Note
This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.
brainprep.workflow.brainprep_quality_assurance¶
- brainprep.workflow.brainprep_quality_assurance(image_files, output_dir, keep_intermediate=False, **kwargs)[source]¶
Subject level quality assurance pre-processing workflow for MRI images.
Applies MRIQC tool [1] with subject level default settings.
- Parameters:
- image_fileslist[File]
Path to the input image files of one subject.
- output_dirDirectory
Directory where the quality assurance related outputs will be saved (i.e., the root of your dataset).
- keep_intermediatebool
If True, retains intermediate results (i.e., the workspace); useful for debugging. Default False.
- **kwargsdict
- entities: lsit[dict]
Dictionaries of parsed BIDS entities.
- Returns:
- Bunch
A dictionary-like object containing:
iqm_files : list[File] — paths to the subject level Image Quality Metrics (IQMs).
Notes
This workflow assumes the input images are organized in BIDS.
References
Examples
>>> from brainprep.config import Config >>> from brainprep.reporting import RSTReport >>> from brainprep.workflow import brainprep_quality_assurance >>> >>> with Config(dryrun=True, verbose=False): ... report = RSTReport() ... outputs = brainprep_quality_assurance( ... image_files=[ ... "/tmp/dataset/rawdata/sub-01/ses-01/anat/" ... "sub-01_ses-01_run-01_T1w.nii.gz", ... "/tmp/dataset/rawdata/sub-01/ses-01/dwi/" ... "sub-01_ses-01_run-01_dwi.nii.gz", ... ], ... output_dir="/tmp/dataset/derivatives", ... ) >>> outputs Bunch( iqm_files: [PosixPath('...'), PosixPath('...')] )
