fsqc.evaluateHypothalamicSegmentation

This module provides a function to evaluate potential missegmentation of the hypothalamus

fsqc.evaluateHypothalamicSegmentation.evaluateHypothalamicSegmentation(SUBJECT, SUBJECTS_DIR, OUTPUT_DIR, CREATE_SCREENSHOT=True, SCREENSHOTS_OUTFILE=None, SCREENSHOTS_ORIENTATION='radiological')

Evaluate potential missegmentation of the hypothalamus.

This script evaluates potential missegmentation of the hypothalamus as created by FreeSurfer 7.2’s module for hypothalamic segmentation: https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits.

If the corresponding arguments are set to ‘True’, the script will also create screenshots. Resulting files will be saved to the same directory as indicated above.

Parameters:

SUBJECTstr

The subject identifier.

SUBJECTS_DIRstr

The directory containing subject data.

OUTPUT_DIRstr

The output directory.

CREATE_SCREENSHOTbool, optional, default: True

Whether to create screenshots.

SCREENSHOTS_OUTFILEstr or list, optional, default: None

File or list of files for screenshots.

SCREENSHOTS_ORIENTATIONstr, optional, default: “radiological”

Orientation for screenshots.

Returns:

None

This function return nothing.

Notes

Required Files: - mri/hypothalamic_subunits_seg.v1.mgz - mri/norm.mgz