def test_ICC_rep_anova():
# see table 2 in P. E. Shrout & Joseph L. Fleiss (1979). "Intraclass Correlations: Uses in
# Assessing Rater Reliability". Psychological Bulletin 86 (2): 420-428
Y = np.array([[9, 2, 5, 8], [6, 1, 3, 2], [8, 4, 6, 8], [7, 1, 2, 6],
[10, 5, 6, 9], [6, 2, 4, 7]])
icc, r_var, e_var, _, dfc, dfe = ICC_rep_anova(Y)
# see table 4
assert round(icc, 2) == 0.71
assert dfc == 3
assert dfe == 15
assert np.isclose(r_var / (r_var + e_var), icc)
def run_icc_meanDist(subjects, dataDir, fsDir, thr, hemi, scan_list):
concat = np.zeros((len(subjects), len(scan_list), 10242))
results = np.zeros((6, 10242))
subcort = np.sort(
nib.freesurfer.io.read_label(
'%s/fsaverage5/label/%s.Medial_wall.label' % (fsDir, hemi)))
for n_scan, scan in enumerate(scan_list):
for n_sub, sub in enumerate(subjects):
concat[n_sub, n_scan] = np.load(
'%s/%s/meanDist/%s_lsd_meanDist_interp_%s_%s_fsa5_%s.npy' %
(dataDir, sub, sub, thr, scan, hemi))
for node in range(10242):
results[:, node] = ICC_rep_anova(concat[:, :, node])
results[:, subcort] = 0
return results
def run_icc_interses_meanDist(subjects, dataDir, fsDir, thr, hemi):
concat = np.zeros((len(subjects), 2, 10242))
results = np.zeros((6, 10242))
subcort = np.sort(
nib.freesurfer.io.read_label(
'%s/fsaverage5/label/%s.Medial_wall.label' % (fsDir, hemi)))
for n_sub, sub in enumerate(subjects):
for n_ses, session in enumerate([
'%s/%s/meanDist/%s_lsd_meanDist_geo_interp_%s_1a_fsa5_%s.npy' %
(dataDir, sub, sub, thr, hemi),
'%s/%s/meanDist/%s_lemon_meanDist_geo_interp_%s_fsa5_%s.npy' %
(dataDir, sub, sub, thr, hemi)
]):
concat[n_sub, n_ses] = np.load(session)
for node in range(10242):
results[:, node] = ICC_rep_anova(concat[:, :, node])
results[:, subcort] = 0
return results
def icc31(Y):
icc31, _, _, _, _, _ = ICC_rep_anova(Y)
return icc31