MRdataset 0.1.3

MRdataset

Quickstart

MRdataset

• a unified interface to various neuroimaging datasets such as DICOM, BIDS and any other generic format etc

• Documentation: https://open-minds-lab.github.io/MRdataset/

Command line usage

MRdataset can be used on the command line interface. For a DICOM dataset:

mrds --data_root /path/to/dataset --style dicom

For a BIDS dataset:

mrds --data_root /path/to/dataset --style bids

API/programmatic usage

To use MRdataset in a project:

import MRdataset

The most important method is import_dataset. It creates an appropriate object depending as per style argument.

First of all, you have to import the relevant module:

from MRdataset import import_dataset

Given a valid folder path to a dataset of MR images (e.g. DICOM images), it creates a MRdataset.base.Project object.:

data_root = '/home/user/datasets/ABCD'
dataset = import_dataset(data_root=data_root,
                         style='dicom',
                         name='ABCD')

By default, the import_dataset expects a DICOM dataset. However, this can be changed using style argument. For example, use style='bids' for importing a BIDS dataset.

The library is highly extensible, and a developer can extend it to their own neuroimaging formats. For example, to create an interface with a new format, say NID (NeuroImaging Dataset), inherit MRdataset.base.Project in a file NID_dataset.py:

from MRdataset import Project
class NIDDataset(Project):
    def __init__():
        pass

     def walk():
        pass

Implement, these two functions. You can directly use style='nid'. Thats it! No more changes required.

History

0.1.0 (2022-05-05)

• First release on PyPI.