Merge pull request #1445 from oesteban/docs/update-natmeth-references

[MAINT/DOC] Clean-up ``__about__``, update with Nat Meth

Author: oesteban

docs/citing.rst

@@ -149,11 +149,11 @@ we recommend to include in your paper.
    <p>
      1. Esteban O, Markiewicz CJ, Blair RW, Moodie CA, Isik AI, Erramuzpe A, Kent JD, Goncalves M,
         DuPre E, Snyder M, Oya H, Ghosh SS, Wright J, Durnez J, Poldrack RA, Gorgolewski KJ.
-        FMRIPrep: a robust preprocessing pipeline for functional MRI.
-        bioRxiv. 2018. 306951; doi:<a href="https://doi.org/10.1101/306951">10.1101/306951</a>
+        fMRIPrep: a robust preprocessing pipeline for functional MRI.
+        Nat Meth. 2018; doi:<a href="https://doi.org/10.1038/s41592-018-0235-4">10.1038/s41592-018-0235-4</a>
    </p>
    <p>
-     2. <span id="fmriprep_citation">FMRIPREP</span> Available from: <a id="fmriprep_doi_url" href="https://doi.org/10.5281/zenodo.852659">10.5281/zenodo.852659</a>.
+     2. <span id="fmriprep_citation">fMRIPrep</span> Available from: <a id="fmriprep_doi_url" href="https://doi.org/10.5281/zenodo.852659">10.5281/zenodo.852659</a>.
      <img src onerror='fillCitation()' alt="" />
    </p>
    <p>

docs/environment.yml

@@ -29,5 +29,5 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows==0.5.1
+    - niworkflows>=0.5.1,<0.5.2
     - tedana>=0.0.5

fmriprep/__about__.py

@@ -4,42 +4,41 @@
 """
 Base module variables
 """
-
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
 
 __author__ = 'The CRN developers'
 __copyright__ = 'Copyright 2018, Center for Reproducible Neuroscience, Stanford University'
-__credits__ = ['Craig Moodie', 'Ross Blair', 'Oscar Esteban', 'Chris Gorgolewski',
-               'Shoshana Berleant', 'Christopher J. Markiewicz', 'Russell A. Poldrack']
+__credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder'
+               'of the repository')
 __license__ = '3-clause BSD'
-__maintainer__ = 'Ross Blair'
-__email__ = '[email protected]'
+__maintainer__ = 'Oscar Esteban'
+__email__ = '[email protected]'
 __status__ = 'Prototype'
 __url__ = 'https://github.com/poldracklab/fmriprep'
 __packagename__ = 'fmriprep'
-__description__ = ("FMRIprep is a functional magnetic resonance image pre-processing pipeline "
-                   "that is designed to provide an easily accessible, state-of-the-art interface "
-                   "that is robust to differences in scan acquisition protocols and that requires "
-                   "minimal user input, while providing easily interpretable and comprehensive "
-                   "error and output reporting.")
+__description__ = """\
+fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data.
+The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility
+of the results"""
 __longdesc__ = """\
 Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize
-data before statistical analysis.
-Generally, researchers create ad hoc preprocessing workflows for each new dataset,
-building upon a large inventory of tools available for each step.
-The complexity of these workflows has snowballed with rapid advances in MR data
-acquisition and image processing techniques.
-FMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and
+the data before statistical analysis.
+Generally, researchers create ad hoc preprocessing workflows for each dataset,
+building upon a large inventory of available tools.
+The complexity of these workflows has snowballed with rapid advances in
+acquisition and processing.
+fMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and
 reproducible preprocessing for task-based and resting fMRI data.
-FMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of
-virtually any dataset, ensuring high-quality preprocessing with no manual intervention,
-while providing easily interpretable and comprehensive error and output reporting.
-It performs basic preprocessing steps (coregistration, normalization, unwarping, noise
-component extraction, segmentation, skullstripping etc.) providing outputs that can be
-easily submitted to a variety of group level analyses, including task-based or resting-state
-fMRI, graph theory measures, surface or volume-based statistics, etc.
+fMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of
+virtually any dataset, ensuring high-quality preprocessing without manual intervention.
+fMRIPrep robustly produces high-quality results on diverse fMRI data.
+Additionally, fMRIPrep introduces less uncontrolled spatial smoothness than observed
+with commonly used preprocessing tools.
+fMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing
+workflow, which can help ensure the validity of inference and the interpretability
+of results.
 
 The workflow is based on `Nipype <https://nipype.readthedocs.io>`_ and encompases a large
 set of tools from well-known neuroimaging packages, including
@@ -52,7 +51,11 @@
 preprocessing, and will be updated as newer and better neuroimaging software becomes
 available.
 
-This tool allows you to easily do the following:
+fMRIPrep performs basic preprocessing steps (coregistration, normalization, unwarping, noise
+component extraction, segmentation, skullstripping etc.) providing outputs that can be
+easily submitted to a variety of group level analyses, including task-based or resting-state
+fMRI, graph theory measures, surface or volume-based statistics, etc.
+fMRIPrep allows you to easily do the following:
 
   * Take fMRI data from *unprocessed* (only reconstructed) to ready for analysis.
   * Implement tools from different software packages.
@@ -63,11 +66,7 @@
   * Automate and parallelize processing steps, which provides a significant speed-up from
     typical linear, manual processing.
 
-FMRIPrep has the potential to transform fMRI research by equipping
-neuroscientists with a high-quality, robust, easy-to-use and transparent preprocessing workflow
-which can help ensure the validity of inference and the interpretability of their results.
-
-[Pre-print doi:`10.1101/306951 <https://doi.org/10.1101/306951>`_]
+[Nat Meth doi:`10.1038/s41592-018-0235-4 <https://doi.org/10.1038/s41592-018-0235-4>`_]
 [Documentation `fmriprep.org <https://fmriprep.readthedocs.io>`_]
 [Software doi:`10.5281/zenodo.852659 <https://doi.org/10.5281/zenodo.852659>`_]
 [Support `neurostars.org <https://neurostars.org/tags/fmriprep>`_]
@@ -85,53 +84,46 @@
 ]
 
 REQUIRES = [
-    'numpy',
-    'lockfile',
-    'future',
-    'scikit-learn',
-    'matplotlib>=2.2.0',
-    'nilearn',
-    'sklearn',
+    'grabbit==0.2.3',
+    'indexed_gzip>=0.8.8',
     'nibabel>=2.2.1',
+    'nilearn',
+    'nipype>=1.1.6',
+    'nitime',
+    'niworkflows>=0.5.1,<0.5.2',
+    'numpy',
     'pandas',
-    'grabbit==0.2.3',
     'pybids==0.6.5',
-    'nitime',
-    'nipype>=1.1.6',
-    'niworkflows==0.5.1',
-    'tedana>=0.0.5',
-    'statsmodels',
-    'seaborn',
-    'indexed_gzip>=0.8.8',
-    'scikit-image',
-    'versioneer',
     'pyyaml',
+    'scikit-image',
+    'statsmodels',
+    'tedana>=0.0.5',
 ]
 
+
 LINKS_REQUIRES = [
 ]
 
 TESTS_REQUIRES = [
-    "mock",
     "codecov",
     "pytest",
 ]
 
 EXTRA_REQUIRES = {
+    'datalad': ['datalad'],
     'doc': [
+        'nbsphinx',
+        'packaging',
+        'pydot>=1.2.3',
+        'pydotplus',
         'sphinx>=1.5.3',
-        'sphinx_rtd_theme',
         'sphinx-argparse',
-        'pydotplus',
-        'pydot>=1.2.3',
-        'packaging',
-        'nbsphinx',
+        'sphinx_rtd_theme',
     ],
-    'tests': TESTS_REQUIRES,
     'duecredit': ['duecredit'],
-    'datalad': ['datalad'],
     'resmon': ['psutil>=5.4.0'],
     'sentry': ['sentry-sdk>=0.5.3'],
+    'tests': TESTS_REQUIRES,
 }
 EXTRA_REQUIRES['docs'] = EXTRA_REQUIRES['doc']
 

fmriprep/data/boilerplate.bib

@@ -1,14 +1,14 @@
 @article{fmriprep1,
     author = {Esteban, Oscar and Markiewicz, Christopher and Blair, Ross W and Moodie, Craig and Isik, Ayse Ilkay and Erramuzpe Aliaga, Asier and Kent, James and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit and Wright, Jessey and Durnez, Joke and Poldrack, Russell and Gorgolewski, Krzysztof Jacek},
-    title = {FMRIPrep: a robust preprocessing pipeline for functional {MRI}},
+    title = {{fMRIPrep}: a robust preprocessing pipeline for functional {MRI}},
     year = {2018},
-    doi = {10.1101/306951},
-    journal = {bioRxiv}
+    doi = {10.1038/s41592-018-0235-4},
+    journal = {Nature Methods}
 }
 
 @article{fmriprep2,
     author = {Esteban, Oscar and Blair, Ross and Markiewicz, Christopher J. and Berleant, Shoshana L. and Moodie, Craig and Ma, Feilong and Isik, Ayse Ilkay and Erramuzpe, Asier and Kent, James D. andGoncalves, Mathias and DuPre, Elizabeth and Sitek, Kevin R. and Gomez, Daniel E. P. and Lurie, Daniel J. and Ye, Zhifang and Poldrack, Russell A. and Gorgolewski, Krzysztof J.},
-    title = {FMRIPrep},
+    title = {fMRIPrep},
     year = 2018,
     doi = {10.5281/zenodo.852659},
     publisher = {Zenodo},

fmriprep/utils/bids.py

@@ -85,7 +85,7 @@ def collect_participants(bids_dir, participant_label=None, strict=False):
         raise BIDSError(
             'Could not find participants. Please make sure the BIDS data '
             'structure is present and correct. Datasets can be validated online '
-            'using the BIDS Validator (http://incf.github.io/bids-validator/).\n'
+            'using the BIDS Validator (http://bids-standard.github.io/bids-validator/).\n'
             'If you are using Docker for Mac or Docker for Windows, you '
             'may need to adjust your "File sharing" preferences.', bids_dir)
 
@@ -210,13 +210,13 @@ def write_derivative_description(bids_dir, deriv_dir):
             'Name': 'fMRIPrep',
             'Version': __version__,
             'CodeURL': DOWNLOAD_URL,
-            },
+        },
         'CodeURL': 'https://github.com/poldracklab/fmriprep',
         'HowToAcknowledge':
-            'Please cite our paper (https://doi.org/10.1101/306951), and '
-            'include the generated citation boilerplate within the Methods '
+            'Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4), '
+            'and include the generated citation boilerplate within the Methods '
             'section of the text.',
-        }
+    }
 
     # Keys that can only be set by environment
     if 'FMRIPREP_DOCKER_TAG' in os.environ:
@@ -239,7 +239,7 @@ def write_derivative_description(bids_dir, deriv_dir):
 
     if 'DatasetDOI' in orig_desc:
         desc['SourceDatasetsURLs'] = ['https://doi.org/{}'.format(
-                                          orig_desc['DatasetDOI'])]
+            orig_desc['DatasetDOI'])]
     if 'License' in orig_desc:
         desc['License'] = orig_desc['License']
 

requirements.txt

@@ -1,4 +1,4 @@
-niworkflows==0.5.1
+niworkflows>=0.5.1,<0.5.2
 grabbit==0.2.3
 pybids==0.6.5
 versioneer