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.freesurfer.reconall_surfreg

brainprep.interfaces.freesurfer.reconall_surfreg(output_dir, entities)

Interhemispheric surface-based registration using the fsaverage_sym template, and FreeSurfer’s xhemireg and surfreg.

Applies the interhemispheric cortical surface-based pre-processing described in [1]. This includes:

1. Registers the right hemisphere to the left hemisphere within the subject’s own space.

2. Registers the left hemisphere to the fsaverage_sym symmetric template.

3. Registers the right hemisphere (already aligned to the left via xhemireg) to fsaverage_sym - use the interhemispheric registration surface (rh.sphere.reg.xhemi) instead of the standard one (rh.sphere.reg).

Parameters:

output_dirDirectory

FreeSurfer working directory containing all the subjects.

entitiesdict

A dictionary of parsed BIDS entities including modality.

Returns:

commandslist[list[str]]

Registration command-lines.

outputstuple[File]

• left_reg_file : File - Left hemisphere registered to fsaverage_sym symmetric template.

• right_reg_file : File - Right hemisphere registered to fsaverage_sym symmetric template via xhemi.

• log_file : File - Generated log file.

Notes

• Removing the left_reg_file if trying to resume.

References

[1]

Douglas N Greve, Lise Van der Haegen, Qing Cai, Steven Stufflebeam, Mert R Sabuncu, Bruce Fischl, and Marc Brysbaert. A surface-based analysis of language lateralization and cortical asymmetry. J. Cogn. Neurosci., 25(9):1477–1492, September 2013.