Merge remote-tracking branch 'upstream/master' into rf/upstream_tshift

Author: oesteban

.circleci/config.yml

@@ -202,9 +202,8 @@ jobs:
           no_output_timeout: 2h
           command: |
             docker run -ti --rm=false \
-              --entrypoint="/usr/local/miniconda/bin/py.test" \
-              poldracklab/fmriprep:latest . \
-              --doctest-modules --ignore=docs --ignore=setup.py
+              --entrypoint="py.test" poldracklab/fmriprep:latest \
+              /root/src/fmriprep/ --doctest-modules --ignore=docs --ignore=setup.py
       - run:
           name: Test fmriprep-wrapper (Python 2)
           command: |
@@ -268,7 +267,7 @@ jobs:
             docker run -ti --rm=false -v $PWD:/_build_html \
               --entrypoint=sphinx-build poldracklab/fmriprep:latest \
               -T -E -b html -d _build/doctrees-readthedocs -W -D \
-              language=en docs/ /_build_html 2>&1 \
+              language=en /root/src/fmriprep/docs/ /_build_html 2>&1 \
               | tee $PWD/builddocs.log
             cat $PWD/builddocs.log
             grep -qv "ERROR" $PWD/builddocs.log
@@ -327,7 +326,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --debug --write-graph --mem_mb 4096 \
@@ -347,7 +346,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --debug --write-graph --use-syn-sdc --mem_mb 4096 \
@@ -374,7 +373,7 @@ jobs:
           command: |
             rm /tmp/data/ds005/sub-01/func/*_run-02_*
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
                 --debug --write-graph --use-syn-sdc --mem_mb 4096 \

.circleci/ds005_outputs.txt

@@ -1,5 +1,8 @@
 fmriprep
 fmriprep/logs
+fmriprep/logs/CITATION.html
+fmriprep/logs/CITATION.md
+fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/anat
 fmriprep/sub-01/anat/sub-01_T1w_brainmask.nii.gz

.circleci/ds005_partial_outputs.txt

@@ -1,5 +1,8 @@
 fmriprep
 fmriprep/logs
+fmriprep/logs/CITATION.html
+fmriprep/logs/CITATION.md
+fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/anat
 fmriprep/sub-01/anat/sub-01_T1w_brainmask.nii.gz

.circleci/ds054_outputs.txt

@@ -1,5 +1,8 @@
 fmriprep
 fmriprep/logs
+fmriprep/logs/CITATION.html
+fmriprep/logs/CITATION.md
+fmriprep/logs/CITATION.tex
 fmriprep/sub-100185
 fmriprep/sub-100185/anat
 fmriprep/sub-100185/anat/sub-100185_T1w_brainmask.nii.gz

.circleci/ds210_outputs.txt

@@ -1,5 +1,8 @@
 fmriprep
 fmriprep/logs
+fmriprep/logs/CITATION.html
+fmriprep/logs/CITATION.md
+fmriprep/logs/CITATION.tex
 fmriprep/sub-02
 fmriprep/sub-02/anat
 fmriprep/sub-02/anat/sub-02_T1w_brainmask.nii.gz

CHANGES.rst

@@ -1,3 +1,15 @@
+1.1.2 (July 6, 2018)
+====================
+
+This release incorporates Nipype improvements that should reduce the
+chance of hanging if tasks are killed for excessive resource consumption.
+
+Thanks to Elizabeth DuPre for documentation updates.
+
+* [DOC] Clarify how to reuse FreeSurfer derivatives (#1189)
+* [DOC] Improve command line option documentation (#1186, #1080)
+* [MAINT] Update core dependencies (#1179, #1180)
+
 1.1.1 (June 7, 2018)
 ====================
 

CONTRIBUTING.md

@@ -1,6 +1,8 @@
-# Contributing to FMRIPREP
+# Contributing to fMRIPrep
 
-Welcome to the FMRIPREP repository! We're excited you're here and want to contribute.  
+Welcome to the fMRIPrep repository! We're excited you're here and want to contribute.
+
+## Practical guide to submitting your contribution
 
 These guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know by opening an [issue][link_issues]!
 
@@ -30,7 +32,9 @@ We appreciate all contributions to FMRIPREP, but those accepted fastest will fol
 
 **1. Comment on an existing issue or open a new issue referencing your addition.**
 
-This allows other members of the FMRIPREP development team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
+This allows other members of the FMRIPREP development team to confirm that you aren't 
+overlapping with work that's currently underway and that everyone is on the same page
+with the goal of the work you're going to carry out.
 
 [This blog][link_pushpullblog] is a nice explanation of why putting this work in up front is so useful to everyone involved.
 

Dockerfile

@@ -113,7 +113,7 @@ RUN conda install -y mkl=2018.0.3 mkl-service;  sync &&\
                      matplotlib=2.2.0 \
                      pandas=0.23.0 \
                      libxml2=2.9.4 \
-                     libxslt=1.1.29\
+                     libxslt=1.1.29 \
                      traits=4.6.0; sync &&  \
     chmod -R a+rX /usr/local/miniconda; sync && \
     chmod +x /usr/local/miniconda/bin/*; sync && \
@@ -131,6 +131,11 @@ RUN apt-get update && \
                     graphviz=2.38.0-12ubuntu2 && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+# Install latest pandoc
+RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
+    dpkg -i pandoc-2.2.2.1-1-amd64.deb && \
+    rm pandoc-2.2.2.1-1-amd64.deb
+
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
@@ -160,9 +165,7 @@ RUN echo "${VERSION}" > /root/src/fmriprep/fmriprep/VERSION && \
     rm -rf ~/.cache/pip
 
 RUN ldconfig
-
-WORKDIR /root/src/fmriprep
-
+WORKDIR /tmp/
 ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]
 
 ARG BUILD_DATE
@@ -171,8 +174,9 @@ ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="FMRIPREP" \
       org.label-schema.description="FMRIPREP - robust fMRI preprocessing tool" \
-      org.label-schema.url="http://fmriprep.readthedocs.io" \
+      org.label-schema.url="http://fmriprep.org" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/poldracklab/fmriprep" \
       org.label-schema.version=$VERSION \
       org.label-schema.schema-version="1.0"
+

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2017, the CRN developers team.
+Copyright (c) 2015-2018, the CRN developers team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -90,6 +90,30 @@ Principles
    the process and decide which subjects should be kept for the group level
    analysis.
 
+
+Limitations and reasons not to use ``fmriprep``
+-----------------------------------------------
+
+1. Very narrow :abbr:`FoV (field-of-view)` images oftentimes do not contain
+   enough information for standard image registration methods to work correctly.
+   Also, problems may arise when extracting the brain from these data.
+   Supporting these particular images is already a future line of the development
+   road-map.
+2. ``fmriprep`` may also underperform for particular populations (e.g. infants) and
+   non-human brains, although appropriate templates can be provided to overcome the
+   issue.
+3. The "EPInorm" approach is currently not supported, although we plan to implement
+   this feature (see `#857 <https://github.com/poldracklab/fmriprep/issues/857>`_).
+4. If you really want unlimited flexibility (which is obviously a double-edged sword).
+5. If you want students to suffer through implementing each step for didactic purposes,
+   or to learn shell-scripting or Python along the way.
+6. If you are trying to reproduce some *in-house* lab pipeline.
+
+(Reasons 4-6 were kindly provided by S. Nastase in his
+`open review <http://academickarma.org/review/j7d5501n779n>`__
+of our `pre-print <https://www.biorxiv.org/content/early/2018/05/06/306951>`__).
+
+
 Acknowledgements
 ----------------