mriqc.workflows package

Submodules

mriqc.workflows.anatomical module

A QC workflow for anatomical MRI

mriqc.workflows.anatomical.airmsk_wf(name='AirMaskWorkflow', save_memory=False, ants_settings=None)

Implements the Step 1 of [Mortamet2009].

mriqc.workflows.anatomical.anat_qc_workflow(name='MRIQC_Anat', settings=None)

One-subject-one-session-one-run pipeline to extract the NR-IQMs from anatomical images

mriqc.workflows.anatomical.combine_masks(head_mask, artifact_msk, out_file=None)

Computes an air mask from the head and artifact masks

mriqc.workflows.anatomical.gradient_threshold(in_file, thresh=1.0, out_file=None)

Compute a threshold from the histogram of the magnitude gradient image

mriqc.workflows.anatomical.headmsk_wf(name='HeadMaskWorkflow')

Computes a head mask as in [Mortamet2009].

mriqc.workflows.anatomical.image_gradient(in_file, compute_abs=True, out_file=None)

Computes the magnitude gradient of an image using numpy

mriqc.workflows.anatomical.mri_reorient_wf(name='ReorientWorkflow')

A workflow to reorient images to ‘RPI’ orientation

mriqc.workflows.anatomical.skullstrip_wf(name='SkullStripWorkflow')

Skull-stripping workflow

mriqc.workflows.core module

The core module combines the existing workflows

mriqc.workflows.core.ms_anat(settings=None, subject_id=None, session_id=None, run_id=None)

Multi-subject anatomical workflow wrapper

mriqc.workflows.core.ms_func(settings=None, subject_id=None, session_id=None, run_id=None)

Multi-subject functional workflow wrapper

mriqc.workflows.functional module

A QC workflow for fMRI data

mriqc.workflows.functional.fmri_bmsk_workflow(name='fMRIBrainMask', use_bet=False)

Comute brain mask of an fmri dataset

mriqc.workflows.functional.fmri_hmc_workflow(name='fMRI_HMC', st_correct=False)

A head motion correction (HMC) workflow for functional scans

mriqc.workflows.functional.fmri_qc_workflow(name='fMRIQC', settings=None)

The fMRI qc workflow

mriqc.workflows.utils module

Helper functions for the workflows

mriqc.workflows.utils.fmri_getidx(in_file, start_idx, stop_idx)

Heuristics to set the start and stop indices of fMRI series

mriqc.workflows.utils.fwhm_dict(fwhm)

Convert a list of FWHM into a dictionary

Module contents