dcmpi 0.0.2.8

DICOM Preprocessing Interface.

DCMPI - DICOM Preprocessing Interface: explore/distill DICOM data.

This software implements an automated information extraction tool from DICOM files containing MRI acquisitions. It is specifically targeted at the output of the Siemens scanners, although it should be easily adaptable to other vendors and eventually even different acquisition modalities.

It features a Graphical User-Interface to manage the most used export options. This is also mirrored by a CLI of the same software.

Additionally, several other command-line tools are provided, which offer a much finer control over the single tasks.

The available tasks are:

• DICOM copy/moving and sorting according to acquisition (this includes a JSON summary of the acquisitions and series)

• extraction of DICOM metadata and experimental storing as JSON

• extraction of acquisition protocol information

• extraction of human-friendly information from the DICOM, stored as JSON

• extraction of the image data and conversion to the popular NIfTI format (this is supported through the software dcm2nii, with partial support for other programs, e.g. isis)

• creation of HTML reports from the DICOM information (PDF conversion is supported via wkhtmltopdf)

• backup of the DICOM files as compressed archives

• monitor of a folder to detect appearance of new DICOM files

The subsequent data analysis is probably best performed using PyMRT, which natively understands the output of DCMPI.

Notes

This work is based on reverse engineering of the DICOM files and as such should not be used as a reliable source of information. Some of the features are only partially supported. Please get in contact if you would like to suggest additional features.

WARNING

This is a research tool and it is provided ‘as is’. DO NOT BASE ANY DIAGNOSIS ON THE INFORMATION PROCESSED BY THIS SOFTWARE!

Installation

The recommended way of installing the software is through PyPI:

$ pip install dcmpi

Alternatively, you can the clone the source repository from GitHub:

$ mkdir dcmpi
$ cd dcmpi
$ git clone [e-mail]:norok2/dcmpi.git
$ python setup.py install

For more details see also INSTALL.rst.

License

This work is licensed through the terms and conditions of the GPLv3+ The use of this software for scientific purpose leading to a publication should be acknowledged through citation of the upcoming paper.

Acknowledgements

This software originated as part of my Ph.D. work at the Max Planck Institute for Human Cognitive and Brain Sciences and the University of Leipzig.

For a complete list of authors please see AUTHORS.rst.

People who have influenced this work are acknowledged in THANKS.rst.

This work was partly funded by the European Union through the Seventh Framework Programme Marie Curie Actions via the “Ultra-High Field Magnetic Resonance Imaging: HiMR” Initial Training Network (FP7-PEOPLE-2012-ITN-316716).