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Added grad_dev input to BEDPOSTX5 interface
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‎.gitignore‎

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/nipype/build
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/nipype/nipype.egg-info
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/doc/_build
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/doc/preproc
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/doc/users/examples
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/doc/api/generated
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*.pyc
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.DS_Store
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nipype/testing/data/von-ray_errmap.nii.gz
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nipype/testing/data/von_errmap.nii.gz
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crash*.pklz
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.coverage
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htmlcov/
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__pycache__/
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*~
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.ipynb_checkpoints/
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.ruby-version

‎.noserc‎

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[nosetests]
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verbosity=3
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with-coverage=1
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cover-branches=1
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cover-xml=1
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cover-xml-file=./coverage.xml
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cover-min-percentage=50
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with-xunit=1

‎.travis.yml‎

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language: python
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python:
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- 2.7
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- 3.4
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- 3.5
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env:
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- INSTALL_DEB_DEPENDECIES=true
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- INSTALL_DEB_DEPENDECIES=false
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before_install:
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
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-O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.6.0-Linux-x86_64.sh
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
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-O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
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-O miniconda.sh; fi
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- chmod +x miniconda.sh
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- "./miniconda.sh -b"
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- export PATH=/home/travis/miniconda/bin:$PATH
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=/home/travis/miniconda2/bin:$PATH; else export PATH=/home/travis/miniconda3/bin:$PATH; fi
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- if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi
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- if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi
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- if $INSTALL_DEB_DEPENDECIES; then bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
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fi
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- bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
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- sudo apt-get update
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- sudo apt-get install xvfb
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- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq --no-install-recommends
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fsl afni elastix; fi
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- if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases;
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fi
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- if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
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- if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
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- export FSLOUTPUTTYPE=NIFTI_GZ
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# Install vtk and fix numpy installation problem
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# Fix numpy problem: https://github.com/enthought/enable/issues/34#issuecomment-2029381
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then travis_retry sudo apt-get install -qq libx11-dev swig;
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echo '[x11]' >> $HOME/.numpy-site.cfg;
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echo 'library_dirs = /usr/lib64:/usr/lib:/usr/lib/x86_64-linux-gnu' >> $HOME/.numpy-site.cfg;
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echo 'include_dirs = /usr/include:/usr/include/X11' >> $HOME/.numpy-site.cfg;
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fi
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install:
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- sudo apt-get install fusefat
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- conda update --yes conda
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- conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
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- source activate testenv
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi
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- conda install --yes numpy scipy nose traits networkx dateutil
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- pip install nibabel
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- conda install --yes numpy scipy nose networkx python-dateutil
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi
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- pip install python-coveralls
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- pip install nose-cov
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- pip install https://github.com/RDFLib/rdflib/archive/master.zip
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- pip install https://github.com/trungdong/prov/archive/rdf.zip
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# Add tvtk (PIL is required by blockcanvas)
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# Install mayavi (see https://github.com/enthought/mayavi/issues/271)
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- if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
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pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz;
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pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools;
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pip install -e git+https://github.com/enthought/blockcanvas.git#egg=blockcanvas;
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pip install -e git+https://github.com/enthought/etsproxy.git#egg=etsproxy;
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pip install https://github.com/dmsurti/mayavi/archive/4d4aaf315a29d6a86707dd95149e27d9ed2225bf.zip;
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pip install -e git+https://github.com/enthought/ets.git#egg=ets;
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fi
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- pip install -r requirements.txt # finish remaining requirements
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- python setup.py install
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script:
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- nosetests --with-doctest --with-cov --cov nipype --cov-config .coveragerc --logging-level=INFO
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- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=DEBUG --verbosity=3
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after_success:
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- coveralls --config_file .coveragerc
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deploy:

‎CHANGES‎

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Next Release
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Release 0.12.0-rc1 (April 20, 2016)
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============
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* ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
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* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
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* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
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* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
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* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
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* FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
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* FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
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* ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
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(https://github.com/nipy/nipype/pull/1090)
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* ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,
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https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
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* ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
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* ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
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* ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
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* TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
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* ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
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* ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
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* FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
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* FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
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* ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
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* FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
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* ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
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* ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
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* API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
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* ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
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* ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
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* FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
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* FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
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* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
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* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
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* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
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* ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
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(https://github.com/nipy/nipype/pull/1460)
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Release 0.11.0 (September 15, 2015)
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============
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‎CONTRIBUTING.md‎

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2020
When opening a new Issue, please take the following steps:
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1. Search GitHub and/or [Neurostars](neurostars.org) for your issue to avoid duplicate reports.
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1. Search GitHub and/or [Neurostars](http://neurostars.org) for your issue to avoid duplicate reports.
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Keyword searches for your error messages are most helpful.
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2. If possible, try updating to master and reproducing your issue,
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because we may have already fixed it.

‎LICENSE‎

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Copyright (c) 2009-2014, NIPY Developers
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All rights reserved.
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Copyright (c) 2009-2016, Nipype developers
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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http://www.apache.org/licenses/LICENSE-2.0
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* Redistributions in binary form must reproduce the above
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copyright notice, this list of conditions and the following
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disclaimer in the documentation and/or other materials provided
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with the distribution.
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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* Neither the name of the NIPY Developers nor the names of any
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contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Prior to release 0.12, Nipype was licensed under a BSD license.

‎Makefile‎

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python setup.py sdist
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@echo "Done building source distribution."
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# XXX copy documentation.zip to dist directory.
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# XXX Somewhere the doc/_build directory is removed and causes
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# this script to fail.
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egg: zipdoc
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@echo "Building egg..."
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clean-ctags:
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rm -f tags
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clean: clean-build clean-pyc clean-so clean-ctags
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clean-doc:
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rm -rf doc/_build
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clean: clean-build clean-pyc clean-so clean-ctags clean-doc
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in: inplace # just a shortcut
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inplace:
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html:
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@echo "building docs"
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make -C doc clean html
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make -C doc clean htmlonly
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specs:
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@echo "Checking specs and autogenerating spec tests"

‎README.rst‎

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:target: https://pypi.python.org/pypi/nipype/
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:alt: License
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.. image:: https://img.shields.io/badge/gitter-join%20chat%20%E2%86%92-brightgreen.svg?style=flat
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:target: http://gitter.im/nipy/nipype
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:alt: Chat
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Current neuroimaging software offer users an incredible opportunity to
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analyze data using a variety of different algorithms. However, this has
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resulted in a heterogeneous collection of specialized applications

‎THANKS.rst‎

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.. -*- mode: rst -*-
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Code contributors
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-----------------
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Contributors to Nipype include but are not limited to:
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.. hlist::
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* Aimi Watanabe
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* Alexander Schaefer
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* Alexandre Gramfort
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* Anisha Keshavan
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* Ariel Rokem
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* Ben Acland
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* Basile Pinsard
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* Brendan Moloney
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* Brian Cheung
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* Charl Linssen
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* Chris Filo Gorgolewski
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* Chris Steele
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* Christian Haselgrove
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* Christopher Burns
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* Cindee Madison
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* Claire Tarbert
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* Colin Buchanan
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* Daniel Ginsburg
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* Daniel Haehn
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* Daniel Margulies
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* Dav Clark
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* David Welch
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* Drew Erickson
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* Erik Kastman
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* Félix C. Morency
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* Gael Varoquaux
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* Hans Johnson
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* Janosch Linkersdörfer
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* Januzz
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* Jarrod Millman
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* Jeff Lai
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* Jessica Forbes
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* John Salvatore
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* Lijie Huang
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* Michael Hallquist
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* Michael Hanke
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* Michael Notter
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* Michael Waskom
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* Nolan Nichols
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* Oliver Hinds
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* Oscar Esteban
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* Rosalia Tungaraza
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* Satrajit Ghosh
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* Sharad Sikka
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* Stephan Gerhard
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* Erik Ziegler
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* Valentin Haenel
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* Xiangzhen Kong
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* Xu Wang
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* Yannick Schwartz
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* Yaroslav O. Halchenko
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See `Github contributors list <https://github.com/nipy/nipype/graphs/contributors>`__.
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For full most up to date list see `Ohloh <https://www.ohloh.net/p/nipype/contributors>`__.
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Funding
9+
-------
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Other contributors
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------------------
11+
Nipype is currently supported by `1R01EB020740-01A1 Nipype: Dataflows for Reproducible Biomedical Research <https://projectreporter.nih.gov/project_info_description.cfm?aid=9053094>`__.
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.. hlist::
13+
Satrajit Ghosh work on this project was partially funded by NIBIB `R03EB008673 <https://projectreporter.nih.gov/project_info_description.cfm?aid=7501200>`__ and by the `INCF <http://www.incf.org>`__ through a contract with TankThink Labs, LLC.
14+
Chris Burns was supported by NIMH grant `5R01MH081909-02 Continued Development and Maintenance of the Neuroimaging in Python Project <https://projectreporter.nih.gov/project_info_description.cfm?aid=7288112>`__. Hans Jonson was supported by
15+
`2 U54 EB005149 - 06 Core 2b Huntington's Disease - Driving Biological Project <http://projectreporter.nih.gov/project_info_description.cfm?aid=8153616>`__,
16+
`S10 RR023392 Enterprise Storage In A Collaborative Neuroimaging Environment <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718>`__,
17+
`R01 NS040068 Neurobiological Predictors of Huntington's Disease <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377>`__,
18+
and `UL1 TR000442 University of Iowa Clinical and Translational Science Program <http://projectreporter.nih.gov/project_info_description.cfm?aid=8467220>`__.
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* Matthew Brett
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* Michael Castelle
71-
* Philippe Ciuciu
72-
* Yann Cointepas
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* Mark D'Esposito
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* Susan Gabrieli
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* Brian Hawthorne
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* Tim Leslie
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* Fernando Perez
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* Tyler Perrachione
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* Jean-Baptiste Poline
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* Alexis Roche
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* Denis Riviere
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* Gretchen Reynolds
83-
* Jonathan Taylor
84-
* Bertrand Thirion
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* Bernjamin Thyreau
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* Mike Trumpis
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* Karl Young
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* Tom Waite
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We would also like to thank `JetBrains <http://www.jetbrains.com/>`__ for providing `Pycharm <http://www.jetbrains.com/pycharm/>`__ licenses.
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Funding
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-------
94-
Satrajit Ghosh work on this project was partially funded by NIBIB R03 EB008673 (PI: Ghosh and Whitfield-Gabrieli) and by the `INCF <http://www.incf.org>`__ through a contract with TankThink Labs, LLC.
95-
Chris Burns was supported by NIMH grant 5R01MH081909-02 (PI: Desposito). Hans Jonson was supported by
96-
`2 U54 EB005149 - 06 Core 2b Huntington's Disease - Driving Biological Project <http://projectreporter.nih.gov/project_info_description.cfm?aid=8153616&icde=16158743&ddparam=&ddvalue=&ddsub=&cr=18&csb=PT&cs=ASC>`__,
97-
`S10 RR023392 Enterprise Storage In A Collaborative Neuroimaging Environment <http://projectreporter.nih.gov/project_info_description.cfm?aid=7209718&icde=16158552&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__,
98-
`R01 NS040068 Neurobiological Predictors of Huntington's Disease <http://projectreporter.nih.gov/project_info_description.cfm?aid=6266377&icde=16158103>`__,
99-
and `UL1 TR000442 University of Iowa Clinical and Translational Science Program <http://projectreporter.nih.gov/project_info_description.cfm?aid=8467220&icde=16159156&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC>`__.
100-

‎Vagrantfile‎

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@@ -20,19 +20,20 @@ $script = <<SCRIPT
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# qconf -aattr queue slots "2, [neuro=3]" main.q
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# install anaconda
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wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
23+
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
2424
chmod +x miniconda.sh
2525
./miniconda.sh -b
26-
echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
26+
echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
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# install nipype dependencies
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$HOME/miniconda/bin/conda update --yes conda
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$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
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$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
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$HOME/miniconda/bin/pip install nibabel --use-mirrors
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$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
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$HOME/miniconda/bin/pip install https://github.com/trungdong/prov/archive/rdf.zip
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$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
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$HOME/miniconda3/bin/conda update --yes conda
30+
$HOME/miniconda3/bin/conda install --yes pip scipy nose networkx lxml future simplejson
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$HOME/miniconda3/bin/conda install --yes python-dateutil jupyter matplotlib
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$HOME/miniconda3/bin/pip install nibabel
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$HOME/miniconda3/bin/pip install prov
34+
$HOME/miniconda3/bin/pip install xvfbwrapper
35+
$HOME/miniconda3/bin/pip install traits
36+
$HOME/miniconda3/bin/pip install https://github.com/nipy/nipype/archive/master.zip
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SCRIPT
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Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|

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