Hippunfold - calculating mean surface metrics over subfields

example_calc_surf_metrics.py

import nibabel as nib

subjects = ['01']
hemis = ['L','R']
subfield_labels={1:'Sub',2:'CA1',3:'CA2',4:'CA3',5:'CA4'}
hipp_metrics = ['thickness','gyrification']
dentate_metrics = ['gyrification']


with open('table.csv','w') as f:

    print('subject,hemi,label,metric,meanvalue',file=f)

    for subject in subjects:
        for hemi in hemis:

            subfields = nib.load(f'hippunfold/sub-{subject}/ses-1/surf/sub-{subject}_ses-1_hemi-{hemi}_space-T1w_den-0p5mm_label-hipp_subfields.label.gii').agg_data()

            for metric in hipp_metrics:

                hippdata = nib.load(f'hippunfold/sub-{subject}/ses-1/surf/sub-{subject}_ses-1_hemi-{hemi}_space-T1w_den-0p5mm_label-hipp_{metric}.shape.gii').agg_data()
                for label,name in subfield_labels.items():

                    meanval = hippdata[subfields==label].mean()
                    print(f'sub-{subject},{hemi},{name},{metric},{meanval:.3f}',file=f)

                if metric in dentate_metrics:  
                    name = 'DG'
                    dgdata = nib.load(f'hippunfold/sub-{subject}/ses-1/surf/sub-{subject}_ses-1_hemi-{hemi}_space-T1w_den-0p5mm_label-dentate_{metric}.shape.gii').agg_data()
                    meanval = dgdata.mean()
                    print(f'sub-{subject},{hemi},{name},{metric},{meanval:.3f}',file=f)