Medical imaging utility scripts. Anonymization, Converters, Scores.
Given an existing folder, this tool proceeds to anonymize any DICOM files, removing all the sensible information and making them ready to be shared and stored without any potential security risk.
The anonymization process progress iteratively and is extended to all the subdirectories of the main folder.
Attention: this tool has been tested on data obtained from a General Electrics MRI scanner. While the script will still work for any DICOM series, it may happen that some key fields will be deleted with images from different manufactures are used (notably the diffusion encoding parameters).
Use the script as a command line tool. Anonymization is in-place:
$ python DICOM_anonymizer.py <folder>Convert a fiber tract file between the following formats: .tck, .trk, .vtk, .vtp, .xml
The conversion can is supported in both senses and for all the combinations. The original file does not get eliminated. The converted output assumes the name of the input, with a different extension.
Use the script as a command line tool:
$ python tracto_converter.py <tractogram_filepath> <new_format>Example:
$ python tracto_converter.py tracto.tck vtkSørensen–Dice coefficient and IOU coefficient computation between two binary masks.
DSC = 2 * TP / (2 * TP + FP + FN) IOU = TP / (TP + FP + FN)
Implementation as 3D Slicer plug-in.
For any inquiries please contact: Alessandro Delmonte @ alessandro.delmonte@institutimagine.org
This project is licensed under the Apache License 2.0 - see the LICENSE file for details