HeuDiConv¶
a heuristic-centric DICOM converter
About¶
heudiconv is a flexible DICOM converter for organizing brain imaging data
into structured directory layouts.
It allows flexible directory layouts and naming schemes through customizable heuristics implementations.
It only converts the necessary DICOMs and ignores everything else in a directory.
You can keep links to DICOM files in the participant layout.
Using dcm2niix under the hood, it’s fast.
It can track the provenance of the conversion from DICOM to NIfTI in W3C PROV format.
It provides assistance in converting to BIDS.
It integrates with DataLad 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).
Installation¶
See our installation page on heudiconv.readthedocs.io .
HOWTO 101¶
In a nutshell – heudiconv operates using a heuristic which, given metadata from DICOMs, would decide how to name
resultant (from conversion using dcm2niix) files. Heuristic convertall could actually be used with no real
heuristic and by simply establish your own conversion mapping through editing produced mapping files.
In most use-cases of retrospective study data conversion, you would need to create your custom heuristic following
existing heuristics as examples and/or
referring to “Heuristic” section in the documentation.
Note that ReproIn heuristic is
generic and powerful enough to be adopted virtually for any study: For prospective studies, you would just need
to name your sequences following the ReproIn convention, and for
retrospective conversions, you often would be able to create a new versatile heuristic by simply providing
remappings into ReproIn as shown in this issue (documentation is coming).
Having decided on a heuristic, you could use the command line:
heudiconv -f HEURISTIC-FILE-OR-NAME -o OUTPUT-PATH --files INPUT-PATHs
with various additional options (see heudiconv --help or
“Usage” in documentation) to tune its behavior to
convert your data.
For detailed examples and guides, please check out ReproIn conversion invocation examples and the user tutorials in the documentation.
How to cite¶
Please use Zenodo record for your specific version of HeuDiConv. We also support gathering all relevant citations via DueCredit.
How to contribute¶
For a detailed into, see our contributing guide.
Our releases are packaged using Intuit auto, with the corresponding workflow including
Docker image preparation being found in .github/workflows/release.yml.
3-rd party heuristics¶
Contributing to HeuDiConv¶
Files organization¶
heudiconv/ is the main Python module where major development is happening, with major submodules being:
cli/- wrappers and argument parsers bringing the HeuDiConv functionality to the command line.external/- general compatibility layers for external functions HeuDiConv depends on.heuristics/- heuristic evaluators for workflows, pull requests here are particularly welcome.
docs/ - documentation directory.
utils/ - helper utilities used during development, testing, and distribution of HeuDiConv.
How to contribute¶
The preferred way to contribute to the HeuDiConv code base is to fork the main repository on GitHub.
If you are unsure what that means, here is a set-up workflow you may wish to follow:
Fork the project repository on GitHub, by clicking on the “Fork” button near the top of the page — this will create a copy of the repository writeable by your GitHub user.
Set up a clone of the repository on your local machine and connect it to both the “official” and your copy of the repository on GitHub:
git clone git://github.com/nipy/heudiconv cd heudiconv git remote rename origin official git remote add origin git://github.com/YOUR_GITHUB_USERNAME/heudiconv
When you wish to start a new contribution, create a new branch:
git checkout -b topic_of_your_contribution
When you are done making the changes you wish to contribute, record them in Git:
git add the/paths/to/files/you/modified can/be/more/than/one git commit
Push the changes to your copy of the code on GitHub, following which Git will provide you with a link which you can click to initiate a pull request:
git push -u origin topic_of_your_contribution
(If any of the above seems overwhelming, you can look up the Git documentation on the web.)
Development environment¶
We support Python 3 only (>= 3.7).
Dependencies which you will need are listed in the repository.
Note that you will likely have these will already be available on your system if you used a
package manager (e.g. Debian’s apt-get, Gentoo’s emerge, or simply PIP) to install the
software.
Development work might require live access to the copy of HeuDiConv which is being developed. If a system-wide release of HeuDiConv is already installed, or likely to be, it is best to keep development work sandboxed inside a dedicated virtual environment. This is best accomplished via:
cd /path/to/your/clone/of/heudiconv
mkdir -p venvs/dev
python -m venv venvs/dev
source venvs/dev/bin/activate
pip install -e .[all]
Additional Hints¶
It is recommended to check that your contribution complies with the following rules before submitting a pull request:
All public functions (i.e. functions whose name does not start with an underscore) should have informative docstrings with sample usage presented as doctests when appropriate.
Docstrings are formatted in NumPy style.
Lines are no longer than 120 characters.
All tests still pass:
cd /path/to/your/clone/of/heudiconv pytest -vvs .
New code should be accompanied by new tests.