mriqc.workflows package¶
Submodules¶
mriqc.workflows.anatomical module¶
A QC workflow for anatomical MRI
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mriqc.workflows.anatomical.
airmsk_wf
(name='AirMaskWorkflow', testing=False, ants_settings=None)[source]¶ Implements the Step 1 of [Mortamet2009].
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mriqc.workflows.anatomical.
anat_qc_workflow
(name='MRIQC_Anat', settings=None)[source]¶ One-subject-one-session-one-run pipeline to extract the NR-IQMs from anatomical images
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mriqc.workflows.anatomical.
combine_masks
(head_mask, artifact_msk, out_file=None)[source]¶ Computes an air mask from the head and artifact masks
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mriqc.workflows.anatomical.
gradient_threshold
(in_file, thresh=1.0, out_file=None)[source]¶ Compute a threshold from the histogram of the magnitude gradient image
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mriqc.workflows.anatomical.
headmsk_wf
(name='HeadMaskWorkflow')[source]¶ Computes a head mask as in [Mortamet2009].
mriqc.workflows.core module¶
The core module combines the existing workflows
mriqc.workflows.functional module¶
A QC workflow for fMRI data
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mriqc.workflows.functional.
fmri_bmsk_workflow
(name='fMRIBrainMask', use_bet=False)[source]¶ Comute brain mask of an fmri dataset
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mriqc.workflows.functional.
fmri_qc_workflow
(name='fMRIQC', settings=None)[source]¶ The fMRI qc workflow
mriqc.workflows.utils module¶
Helper functions for the workflows
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mriqc.workflows.utils.
fd_jenkinson
(in_file, rmax=80.0, out_file=None)[source]¶ Compute the FD [Jenkinson2002] on a 4D dataset, after AFNI-
3dvolreg
has been executed (generally a file named*.affmat12.1D
).Parameters: Returns: the output file with the FD, and the average FD along the time series
Return type: tuple(str, float)
Note
infile
should have one 3dvolreg affine matrix in one row - NOT the motion parametersNote
Acknowledgments
We thank Steve Giavasis (@sgiavasis) and Krishna Somandepali for their original implementation of this code in the [QAP].