mrQA suite of tools offering automatic evaluation of protocol compliance
Project description
Quickstart
mrQA suite of tools
automatic evaluation of protocol compliance
Documentation: https://open-minds-lab.github.io/mrQA/
Tutorial: https://nbviewer.org/github/Open-Minds-Lab/mrQA/blob/master/examples/usage.ipynb
CLI usage
A protocol compliance report can be generated directly from the command line interface. For a DICOM dataset:
mr_proto_compl --data_root /path/to/dataset --style xnat
For a BIDS dataset:
mr_proto_compl --data_root /path/to/dataset --style bids
Python usage
To use mrQA in a project:
import mrQA
The most important methods for checking protocol compliance is check_compliance. It calls all the required functions.
To infer the most frequent values for each acquisition parameter
Aggregate the non-compliance information to generate an HTML report
First of all, you have to import the relevant modules and classes:
from MRdataset import import_dataset from mrQA import check_compliance
Given a dataset of MR images, (e.g. DICOM images), we create MRdataset.base.Project object. This can be achieved simply by MRdataset.import_dataset method, which requires a valid folder path. For details on MRdataset, please see its documentation.
data_root = '/home/user/datasets/ABCD' output_dir = '/home/user/MR_reports/' dataset = import_dataset(data_root=data_root, style='xnat', name='ABCD') check_compliance(dataset=dataset, output_dir=output_dir)
And that’s it! Please note some important points:
It will generate a corresponding HTML file in the output_dir which contains the complete report.
style denotes the specific format of neuroimaging dataset. For example, use xnat for DICOM datasets and bids for BIDS datasets
name is an identifier which can be used to reload the the cached files later.If no name is specified, it uses a random identifier.
History
0.1.0 (2022-05-20)
First release on PyPI.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.