pynibs.congruence package¶

pynibs.congruence holds the initial congruence factor implementation as described in Weise, Numssen, et al., 2020 [1]. This code is mainly stored here for reproducibility reasons. The current approach (Numssen et al., 2021; [2]) uses the pynibs.regression methods.

References

[1]

Weise, K., Numssen, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020). A novel approach to localize cortical TMS effects. Neuroimage, 209, 116486.

[2]

Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. NeuroImage, 245, 118654.

Submodules¶

pynibs.congruence.congruence module¶

pynibs.congruence.congruence.cf_curveshift_kernel(e_curve, mep_curve)¶

Curve congruence (overlap) measure for multiple MEP curves per element. Determines the average displacement between the MEP curves. The congruence factor is weighted by median(E) and summed up. This favors elements which have greater E, as these are more likely to produce MEPs.

$dE = \begin{bmatrix} dE_{11} & dE_{12} & ... & dE_{1n} \\ dE_{21} & dE_{22} & ... & dE_{2n} \\ ... & ... & ... & ... \\ dE_{n1} & dE_{n2} & ... & dE_{nn} \\ \end{bmatrix}$

-> congruence_factor ~ np.linalg.norm(dE)/median(E)/n_cond/2

Parameters:

e_curve (list of np.ndarray of float) – (n_cond) List over all conditions of electric field values corresponding to the mep amplitudes.
mep_curve (list of np.ndarray of float) – (n_cond) List over all conditions of mep values corresponding to the electric field.

Returns:

congruence_factor – Congruence factor for the n_cond electric field and MEP curves.

Return type:

float

pynibs.congruence.congruence.cf_curveshift_workhorse(elm_idx_list, mep, mep_params, e, n_samples=100)¶

Worker function for congruence factor computation - call from multiprocessing.Pool. Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The computations are parallelized in terms of element indices (elm_idx_list). n_samples are taken from fitted_mep, within the range of the Mep.

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for.
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float) –
(n_mep_params_total) List of all mep parameters of curve fits used to calculate the MEP, accumulated into one array.
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …]
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest.
- len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
n_samples (int, default=100) – Number of data points to generate discrete mep and e curves.

Returns:

congruence_factor – (n_roi, n_datasets) Congruence factor in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

pynibs.congruence.congruence.cf_curveshift_workhorse_stretch_correction(elm_idx_list, mep, mep_params, e, n_samples=100)¶

Worker function for congruence factor computation - call from multiprocessing.pool Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The computations are parallelized in terms of element indices (elm_idx_list). n_samples are taken from fitted_mep, within the range of the Mep.

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float) –
(n_mep_params_total) List of all mep parameters of curve fits used to calculate the MEP, accumulated into one array.
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …]
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- e.g.: len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
n_samples (int, default=100) – Number of data points to generate discrete mep and e curves.

Returns:

congruence_factor – (n_roi, n_datasets) Congruence factor in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

pynibs.congruence.congruence.cf_curveshift_workhorse_stretch_correction_new(mep, mep_params, e, n_samples=100, ref_idx=0)¶

Worker function for congruence factor computation - call from multiprocessing.Pool. Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The computations are parallelized in terms of element indices (elm_idx_list). n_samples are taken from fitted_mep, within the range of the Mep.

Parameters:

mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float [n_mep_params_total]) –
List of all mep parameters of curve fits used to calculate the MEP (accumulated into one array)
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …]
e (np.ndarray of float) – (n_elm, n_cond) Electric field in elements.
n_samples (int, default=100) – Number of data points to generate discrete mep and e curves.

Returns:

congruence_factor – (n_elm) Congruence factor in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

pynibs.congruence.congruence.cf_curveshift_workhorse_stretch_correction_sign_new(mep, mep_params, e, n_samples=100, ref_idx=0)¶

Worker function for congruence factor computation - call from multiprocessing.Pool. Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The computations are parallelized in terms of element indices (elm_idx_list). ``n_sample``s are taken from fitted_mep, within the range of the Mep.

Parameters:

mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float) –
(n_mep_params_total) List of all mep parameters of curve fits used to calculate the MEP, accumulated into one array.
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …]
e (np.ndarray of float) – (n_elm, n_cond) Electric field in elements.
n_samples (int, default=100) – Number of data points to generate discrete mep and e curves.

Returns:

congruence_factor – (n_elm, 1) Congruence factor in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

pynibs.congruence.congruence.cf_curveshift_workhorse_stretch_correction_variance(elm_idx_list, mep, mep_params, e, n_samples=100)¶

Worker function for congruence factor computation - call from multiprocessing.Pool. Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The computations are parallelized in terms of element indices (elm_idx_list). n_samples are taken from fitted_mep, within the range of the Mep.

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for.
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions
mep_params (np.ndarray of float [n_mep_params_total]) –
List of all mep parameters of curve fits used to calculate the MEP (accumulated into one array)
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …]
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- e.g.: len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
n_samples (int, default=100) – Number of data points to generate discrete mep and e curves

Returns:

congruence_factor – Congruence factor in each element specified in elm_idx_list and for each input dataset

Return type:

np.ndarray of float [n_roi, n_datasets]

pynibs.congruence.congruence.cf_variance_sign_workhorse(elm_idx_list, mep, mep_params, e)¶

Worker function for congruence factor computation - call from multiprocessing.Pool. Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements.

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for.
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float) – (n_mep_params_total) List of all mep parameters of curve fits used to calculate the MEP, accumulated into one array), e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …])
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))

Returns:

congruence_factor – (n_roi, n_datasets) Congruence factor in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

pynibs.congruence.congruence.cf_variance_workhorse(elm_idx_list, mep, mep_params, e, old_style=True)¶

Worker function for congruence factor computation - call from multiprocessing.Pool. Calculates congruence factor for e = (E_mag, E_norm and/or E_tan) for given zaps and elements.

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for.
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float) –
(n_mep_params_total) List of all mep parameters used to calculate the MEP, accumulated into one array).
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …])
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
old_style (bool, default: True) – True: Weight var(x_0_prime(r)) with mean(e(r) * mean(Stimulator Intensity), taken from mep False: Weight var(x_0_prime(r)) with mean(E(r)), taken from e

Returns:

congruence_factor – (n_roi, n_datasets) Congruence factor in each element specified in elm_idx_list and for each input dataset

Return type:

np.ndarray of float

pynibs.congruence.congruence.extract_condition_combination(fn_config_cfg, fn_results_hdf5, conds, fn_out_prefix)¶

Extract and plot congruence factor results for specific condition combinations from permutation analysis.

Parameters:

fn_config_cfg (str) – Filename of .cfg file the permutation study was cinducted with
fn_results_hdf5 (str) – Filename of .hdf5 results file generated by 00_run_c_standard_compute_all_permutations.py containing congruence factors and condition combinations.
conds (list of str) – (n_cond) List containing condition combinations to extract and plot, e.g. ['P_0', 'I_225', 'M1_0', 'I_675', 'P_225']).
fn_out_prefix (str) – Prefix of output filenames of *_data.xdmf, *_data.hdf5 and *_geo.hdf5.

Returns:

<fn_out_prefix_data.xdmf> (.xdmf file) – Output file linking *_data.hdf5 and *_geo.hdf5 file to plot in paraview.
<fn_out_prefix_data.hdf5> (.hdf5 file) – Output .hdf5 file containing the data.
<fn_out_prefix_geo.xdmf> (.hdf5 file) – Output .hdf5 file containing the geometry information.

pynibs.congruence.ext_metrics module¶

pynibs.congruence.ext_metrics.dvs_likelihood(params, x, y, verbose=True, normalize=False, bounds=[(1, 2), (1, 2)])¶

pynibs.congruence.ext_metrics.e_cog_workhorse(elm_idx_list, mep, mep_params, e)¶

Worker function for electric field center of gravity (e_cog) computation after Opitz et al. (2013) [1] - call from multiprocessing.Pool. Calculates the e_cog for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The electric field is weighted by the mean MEP amplitude (turning point of the sigmoid) and summed up. The computations are parallelized in terms of element indices (elm_idx_list).

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for.
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float) –
(n_mep_params_total) List of all mep parameters of curve fits used to calculate the MEP, accumulated into one array.
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1,
mep_#2_para_#1, …]
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- e.g.: len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))

Returns:

e_cog – (n_roi, n_datasets) RSD inverse in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

Notes

[1]

Opitz, A., Legon, W., Rowlands, A., Bickel, W. K., Paulus, W., & Tyler, W. J. (2013). Physiological observations validate finite element models for estimating subject-specific electric field distributions induced by transcranial magnetic stimulation of the human motor cortex. Neuroimage, 81, 253-264.

pynibs.congruence.ext_metrics.e_focal_workhorse(elm_idx_list, e)¶

Worker function to determine the site of stimulation after Aonuma et al. (2018) [1], call from multiprocessing.Pool. Calculates the site of stimulation for e = (E_mag, E_norm and/or E_tan) for given zaps and elements by multiplying the electric fields with each other. The computations are parallelized in terms of element indices (elm_idx_list).

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))

Returns:

e_focal – (n_roi, n_datasets) Focal electric field in each element specified in elm_idx_list and for each input.

Return type:

np.ndarray of float

Notes

[1]

Aonuma, S., Gomez-Tames, J., Laakso, I., Hirata, A., Takakura, T., Tamura, M., & Muragaki, Y. (2018). A high-resolution computational localization method for transcranial magnetic stimulation mapping. NeuroImage, 172, 85-93.

pynibs.congruence.ext_metrics.rsd_inverse_workhorse(elm_idx_list, mep, e)¶

Worker function for RSD inverse computation after Bungert et al. (2017) [1], call from multiprocessing.Pool. Calculates the RSD inverse for e = (E_mag, E_norm and/or E_tan) for given zaps and elements. The computations are parallelized in terms of element indices (elm_idx_list).

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for
mep (list of Mep) – (n_cond) List of fitted Mep object instances for all conditions.
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))

Returns:

rsd_inv – (n_roi, n_datasets) RSD inverse in each element specified in elm_idx_list and for each input dataset.

Return type:

np.ndarray of float

Notes

[1]

Bungert, A., Antunes, A., Espenhahn, S., & Thielscher, A. (2016). Where does TMS stimulate the motor cortex? Combining electrophysiological measurements and realistic field estimates to reveal the affected cortex position. Cerebral Cortex, 27(11), 5083-5094.

pynibs.congruence.stimulation_threshold module¶

pynibs.congruence.stimulation_threshold.intensity_thresh(mep_curve, intensities, mep_threshold)¶

Determines the stimulation threshold of one particular condition (usually the most sensitive e.g. M1-45). The stimulation threshold is the stimulator intensity value in [A/us] where the mep curves exceed the value of mep_threshold (in [mV]).

Parameters:

mep_curve (list [1] of np.ndarray of float [n_samples]) – MEP curve values for every conditions
intensities (list [1] of np.ndarray of float [n_samples]) – To the MEP values corresponding stimulator intensities in [A/us]
mep_threshold (float) – MEP value in [mV], which has to be exceeded for threshold definition

Returns:

stim_threshold_avg – Average stimulation threshold in [V/m] where c_factor is greater than c_factor_percentile

Return type:

float

pynibs.congruence.stimulation_threshold.mean_mep_threshold(elm_idx, mep_curve, intensities, e, mep_threshold)¶

Determines the stimulation threshold by calculating the average electric field over all conditions, where the mep curves exceed the value of mep_threshold (in [mV]).

Parameters:

elm_idx (list of np.ndarray of int) – [n_datasets](n_elements) Element indices where the congruence factor exceeds a certain percentile, defined during the call of stimulation_threshold().
mep_curve (list of np.ndarray of float) – [n_conditions](n_samples) MEP curve values for every condition.
intensities (list of np.ndarray of float) – [n_conditions](n_samples) To the MEP values corresponding stimulator intensities in [A/us].
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- e.g.: len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
mep_threshold (float) – MEP value in [mV], which has to be exceeded for threshold definition.

Returns:

stim_threshold_avg – Average stimulation threshold in [V/m] where c_factor is greater than c_factor_percentile

Return type:

float

pynibs.congruence.stimulation_threshold.sigmoid_thresh(elm_idx, mep_curve, intensities, e, mep_threshold)¶

Determines the stimulation threshold by calculating an equivalent pynibs.expio.Mep.sigmoid over all conditions. The stimulation threshold is the electric field value where the mep curves exceed the value of mep_threshold (in [mV]).

Parameters:

elm_idx (list of np.ndarray of int) – [n_datasets](n_elements) Element indices where the congruence factor exceeds a certain percentile, defined during the call of stimulation_threshold().
mep_curve (list of np.ndarray of float) – [n_conditions](n_samples) MEP curve values for every condition.
intensities (list of np.ndarray of float) – [n_conditions](n_samples) To the MEP values corresponding stimulator intensities in [A/us].
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- e.g.: len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
mep_threshold (float) – MEP value in [mV], which has to be exceeded for threshold definition

Returns:

stim_threshold_avg – Average stimulation threshold in [V/m] where c_factor is greater than c_factor_percentile

Return type:

float

pynibs.congruence.stimulation_threshold.stimulation_threshold(elm_idx_list, mep, mep_params, n_samples, e, c_factor_percentile=95, mep_threshold=0.5, c_factor=None, c_function=None, t_function=None)¶

Computes the stimulation threshold in terms of the electric field in [V/m]. The threshold is defined as the electric field value where the mep exceeds mep_threshold. The average value is taken over all mep curves in each condition and over an area where the congruence factor exceeds c_factor_percentile.

Parameters:

elm_idx_list (np.ndarray) – (chunksize) List of element indices, the congruence factor is computed for.
mep (list of Mep object instances) – (n_cond) List of fitted Mep object instances for all conditions.
mep_params (np.ndarray of float [n_mep_params_total]) –
List of all mep parameters of curve fits used to calculate the MEP (accumulated into one array)
- e.g. [mep_#1_para_#1, mep_#1_para_#2, mep_#1_para_#3, mep_#2_para_#1, mep_#2_para_#1, …]
n_samples (int) – Number of data points to generate discrete mep and e curves.
e (list of list of np.ndarray of float) –
[n_cond][n_datasets][n_elm] Tuple of n_datasets of the electric field to compute the congruence factor for, e.g. (e_mag, e_norm, e_tan). Each dataset is a list over all conditions containing the electric field component of interest
- e.g.: len(e) = n_cond
- len(e[0]) = n_comp (e.g: e_mag = e[0]))
c_factor_percentile (float) – Percentile of the c_factor taken into account for the threshold evaluation. Only c_factors are considered exceeding this.
mep_threshold (float) – MEP value in [mV], which has to be exceeded for threshold definition.
c_factor (np.ndarray of float) –
(n_roi –
dataset. (n_datasets) Congruence factor in each element specified in elm_idx_list and for each input) –
c_function (function) –
Defines the function to use during c_gpc to calculate the congruence factor.
- congruence_factor_curveshift_workhorse: determines the average curve shift
- congruence_factor_curveshift_workhorse_stretch_correction: determines the average curve shift
- congruence_factor_curveshift_workhorse_stretch_correction_variance: determines the average curve shift
- congruence_factor_variance_workhorse: evaluates the variance of the shifting and stretching parameters
t_function (function) –
Defines the function to determine the stimulation_threshold.
- stimulation_threshold_mean_mep_threshold: uses mep_threshold to determine the corresponding e_threshold over all conditions and takes the average values as the stimulation threshold
- stimulation_threshold_pynibs.sigmoid: Fits a new pynibs.sigmoid using all datapoints in the mep-vs-E space and evaluates the threshold from the turning point or the intersection of the derivative in the crossing point with the e-axis

Returns:

stim_threshold_avg – Average stimulation threshold in [V/m] where c_factor is greater than c_factor_percentile.

Return type:

float

pynibs.congruence package

pynibs.congruence package¶

Submodules¶

pynibs.congruence.congruence module¶

pynibs.congruence.ext_metrics module¶

pynibs.congruence.stimulation_threshold module¶

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