fsqc.evaluateHippocampalSegmentation

This module provides a function to evaluate potential missegmentation of the hippocampus and amygdala

fsqc.evaluateHippocampalSegmentation.evaluateHippocampalSegmentation(SUBJECT, SUBJECTS_DIR, OUTPUT_DIR, CREATE_SCREENSHOT=True, SCREENSHOTS_OUTFILE=None, SCREENSHOTS_ORIENTATION='radiological', HEMI='lh', LABEL='T1.v21')

Evaluate potential missegmentation of the hippocampus and amygdala.

This script evaluates potential missegmentation of the hippocampus and amygdala as created by FreeSurfer 7.1’s dedicated module: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

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.

HEMIstr, optional, default: “lh”

Hemisphere to evaluate, either ‘lh’ or ‘rh’.

LABELstr, optional, default: “T1.v21”

Label for hippocampal and amygdala segmentation.

Returns:

None

This function returns nothing.

Notes

Required Files: - mri/[lr]h.hippoAmygLabels-<LABEL>.FSvoxelSpace.mgz - mri/norm.mgz