  },
+
+  ```
+
+
+  Of course, if you want to opt-out this time there is no
+  problem at all with adding your name later.
+  You will be always welcome to add it in the future whenever
+  you feel it should be listed.

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.pytest_cache/
 
 # C extensions
 *.so

Dockerfile

@@ -164,6 +164,10 @@ RUN echo "${VERSION}" > /root/src/fmriprep/fmriprep/VERSION && \
     pip install .[all] && \
     rm -rf ~/.cache/pip
 
+RUN install -m 0755 \
+    /root/src/fmriprep/scripts/generate_reference_mask.py \
+    /usr/local/bin/generate_reference_mask
+
 RUN ldconfig
 WORKDIR /tmp/
 ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]

docs/installation.rst

@@ -136,7 +136,7 @@ If the data to be preprocessed is also on the HPC, you are ready to run fmriprep
         --omp-nthreads 16
 
 
-    or, unset the ``PYTHONPATH`` variable before running: ::
+   or, unset the ``PYTHONPATH`` variable before running: ::
 
       $ unset PYTHONPATH; singularity run ~/poldracklab_fmriprep_latest-2016-12-04-5b74ad9a4c4d.img \
         /work/04168/asdf/lonestar/ $WORK/lonestar/output \

fmriprep/workflows/bold/tests/__init__.py

@@ -0,0 +1,56 @@
+''' Testing module for fmriprep.workflows.bold.util '''
+import pytest
+import os
+
+import numpy as np
+from nipype.utils.filemanip import fname_presuffix
+from nilearn.image import load_img
+from ..util import init_bold_reference_wf
+
+
+def symmetric_overlap(img1, img2):
+    mask1 = load_img(img1).get_data() > 0
+    mask2 = load_img(img2).get_data() > 0
+
+    total1 = np.sum(mask1)
+    total2 = np.sum(mask2)
+    overlap = np.sum(mask1 & mask2)
+    return overlap / np.sqrt(total1 * total2)
+
+
+@pytest.mark.skipif(not os.getenv('FMRIPREP_REGRESSION_SOURCE') or
+                    not os.getenv('FMRIPREP_REGRESSION_TARGETS'),
+                    reason='FMRIPREP_REGRESSION_{SOURCE,TARGETS} env vars not set')
+@pytest.mark.parametrize('input_fname,expected_fname', [
+    (os.path.join(os.getenv('FMRIPREP_REGRESSION_SOURCE', ''),
+                  base_fname),
+     fname_presuffix(base_fname, suffix='_mask', use_ext=True,
+                     newpath=os.path.join(
+                         os.getenv('FMRIPREP_REGRESSION_TARGETS', ''),
+                         os.path.dirname(base_fname))))
+    for base_fname in (
+        'ds000116/sub-12_task-visualoddballwithbuttonresponsetotargetstimuli_run-02_bold.nii.gz',
+        'ds000133/sub-06_ses-post_task-rest_run-01_bold.nii.gz',
+        'ds000140/sub-32_task-heatpainwithregulationandratings_run-02_bold.nii.gz',
+        'ds000157/sub-23_task-passiveimageviewing_bold.nii.gz',
+        'ds000210/sub-06_task-rest_run-01_echo-1_bold.nii.gz',
+        'ds000210/sub-06_task-rest_run-01_echo-2_bold.nii.gz',
+        'ds000210/sub-06_task-rest_run-01_echo-3_bold.nii.gz',
+        'ds000216/sub-03_task-rest_echo-1_bold.nii.gz',
+        'ds000216/sub-03_task-rest_echo-2_bold.nii.gz',
+        'ds000216/sub-03_task-rest_echo-3_bold.nii.gz',
+        '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',
+        )
+    ])
+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
+    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)
+
+    assert overlap > 0.95, input_fname

fmriprep/workflows/bold/tests/test_util.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+import sys
+from nipype.pipeline import engine as pe
+from nipype.interfaces import utility as niu
+from fmriprep.workflows.bold.util import init_bold_reference_wf
+
+
+def sink_mask_file(in_file, orig_file, out_dir):
+    import os
+    from nipype.utils.filemanip import fname_presuffix, copyfile
+    os.makedirs(out_dir, exist_ok=True)
+    out_file = fname_presuffix(orig_file, suffix='_mask', newpath=out_dir)
+    copyfile(in_file, out_file, copy=True, use_hardlink=True)
+    return out_file
+
+
+def init_main_wf(bold_file, out_dir, base_dir=None, name='main_wf'):
+    wf = init_bold_reference_wf(enhance_t2=True,
+                                omp_nthreads=4,
+                                name=name)
+    wf.base_dir = base_dir
+    wf.inputs.inputnode.bold_file = bold_file
+
+    sink = pe.Node(niu.Function(function=sink_mask_file),
+                   name='sink')
+    sink.inputs.out_dir = out_dir
+    sink.inputs.orig_file = bold_file
+    wf.connect([
+        (wf.get_node('outputnode'), sink, [('bold_mask', 'in_file')]),
+        ])
+    return wf
+
+
+def main():
+    main_wf = init_main_wf(sys.argv[1], sys.argv[2])
+    main_wf.run(plugin='MultiProc')
+
+
+if __name__ == '__main__':
+    main()