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pyBIDSconv

pyBIDSconv is a GUI based tool to convert MR dicom data into the BIDS structure.

See detailed description about the usage of pyBIDSconv in the User Manual. More information about the BIDS structure can be found here

The only thing you need to do is to create categorization file for your scanner or institute. An example of the categorization file for a SIEMENS Prisma can be found in the example files. More information about the content of the configuration file can be found in the pyBIDSconv_Manual.

In an additional configuration file you can specify specific cases of in- or exclusions of your dicom data to the conversion process. An example of a configuration file for a SIEMENS Prisma can be found in the example files. More information about the content of the configuration file can be found in the pyBIDSconv_Manual. An editor for the configuration file is available in the GUI menu under tools.

Based on these two files pyBIDSconv will do the categorization of the dicom data of one subject at each time to the appropriate BIDS structure folder automatically and shows you the catagorization on the screen where you can do the additions (e.g. task names of functional scans) or change manually. Beside the conversation from the subject dicom folder to the BIDS structure nearly all sidecar files (.json and .txt) for BIDS are created or updated automatically. (This only work when you start the BIDS structure with pyBIDSconv).

Install

Copy the pyBIDSconv folder in a folder of your choice on your system and add the directory to your PYTHONPATH.

Dependencies

For using pyBIDSconv you need to have dcm2niix installed.
For using pyBIDSconv source code: pyBIDSconv is developed in python 2.7 and the following packages need to be installed: pydicom, numpy, wxpython, pandas. (pyBIDSconv was developed and tested with the following versions: python: 2.7.14, numpy: 1.13.3, wx: 4.0.0rc1, dicom: 0.9.9, pandas: 0.20.3). You can use the the requirement.txt file to install the required packages: pip install -r requirement.txt

Licence

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License (GPLv3) as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;

Author:
Michael Lindner
University of Reading, 2018
School of Psychology and Clinical Language Sciences
Contact: contact email