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‎README.rst

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heudiconv: 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
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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
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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
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original data under git/git-annex version control, while automatically
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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/conf.py

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# -*- coding: utf-8 -*-
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#
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# Configuration file for the Sphinx documentation builder.
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#
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# This file does only contain a selection of the most common options. For a
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# full list see the documentation:
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# http://www.sphinx-doc.org/en/master/config
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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# import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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# -- Project information -----------------------------------------------------
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project = 'heudiconv'
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copyright = '2019, Heudiconv team'
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author = 'Heudiconv team'
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# The short X.Y version
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version = ''
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# The full version, including alpha/beta/rc tags
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release = '0.5.4'
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# -- General configuration ---------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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#
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# needs_sphinx = '1.0'
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx.ext.autodoc',
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'recommonmark',
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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#
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# source_suffix = ['.rst', '.md']
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source_suffix = '.rst'
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# The master toctree document.
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master_doc = 'index'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = None
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'alabaster'
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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#
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# html_theme_options = {}
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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# Custom sidebar templates, must be a dictionary that maps document names
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# to template names.
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#
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# The default sidebars (for documents that don't match any pattern) are
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# defined by theme itself. Builtin themes are using these templates by
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# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
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# 'searchbox.html']``.
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#
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# html_sidebars = {}
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# -- Options for HTMLHelp output ---------------------------------------------
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'heudiconvdoc'
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# -- Options for LaTeX output ------------------------------------------------
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#
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# 'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#
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# 'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#
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# 'preamble': '',
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# Latex figure (float) alignment
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#
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# 'figure_align': 'htbp',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title,
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# author, documentclass [howto, manual, or own class]).
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latex_documents = [
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(master_doc, 'heudiconv.tex', 'heudiconv Documentation',
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'Heudiconv team', 'manual'),
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]
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# -- Options for manual page output ------------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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(master_doc, 'heudiconv', 'heudiconv Documentation',
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[author], 1)
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]
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# -- Options for Texinfo output ----------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'heudiconv', 'heudiconv Documentation',
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author, 'heudiconv', 'One line description of project.',
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'Miscellaneous'),
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]
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# -- Options for Epub output -------------------------------------------------
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# Bibliographic Dublin Core info.
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epub_title = project
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# The unique identifier of the text. This can be a ISBN number
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# or the project homepage.
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#
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# epub_identifier = ''
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# A unique identification for the text.
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#
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# epub_uid = ''
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# A list of files that should not be packed into the epub file.
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epub_exclude_files = ['search.html']
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# -- Extension configuration -------------------------------------------------

‎docs/heuristics.rst

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## The heuristic file
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The heuristic file controls how information about the dicoms is used to convert
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to a file system layout (e.g., BIDS). This is a python file that must have the
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function `infotodict`, which takes a single argument `seqinfo`.
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### `seqinfo` and the `s` variable
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`seqinfo` is a list of namedtuple objects, each containing the following fields:
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* total_files_till_now
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* example_dcm_file
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* series_id
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* dcm_dir_name
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* unspecified2
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* unspecified3
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* dim1
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* dim2
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* dim3
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* dim4
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* TR
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* TE
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* protocol_name
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* is_motion_corrected
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* is_derived
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* patient_id
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* study_description
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* referring_physician_name
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* series_description
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* image_type
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```
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128 125000-1-1.dcm 1 - -
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- 160 160 128 1 0.00315 1.37 AAHScout False
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```
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### The dictionary returned by `infotodict`
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This dictionary contains as keys a 3-tuple `(template, a tuple of output types,
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annotation classes)`.
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template - how the file should be relative to the base directory
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tuple of output types - what format of output should be created - nii.gz, dicom,
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etc.,.
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annotation classes - unused
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```
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Example: ('func/sub-{subject}_task-face_run-{item:02d}_acq-PA_bold', ('nii.gz',
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'dicom'), None)
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```
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A few fields are defined by default and can be used in the template:
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- item: index within category
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- subject: participant id
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- seqitem: run number during scanning
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- subindex: sub index within group
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- session: session info for multi-session studies and when session has been
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defined as a parameter for heudiconv
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Additional variables may be added and can be returned in the value of the
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dictionary returned from the function.
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`info[some_3-tuple] = [12, 14, 16]` would assign dicom sequence groups 12, 14
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and 16 to be converted using the template specified in `some_3-tuple`.
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if the template contained a non-sanctioned variable, it would have to be
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provided in the values for that key.
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```
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some_3_tuple = ('func/sub-{subject}_task-face_run-{item:02d}_acq-{acq}_bold', ('nii.gz',
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'dicom'), None)
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```
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In the above example `{acq}` is not a standard variable. In this case, values
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for this variable needs to be added.
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```
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info[some_3-tuple] = [{'item': 12, 'acq': 'AP'},
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{'item': 14, 'acq': 'AP'},
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{'item': 16, 'acq': 'PA'}]
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```

‎docs/index.rst

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.. heudiconv documentation master file, created by
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sphinx-quickstart on Mon Mar 25 15:42:31 2019.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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.. include:: ../README.rst
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Contents
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--------
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.. toctree::
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:maxdepth: 2
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installation
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../CHANGELOG.md
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usage
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heuristics
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tutorials
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reference

‎docs/installation.rst

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Installation
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------------
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``Heudiconv`` is packaged and available from many different sources.
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Local
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-----
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Released versions of HeuDiConv are available on `PyPI <https://pypi.org/project/heudiconv/>`
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and `conda <https://github.com/conda-forge/heudiconv-feedstock#installing-heudiconv>`.
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If installing through ``PyPI``, eg::
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pip install heudiconv[all]
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Manual installation of `dcm2niix <https://github.com/rordenlab/dcm2niix#install>`
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is required.
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On Debian-based systems we recommend using `NeuroDebian <http://neuro.debian.net>`
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which provides the `heudiconv package <http://neuro.debian.net/pkgs/heudiconv.html>`.
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Docker
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------
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If `Docker <https://docs.docker.com/install/>` is available on your system, you
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can visit `our page on Docker Hub <https://hub.docker.com/r/nipy/heudiconv/tags>`
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to view available releases. To pull the latest release, run::
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$ docker pull nipy/heudiconv:0.5.4
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Singularity
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-----------
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If `Singularity <https://www.sylabs.io/singularity/>` is available on your system,
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you can use it to pull and convert our Docker images! For example, to pull and
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build the latest release, you can run::
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$ singularity pull docker://nipy/heudiconv:0.5.4

‎docs/tutorials.rst

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Luckily(?), we live in an era of plentiful information. Below are some links to
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other users' tutorials covering their experience with ``heudiconv``.
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- `YouTube tutorial <https://www.youtube.com/watch?v=O1kZAuR7E00>` by
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`James Kent <https://github.com/jdkent>`
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- `Walkthrough <http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/>`
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by the `Standard Center for Reproducible Neuroscience <http://reproducibility.stanford.edu/>`
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- `Sample Conversion: Coastal Coding 2019 <http://www.repronim.org/coco2019-training/presentations/heudiconv/#1>`
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- `U of A Neuroimaging Core <https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html>`
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by `Dianne Patterson <https://github.com/dkp>`
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* Note: some of these tutorials may not be 100% up to date with the latest releases
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of ``heudiconv``, so refer to this documentation first.

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