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.interfaces.qualcheck.euler_numbers

brainprep.interfaces.qualcheck.euler_numbers(output_dir, euler_threshold=-217, dryrun=False)

FreeSurfer recon-all quality control.

Parse the FreeSurfer’s Euler numbers for all subjects and applies the quality control described in [1].

Parameters:

output_dirDirectory

FreeSurfer working directory containing all the subjects.

euler_thresholdint

Quality control threshold on the Euler number. Default 217.

dryrunbool

If True, skip actual computation and file writing. Default False.

Returns:

euler_numbers_fileFile

A TSV file containing FreeSurfer’s averaged Euler numbers. The table includes the columns participant_id, session, run, and euler_number, as well as a binary qc column indicating the quality control result.

Notes

A qc column is added to the output table. It contains a binary flag indicating whether the euler score exceeds the threshold: qc = 1 if euler_number > euler_threshold, otherwise qc = 0.

References

[1]

Adon F G Rosen, David R Roalf, Kosha Ruparel, Jason Blake, Kevin Seelaus, Lakshmi P Villa, Rastko Ciric, Philip A Cook, Christos Davatzikos, Mark A Elliott, Angel Garcia de La Garza, Efstathios D Gennatas, Megan Quarmley, J Eric Schmitt, Russell T Shinohara, M Dylan Tisdall, R Cameron Craddock, Raquel E Gur, Ruben C Gur, and Theodore D Satterthwaite. Quantitative assessment of structural image quality. Neuroimage, 169:407–418, April 2018.