aslprep.interfaces.reference module

Interfaces for building reference images.

class SelectHighestContrastVolumes(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Apply the SCORE and SCRUB algorithms.

The Structural Correlation-based Outlier Rejection (SCORE) algorithm is applied to the CBF time series to discard CBF volumes with outlying values [1] before computing the mean CBF. The Structural Correlation with RobUst Bayesian (SCRUB) algorithm is then applied to the CBF maps using structural tissue probability maps to reweight the mean CBF [2].

References

[1]

Sudipto Dolui, Ze Wang, Russell T. Shinohara, David A. Wolk, John A. Detre, and for the Alzheimer’s Disease Neuroimaging Initiative. Structural Correlation-based Outlier Rejection (SCORE) algorithm for arterial spin labeling time series: SCORE: Denoising Algorithm for ASL. Journal of Magnetic Resonance Imaging, 45(6):1786–1797, June 2017. URL: http://doi.wiley.com/10.1002/jmri.25436 (visited on 2020-04-13), doi:10.1002/jmri.25436.

[2]

Sudipto Dolui, David A. Wolk, David A. Wolk, and John A. Detre. Scrub: a structural correlation and empirical robust bayesian method for asl data. International Society for Magnetic Resonance in Medicine, 2016. doi:http://archive.ismrm.org/2016/2880.html.

Mandatory Inputs:

• asl_file (a pathlike object or string representing an existing file) – ASL file.

• aslcontext (a pathlike object or string representing an existing file) – ASL context file.

• prioritize_m0 (a boolean) – Whether to prioritize the M0 scan (useful for GE data) or not.

Optional Inputs:

m0scan (a pathlike object or string representing an existing file) – M0 scan file. Only provided if M0Type is ‘separate’.

Outputs:

selected_volumes_file (a pathlike object or string representing a file) – File containing the highest-contrast available volumes.