QAnT extracts no-reference IQMs (image quality metrics) representing noise/information measurements as well as DICOM metadata (Tags).

The initial goal of this project was to extract IQMs and dicom tags from structural MRI images in order to automatically determine a site/scanners effect of the images.

ENVNAME="QAnT"
conda create -n $ENVNAME python==3.7.7 -y
conda activate $ENVNAME

pip install git+https://github.com/Alxaline/QAnT.git

git clone https://github.com/Alxaline/QAnT.git
cd QAnT
pip install -e .

https://comscan.readthedocs.io/en/latest/

This tool takes datasets in the file formats (.dcm, .nii, .nii.gz) as the input. To parse DICOM files, the script need to have dicom series in an independent folder, i.e. a unique folder for a volume with all .dcm slices inside.

You need to provide a parameter file for extraction. An example is available in QAnT/example_parameters/default_parameters.yaml

The tool is multi-process in order to speed up the extraction process.

You can directly use the cli:

qant-extractor [-h] -i INPUT_DIR [INPUT_DIR ...] -o OUTPUT_FILEPATH [-p PARAM] [-j N] [-v]

or in python mode:

usage: python -m QAnT.extractor [-h] -i INPUT_DIR [INPUT_DIR ...] -o OUTPUT_FILEPATH
                    [-p PARAM] [-j N] [-v]

QAnT: image Quality Assessment and dicom Tags extraction

optional arguments:
  -h, --help            show this help message and exit

Required:
  -i INPUT_DIR [INPUT_DIR ...], --input_dir INPUT_DIR [INPUT_DIR ...]
                        Input directories path with DICOM files to be parsed.
                        Can be a list of directory
  -o OUTPUT_FILEPATH, --output_filepath OUTPUT_FILEPATH
                        Output filepath for saving the content in csv files.
                        Need to have the .csv extensions
  -p PARAM, --param PARAM
                        Parameter file containing the settings to be used in
                        extraction. If not provided use default setting.
  --inclusion_keywords INCLUSION_KEYWORDS [INCLUSION_KEYWORDS ...]
                        Inclusion keywords to parse files. fnmatch style, i.e
                        ['a*', 'b*']
  --exclusion_keywords EXCLUSION_KEYWORDS [EXCLUSION_KEYWORDS ...]
                        Exclusion keywords to parse files. fnmatch style, i.e
                        ['a*', 'b*']

Options:
  -j N, --n_jobs N      Specifies the number of threads to use for parallel
                        processing (default: all)
  -v, --verbosity       increase output verbosity (e.g., -vv is more than -v)

You can visualize results csv file in the application interface.

You can directly use the cli:

qant-interface

or in python mode:

usage: python -m QAnT.interface

If you find this repository useful for your research, please cite our work:

Carré, A., Battistella, E., Niyoteka, S. et al. AutoComBat: a generic method for harmonizing MRI-based radiomic features. Sci Rep 12, 12762 (2022). https://doi.org/10.1038/s41598-022-16609-1

BibTeX:

@article{carreAutoComBatGenericMethod2022,
    title = {AutoComBat: a generic method for harmonizing MRI-based radiomic features},
    volume = {12},
    issn = {2045-2322},
    url = {https://www.nature.com/articles/s41598-022-16609-1},
    doi = {10.1038/s41598-022-16609-1},
    language = {en},
    number = {1},
    urldate = {2022-07-27},
    journal = {Scientific Reports},
    author = {Carré, Alexandre and Battistella, Enzo and Niyoteka, Stephane and Sun, Roger and Deutsch, Eric and Robert, Charlotte},
    year = {2022},
    keywords = {Cancer imaging, Computational science, Tumour biomarkers},
    pages = {12762},
}

Based on: MRQy

Sadri AR, Janowczyk A, Zhou R, Verma R, Beig N, Antunes J, Madabhushi A, Tiwari P, Viswanath SE. Technical Note: MRQy - An open-source tool for quality control of MR imaging data. Med Phys. 2020 Dec;47(12):6029-6038. doi: 10.1002/mp.14593.