Merge branch 'enh/write-deriv-metadata' of github.com:oesteban/fmriprep into enh/write-deriv-metadata

Author: oesteban

.zenodo.json

@@ -1,4 +1,6 @@
 {
+  "title": "fMRIPrep: a robust preprocessing pipeline for functional MRI",
+  "description": "<p>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.</p>",
   "creators": [
     {
       "name": "Esteban, Oscar",
@@ -14,104 +16,124 @@
       "affiliation": "Department of Psychology, Stanford University",
       "orcid": "0000-0002-6533-164X"
     },
+    {
+      "name": "Poldrack, Russell A.",
+      "affiliation": "Department of Psychology, Stanford University",
+      "orcid": "0000-0001-6755-0259"
+    },
+    {
+      "name": "Gorgolewski, Krzysztof J.",
+      "affiliation": "Department of Psychology, Stanford University",
+      "orcid": "0000-0003-3321-7583"
+    }
+  ],
+  "contributors": [
     {
       "name": "Berleant, Shoshana L.",
-      "affiliation": "Department of Psychology, Stanford University"
+      "affiliation": "Department of Psychology, Stanford University",
+      "type": "Researcher"
     },
     {
       "name": "Moodie, Craig",
       "affiliation": "Stanford University",
-      "orcid": "0000-0003-0867-1469"
+      "orcid": "0000-0003-0867-1469",
+      "type": "Researcher"
     },
     {
       "name": "Ma, Feilong",
       "affiliation": "Dartmouth College",
-      "orcid": "0000-0002-6838-3971"
+      "orcid": "0000-0002-6838-3971",
+      "type": "Researcher"
     },
     {
       "name": "Isik, Ayse Ilkay",
       "affiliation": "Max Planck Institute for Empirical Aesthetics",
-      "orcid": "0000-0002-1652-9297"
+      "orcid": "0000-0002-1652-9297",
+      "type": "Researcher"
     },
     {
       "name": "Erramuzpe, Asier",
       "affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
-      "orcid": "0000-0002-9402-2184"
+      "orcid": "0000-0002-9402-2184",
+      "type": "Researcher"
     },
     {
       "name": "Kent, James D.",
       "affiliation": "Neuroscience Program, University of Iowa",
-      "orcid": "0000-0002-4892-2659"
+      "orcid": "0000-0002-4892-2659",
+      "type": "Researcher"
     },
     {
       "name": "Goncalves, Mathias",
       "affiliation": "MIT",
-      "orcid": "0000-0002-7252-7771"
+      "orcid": "0000-0002-7252-7771",
+      "type": "Researcher"
     },
     {
       "name": "DuPre, Elizabeth",
       "affiliation": "Montreal Neurological Institute, McGill University",
-      "orcid": "0000-0003-1358-196X"
+      "orcid": "0000-0003-1358-196X",
+      "type": "Researcher"
     },
     {
       "name": "Sitek, Kevin R.",
       "affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
-      "orcid": "0000-0002-2172-5786"
+      "orcid": "0000-0002-2172-5786",
+      "type": "Researcher"
     },
     {
       "name": "Gomez, Daniel E. P.",
       "affiliation": "Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen",
-      "orcid": "0000-0001-8635-021X"
+      "orcid": "0000-0001-8635-021X",
+      "type": "Researcher"
     },
     {
       "name": "Lurie, Daniel J.",
       "affiliation": "Department of Psychology, University of California, Berkeley",
-      "orcid": "0000-0001-8012-6399"
+      "orcid": "0000-0001-8012-6399",
+      "type": "Researcher"
     },
     {
       "name": "Ye, Zhifang",
       "affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University",
-      "orcid": "0000-0003-0489-2619"
+      "orcid": "0000-0003-0489-2619",
+      "type": "Researcher"
     },
     {
       "name": "Salo, Taylor",
       "affiliation": "Department of Psychology, Florida International University",
-      "orcid": "0000-0001-9813-3167"
+      "orcid": "0000-0001-9813-3167",
+      "type": "Researcher"
     },
     {
       "name": "Valabregue, Romain",
       "affiliation": "Cenir, ICM, Paris",
-      "orcid": "0000-0002-1814-9570"
+      "orcid": "0000-0002-1814-9570",
+      "type": "Researcher"
     },
     {
       "name": "Amlien, Inge K.",
       "affiliation": "Department of Psychology, University of Oslo",
-      "orcid": "0000-0002-8508-9088"
+      "orcid": "0000-0002-8508-9088",
+      "type": "Researcher"
     },
     {
       "name": "Liem, Franz",
       "affiliation": "University of Zurich",
-      "orcid": "0000-0003-0646-4810"
+      "orcid": "0000-0003-0646-4810",
+      "type": "Researcher"
     },
     {
       "name": "Jacoby, Nir",
       "affiliation": "Department of Psychology, Columbia University",
-      "orcid": "0000-0001-7936-9991"
+      "orcid": "0000-0001-7936-9991",
+      "type": "Researcher"
     },
     {
       "name": "Stojic, Hrvoje",
       "affiliation": "University College London",
-      "orcid": "0000-0002-9699-9052"
-    },
-    {
-      "name": "Poldrack, Russell A.",
-      "affiliation": "Department of Psychology, Stanford University",
-      "orcid": "0000-0001-6755-0259"
-    },
-    {
-      "name": "Gorgolewski, Krzysztof J.",
-      "affiliation": "Department of Psychology, Stanford University",
-      "orcid": "0000-0003-3321-7583"
+      "orcid": "0000-0002-9699-9052",
+      "type": "Researcher"
     }
   ],
   "keywords": [
@@ -122,6 +144,18 @@
     "fMRI",
     "BIDS"
   ],
+  "related_identifiers": [
+    {
+      "identifier": "https://fmriprep.org",
+      "relation": "documents",
+      "scheme": "url"
+    },
+    {
+      "identifier": "10.1038/s41592-018-0235-4",
+      "relation": "isPartOf",
+      "scheme": "doi"
+    }
+  ],
   "license": "BSD-3-Clause",
   "upload_type": "software"
 }

CHANGES.rst

@@ -1,3 +1,16 @@
+1.3.1.post2 (March 13, 2019)
+============================
+
+A hotfix release addressing issues related to TemplateFlow for Singularity users, via pinning templateflow>=0.1.2.
+
+1.3.1.post1 (March 11, 2019)
+============================
+
+A hotfix release addressing issues related to TemplateFlow for Singularity users.
+
+* FIX: Make sure ``--cifti-output`` requires at least one of ``fsaverage{5,6}`` (#1514) @oesteban
+* [FIX] Avoid using ``$HOME`` for storing templates (#1529) @chrisfilo
+
 1.3.1 (March 6, 2019)
 =====================
 

Dockerfile

@@ -160,6 +160,8 @@ RUN python -c "from matplotlib import font_manager" && \
     sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
 
 # Precaching atlases
+ENV TEMPLATEFLOW_HOME="/opt/templateflow"
+RUN mkdir -p $TEMPLATEFLOW_HOME
 RUN pip install --no-cache-dir "templateflow>=0.1.3,<0.2.0a0" && \
     python -c "from templateflow import api as tfapi; \
                tfapi.get('MNI152Lin'); \

requirements.txt

@@ -1,2 +1,3 @@
 git+https://github.com/poldracklab/niworkflows.git@93eb80e1b920d1dfbfee42cbec3b2fc2fc31b2d0#egg=niworkflows-0.8.0
 git+https://github.com/oesteban/smriprep.git@be809a79d87d906c513730634d51cb196a01297b#egg=smriprep-0.1.0
+templateflow<0.2.0a0,>=0.1.3