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Merge pull request #327 from nipy/doc/rtd
DOC: readthedocs
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‎.gitignore

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.coverage
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*.egg-info/
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.idea/
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venvs/
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_build/

‎CHANGELOG.md

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### Fixed
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- TODO: fix: embedding issue (([#306][]))
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- TODO: ([#304][]) from mgxd/fix/queue
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- TODO: ([#301][]) from franklin-feingold/master
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- TODO: fix/queue
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- TODO: ([#293][]) from mgxd/multiecho
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- correctly handle the case when `outtype` of heuristic has "dicom"
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before '.nii.gz'. Previously would have lead to absent additional metadata
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extraction etc
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extraction etc ([#310][])
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### Removed
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- Many other various issues
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## [0.4] - 2017-10-15
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A usable release to support [DBIC] use-case
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A usable release to support [DBIC][] use-case
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### Added
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- more testing
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### Changes
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- Dockerfile updates (added pigz, progressed forward [dcm2niix])
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- Dockerfile updates (added pigz, progressed forward [dcm2niix][])
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### Fixed
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- correct date/time in BIDS `_scans` files
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- sort entries in `_scans` by date and then filename
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## [0.3] - 2017-07-10
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A somewhat working release on the way to support [DBIC] use-case
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A somewhat working release on the way to support [DBIC][] use-case
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### Added
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- more tests
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- groupping of dicoms by series if provided
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- many more features and fixes
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## [0.2] - 2016-10-20
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An initial release on the way to support [DBIC] use-case
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An initial release on the way to support [DBIC][] use-case
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### Added
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- basic Python project assets (`setup.py`, etc)
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- basic tests
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- [datalad] support
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- [datalad][] support
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- dbic_bids heuristic
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- `--dbg` command line flag to enter `pdb` environment upon failure
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## Fixed
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[DBIC]: http://dbic.dartmouth.edu
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[datalad]: http://datalad.org
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[dcm2niix]: https://github.com/rordenlab/dcm2niix
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[#293]: https://github.com/nipy/heudiconv/issues/293
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[#301]: https://github.com/nipy/heudiconv/issues/301
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[#304]: https://github.com/nipy/heudiconv/issues/304
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[#306]: https://github.com/nipy/heudiconv/issues/306
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[#310]: https://github.com/nipy/heudiconv/issues/310

‎README.rst

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=============
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**HeuDiConv**
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=============
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`a heuristic-centric DICOM converter`
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.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:unstable-brightgreen.svg?logo=docker&style=flat
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:target: https://hub.docker.com/r/nipy/heudiconv/tags/
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:alt: Our Docker image
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.. image:: https://travis-ci.org/nipy/heudiconv.svg?branch=master
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:target: https://travis-ci.org/nipy/heudiconv
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:alt: TravisCI
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.. image:: https://codecov.io/gh/nipy/heudiconv/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/nipy/heudiconv
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:alt: CodeCoverage
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.. image:: https://readthedocs.org/projects/heudiconv/badge/?version=latest
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:target: http://heudiconv.readthedocs.io/en/latest/?badge=latest
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:alt: Readthedocs
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About
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-----
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``heudiconv`` is a flexible DICOM converter for organizing brain imaging data
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into structured directory layouts.
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- it allows flexible directory layouts and naming schemes through customizable heuristics implementations
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- it only converts the necessary DICOMs, not everything in a directory
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- you can keep links to DICOM files in the participant layout
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- using dcm2niix under the hood, it's fast
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- it can track the provenance of the conversion from DICOM to NIfTI in W3C PROV format
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- it provides assistance in converting to `BIDS <http://bids.neuroimaging.io/>`_.
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- it integrates with `DataLad <https://www.datalad.org/>`_ to place converted and original data under git/git-annex version control, while automatically annotating files with sensitive information (e.g., non-defaced anatomicals, etc)

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/api.rst

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=============
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API Reference
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=============
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.. toctree::
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:maxdepth: 1
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api/bids
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api/convert
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api/dicoms
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api/parser
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api/queue
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api/utils

‎docs/api/bids.rst

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====
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BIDS
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====
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.. automodule:: heudiconv.bids

‎docs/api/convert.rst

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==========
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Conversion
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==========
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.. automodule:: heudiconv.convert

‎docs/api/dicoms.rst

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======
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DICOMS
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======
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.. automodule:: heudiconv.dicoms

‎docs/api/parser.rst

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=======
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Parsing
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=======
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.. automodule:: heudiconv.parser

‎docs/api/queue.rst

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=============
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Batch Queuing
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=============
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.. automodule:: heudiconv.queue

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