Individual site data¶

This page contains descriptions and examples to load our example data, re-order subcortical labels, and z-score values!

Load example data¶

This is an example dataset that includes 10 healthy controls (7 females, age±SD=33.3±8.8 years) and 10 individuals with epilepsy (7 females, age±SD=39.8±14.8 years).

Covariates | As per ENIGMA-Epilepsy protocol, covariate information includes SubjID (subjectID), Dx (diagnosis, 0=controls, 1=patients), SDx (sub-diagnosis, 0=controls, 1=non-lesional patients, 2=genetic generalized epilepsy (IGE/GGE) patients, 3=left TLE, 4=right TLE), Age (in years), Sex (1=males, 2=females), Handedness (1=right, 2=left), AO (age at onset in years, patients only), DURILL (duration of illness in years, patients only), and ICV (intracranial volume).

Subcortical volume | Subcortical grey matter volumes regroup data from 12 subcortical regions, bilateral hippocampus, and bilateral ventricles.

Cortical thickness | Cortical thickness was measured at each vertex as the Euclidean distance between white and pial surfaces, and subsequently averaged within each of the Desikan-Killiany parcels.

Cortical surface area | The cortical surface area of every Desikan-Killiany parcel is also provided as part of ENIGMA imaging protocols; this morphological measure is defined by the sum of the area of each of the triangles within the parcel.

>>> from enigmatoolbox.datasets import load_example_data

>>> # Load all example data from an individual site
>>> cov, metr1_SubVol, metr2_CortThick, metr3_CortSurf = load_example_data()

% Load all example data from an individual site
[cov, metr1_SubVol, metr2_CortThick, metr3_CortSurf] = load_example_data();

Re-order subcortical regions¶

The column order from ENIGMA-derived subcortical volume matrices does not match the order in the connectivity matrices nor the pre-requisite for our subcortical visualization tools. But, hey, don’t you worry! To re-order ENIGMA-derived subcortical volume data, you may use our reorder_sctx() function, which will re-order the columns of the subcortical volume dataset accordingly (i.e., alphabetically, with all left hemisphere structures first followed by all right hemisphere structures).

>>> from enigmatoolbox.utils.useful import reorder_sctx

>>> # Re-order the subcortical data alphabetically and by hemisphere
>>> metr1_SubVol_r = reorder_sctx(metr1_SubVol)

% Re-order the subcortical data alphabetically and by hemisphere
metr1_SubVol_r = reorder_sctx(metr1_SubVol);

Z-score data¶

With our example data loaded and re-ordered, we can then z-score data in patients, relative to controls, so that lower values correspond to greater atrophy. For simplicity, we also compute the mean z-score across all left TLE patients. These mean, z-scored vectors will be used in subsequent tutorials as measures of subcortical and cortical atrophy!

Prerequisites
↪ Re-order subcortical data

>>> from enigmatoolbox.utils.useful import zscore_matrix

>>> # Z-score patients' data relative to controls (lower z-score = more atrophy)
>>> group = cov['Dx'].to_list()
>>> controlCode = 0
>>> SV_z = zscore_matrix(metr1_SubVol_r.iloc[:, 1:-1], group, controlCode)
>>> CT_z = zscore_matrix(metr2_CortThick.iloc[:, 1:-5], group, controlCode)
>>> SA_z = zscore_matrix(metr3_CortSurf.iloc[:, 1:-5], group, controlCode)

>>> # Mean z-score values across individuals with from a specific group (e.g., left TLE, that is SDx == 3)
>>> SV_z_mean = SV_z.iloc[cov[cov['SDx'] == 3].index, :].mean(axis=0)
>>> CT_z_mean = CT_z.iloc[cov[cov['SDx'] == 3].index, :].mean(axis=0)
>>> SA_z_mean = SA_z.iloc[cov[cov['SDx'] == 3].index, :].mean(axis=0)

% Z-score patients' data relative to controls (lower z-score = more atrophy)
group        = cov.Dx;
controlCode  = 0;
SV_z         = zscore_matrix(metr1_SubVol_r(:, 2:end-1), group, controlCode);
CT_z         = zscore_matrix(metr2_CortThick(:, 2:end-5), group, controlCode);
SA_z         = zscore_matrix(metr3_CortSurf(:, 2:end-5), group, controlCode);

% Mean z-score values across individuals with from a specific group (e.g., left TLE, that is SDx == 3)
SV_z_mean    = array2table(mean(SV_z{find(cov.SDx == 3), :}, 1), ...
                           'VariableNames', SV_z.Properties.VariableNames);
CT_z_mean    = array2table(mean(CT_z{find(cov.SDx == 3), :}, 1), ...
                           'VariableNames', CT_z.Properties.VariableNames);
SA_z_mean    = array2table(mean(SA_z{find(cov.SDx == 3), :}, 1), ...
                           'VariableNames', SA_z.Properties.VariableNames);