sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8d6f66f376e611f75f224da1c48e01ca484579494877f8d5dc3c676efc4eb247 | MATLAB | 6,044 | 161 | function save_color_tables(in_dir, out_dir)
arguments
in_dir (1,1) string { mustBeFolder }
out_dir (1,1) string { mustBeFolder }
end
in_dir = fullfile(in_dir);
[vertices,label,colortable] = read_annotation(fullfile(in_dir, 'label', 'lh.aparc.a2009s.annot'));
save(fullfile(out_... |
fb0d6e8c8f8a5c95d128b0222bc71c9b7da3852957835b164ce6d64212f98c2b | MATLAB | 6,050 | 140 | %% initialize
clear; clc;
currentPath = pwd;
cd ../temp
load('tempFileForAnalysis.mat');
cd(pathBIDS);
cd derivatives
pathDeriv = pwd;
cd(pathDeriv);
cd('spm-preproc'); % For saving preprocessed file from SPM
pathPrepFile = pwd;
prepSubjFolders = dir('sub*');
cd(pathDeriv);
cd('behavior');
pathBehav = pwd;
load('be... |
cb00f25c6bb74a933f15c1a7ddb41088ad0e04631a5945f6c7404d1f1de0ca2f | MATLAB | 6,059 | 186 | function [matPeakDomain,indKeepPeaks] = mergepeaks(vecT,vecV,vecP)
%mergepeaks Merge peaks based on prominence
% [matPeakDomain,indKeepPeaks] = mergepeaks(vecT,vecV,vecP)
%
%Inputs:
% - vecT: timestamp vector
% - vecV: value vector
% - vecP: peak locations
%
%Outputs:
% - matPeakDomain: [P x 3] matrix,
% ... |
a69fc3a7839793a8bee4fafc28c4210a1ecb88a86702cd1d26632b81c2654c36 | MATLAB | 6,077 | 224 | function [dist_vec, angle_vec, mag_vec, dispersion_vec] = zef_rec_diff( ...
zef, ...
inverse_method, ...
noise_db, ...
diff_type, ...
dispersion_radius ...
)
arguments
zef (1,1) struct
inverse_method (1,1) function_handle
noise_db (1,1) double { mustBeNonpositive } = ... |
48930de5fb7c3b5b10787bfcd80e92bdeda46298b448dbc6a1ce7e7cbe3b9da3 | MATLAB | 6,080 | 149 | %% initialize
clear; clc;
currentPath = pwd;
cd ../temp
load('tempFileForAnalysis.mat');
cd(pathBIDS);
cd derivatives
pathDeriv = pwd;
cd(pathDeriv);
cd('spm-preproc'); % For saving preprocessed file from SPM
pathPrepFile = pwd;
prepSubjFolders = dir('sub*');
cd(pathDeriv);
cd('behavior');
pathBehav = pwd;
load('be... |
9cca7c9537137d4eecc6959da6d1073e6c7d88a02b68106c17a830fdff566620 | MATLAB | 6,084 | 180 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function [z,reconstruction_information] = zef_ias_iteration(zef)
inverse_gamma_ind = [1:4];
gamma_ind = [5:10];
h = zef_waitbar(0,1,['IAS MAP iteration.']);
[s_ind_1] = unique(eval('zef.source_interpo... |
4586bd94683432ef8ba964c8ffb7272712e2479a54a19619f5d4bddec96e31e5 | MATLAB | 6,089 | 113 | function zef = zef_Abbott_infinity_strip_multiple_probe(zef)
zef.strip_struct.dir_vec(1,:) = 1/norm(zef.strip_struct.dir_vec(1,:))*zef.strip_struct.dir_vec(1,:);
zef.strip_struct.dir_vec(2,:) = 1/norm(zef.strip_struct.dir_vec(2,:))*zef.strip_struct.dir_vec(2,:);
strip_struct.probe_num = zef.strip_struct.probe_num;
st... |
eca4f2b9554654b06bd07e74f0162d7805a3e99ef5f60f9d43e930418293610f | MATLAB | 6,100 | 216 | function zef_source_tree_cell_edited(~, tbl, event, whichTable)
if nargin < 4 || isempty(whichTable)
error('Provide whichTable = "SourceParameters" or "SignalParameters".');
end
whichTable = lower(char(string(whichTable)));
% === 0) Always work on the latest zef from base (prevents reverting t... |
c8f9afbf8d58a2e98b78ad98c378b8cd4f2b318004c134a2ee1a6680d17b87ab | MATLAB | 6,118 | 112 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function zef = zef_update_parcellation(zef)
if nargin==0
zef = evalin('base','zef');
end
set(zef.h_parcellation_name,'string',zef.parcellation_name);
set(zef.h_parcellation_tolerance,'string',num... |
21d6fecaacb9f4f8176726294609211743b13ee24abd7cc9d3ab3d03c3c3b5c8 | MATLAB | 6,141 | 138 | function Smoco = td_moco2( Yraw, bound, grid_size, maxShift, binWidth, rigid, n_iter, shifts_method, saveY )
% modified from normCorr demo.m
% | Parameter name | Description |
% |----------------|-------------|
% | ```d1,d2,d3``` | dimensions of field of view |
% | ```grid_size``` | size of non-overlapping portion... |
23ebc6c01279a40d5c3777e3749327163b7f3785b756dc2d817d1dd7bb5afa8a | MATLAB | 6,164 | 148 | function [domain_labels, distance_vec, label_vec] = zef_mesh_relabeling(zef, tetra, nodes, domain_labels, distance_vec, use_labeling_priority, h)
if nargin < 5
priority_mode = zef.priority_mode;
end
if nargin < 6
h = zef_waitbar(0,'Mesh re-labeling.')
close_waitbar = true;
else
close_waitbar = false;
end
I = ... |
fe8e5ba68ede7fdca8baead10d19f14aabab9df2c9d468cf8331ef6388bf5e86 | MATLAB | 6,171 | 224 | function [ignore,dat]=sw_ignore_data(dat,opt)
% %sleepwalker help---------------------------------------------------------
% sw_ignore_data to ignore parts of the data (e.g. ignore A,W,R)
% sleepwalker ignore data i.e. to NOT be include in detections
%
% inputs: dat = data structure
% opt.ignore = options ... |
3a089a7cccd45b09271f1e75eb16f740ab60a5aa1e5104e24360903695d96ca4 | MATLAB | 6,172 | 148 | function combineSyncResults(parameters)
%
% Combine the sync results for randomly generated networks as specified in the
% parameters object (or file)
%
% Inputs:
% - parameters - an object containing the expected properties, or a string
% describing the filename to run load this object in.
% Importantly, the ... |
2360ca302c99ba5f98967bee90a642b887f7df89a10bc9be4587d4a350cb9572 | MATLAB | 6,173 | 182 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function [z, reconstruction_information] = zef_dipoleScan(zef)
invMethod=eval( 'zef.dipole_app.InversionmethodDropDown.Value');
regType=eval( 'zef.dipole_app.regType.Value');
inv_leadfield_lambda=eval... |
2a78233ea2639490afee9a098297d918184cfd2dc307182b58053c9a52c7db67 | MATLAB | 6,186 | 161 | function [intResultFlag,sRP] = RP_ExportFile(sFile,sRP)
%get synthesized data
sSynthesis = sFile.sSynthesis;
sLoad = load(fullpath(sSynthesis.folder,sSynthesis.name));
sSynthData = sLoad.sSynthData;
sMetaVar = sRP.sMetaVar;
sProbeCoords = sFile.sProbeCoords;
fprintf('Exporting %s ... [%s]\n',sSynthesis.name,ge... |
288795c85e828bcd00bb8eba9ff29eb7a7a99961d5f88fec5a364f6d5960cf1f | MATLAB | 6,200 | 190 | function h = zef_plot_selected_source_to_axes_stem(treeObj, h_axes, varargin)
%ZEF_PLOT_SELECTED_SOURCE_TO_AXES_STEM Plot selected UI-tree node as a 3D stem/arrow (zef_plot_3D_arrow).
%
% Reads selection from treeObj (uitree) and uses nodeUI.NodeData fields:
% NodeData.SourcePosition.Value (1x3)
% NodeData.Sou... |
ed8140b9728f08769fc2bd7fcf94057a9fb55eae63befc7abb9921f3e356d5e6 | MATLAB | 6,202 | 122 | function [coupling] = extract_voxel_based_structure_function_coupling(subject, dataset, part)
% The goal of this script is to calculate the structure-function coupling
% across each voxel. It assumes that the voxel-based (thresholded) structural
% and functional connectivity matrices for that subject have been generat... |
7f55cd7e1ab099638de81639a77248179536a0a9338d9c9e45594e2ed010476d | MATLAB | 6,217 | 228 | function CBH = cbhandle(varargin)
%CBHANDLE Gets the handle of current colorbar or its peer axes.
%
% SYNTAX:
% CBH = cbhandle;
% CBH = cbhandle(H,...);
% CBH = cbhandle(...,'force');
% CBH = cbhandle(...,'unhide');
% PAH = cbhandle(...,'peer');
%
% INPUTS:
% 'force' - Forces to create co... |
115b0b4ef8e1d1f446a36619d5a990cd0de823488df65ed529cae9628fb893c8 | MATLAB | 6,220 | 159 | % Example of motor imagery classification
% File data/MotorImagery.mat contain preprocessed data from the subject A09
% from the BCI competition IV, dataset IIa.
% Applied preprocessing step are :
%
% - frequency filtering between 8 and 30 Hz (5-th order butterworth)
% - time based epoching between 3.5 to 5.5 s a... |
1eb13f79b3fcf44460035735d8a15679afe9530ace8af8877b499461e37b917c | MATLAB | 6,251 | 190 | function h = cline(varargin)
%cline Draw colored lines. Syntax:
% h = cline([hAx],vecX, vecY, vecZ, vecC, boolPatch)
%
%The original cline() function works with patch objects, which cannot
%be exported to a vector image (e.g., pdf or eps). I therefore built
%this function that has an identical syntax, but instead... |
29f47be69a37eb53baea207cfeb4d9ecdec7dd88c7848e41e1edeba1ea935160 | MATLAB | 6,251 | 193 | function [flips,scorepath,covmats_unflipped] = findflip(data,T,options)
% Finds an optimal permutation of the channels, where goodness is measured
% as the mean lagged partial cross-correlation across pair of channels and lags.
% In other words, it finds a permutation where the signs of the lagged
% partial correlatio... |
fcee4c6264b131f9a2695e1e70539c82092add7a0bdde1c635c691ace6609d99 | MATLAB | 6,253 | 159 | %Copyright © 2018- Joonas Lahtinen, Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
%Plot estimated amplitudes as a bar plot
function zef_plot_GMM_amplitudes
%check if the amplitudes exists
if ~evalin('base','isfield(zef.GMM,''amplitudes'')')
error('Amplitudes a... |
5d7550045ecf5ba9e17f44aa6d5780d8db643f4528d07ae0774e7904c366616d | MATLAB | 6,254 | 196 | function OT_redraw(varargin)
%DC_redraw Sets and redraws windows
% DC_redraw([redrawImage=true])
%get structures
global sOT;
global sFig;
%check whether to plot in new figure
intNewFigure = get(sFig.ptrButtonNewFig,'Value');
%check if data has been loaded
if isempty(sOT) || isempty(sFig)
return;
els... |
d4f86ebdd58c64f2baea99d9d30cdc6f8dcac2095768dfe2359e02d947ff5eaf | MATLAB | 6,260 | 211 | function nbins = calcnbins(x, method, minimum, maximum)
% Calculate the "ideal" number of bins to use in a histogram, using a
% choice of methods.
%
% NBINS = CALCNBINS(X, METHOD) calculates the "ideal" number of bins to use
% in a histogram, using a choice of methods. The type of return value
% depends upon the meth... |
54fb7f45263a1b76ef63c653e017ed9dec21551de5477246ac72a85beb915dd4 | MATLAB | 6,287 | 253 | function Data = extract_spike_window(parm, y, print_mode)
% extract_spike_window
% Data = extract_spike_window(parm, y)
% ----- parameters for window extraction
% parm.fs = sampling rate for observed data [Hz]
% parm.Twin = time window length [sec]
% parm.Tpre = time period before peak ons... |
bf93ef0e5747f13c3c6dcfbaaae46fb180d6268ad8a3b4a5614a5dd29a27666b | MATLAB | 6,331 | 282 | function [mag_fig, rdm_fig] = eccentricity_diff_fig_fn( ...
source_points, ...
mags, ...
rdms, ...
legend_labels, ...
n_intervals, ...
x_scale, ...
min_ecc, ...
mag_handle_num, ...
rdm_handle_num ...
)
% eccentricity_diff_fig_fn
%
% A function that generates two figures comparin... |
b5322a6a92c0501d76e36c55eeafd43bdf9db43c5379cef990cc8cde9e5afd02 | MATLAB | 6,337 | 123 | % script to test sleepwalker functions
%% data file location:
path_file='data/csc_PrL_rest.ncs';
% global settings
opt.signaltype= 'lfp'; %detect sleep events in lfp;
opt.noisewin =1;
%% delta detection
% settings
optd=[];
optd=opt;
optd.detect= 'delta'; % detect slow wave/delt... |
10a690a6b89d08f2e46705f1c36fb09c0f1e3d181d8b1d7693639b0a5881eb94 | MATLAB | 6,340 | 240 | function tree = zef_build_source_tree(parentObj)
%ZEF_BUILD_SOURCE_TREE Build a struct "tree" from a UI tree / checkbox tree.
% Works with both checkboxtree (CheckedNodes exists) and plain tree
% (no CheckedNodes). In the plain tree case, "IsChecked" is inferred from
% SelectedNodes (if available) or node.Checked... |
959813211efa12ac76ca1ae9ad99ea6e18c28bdb2d2e80f836f7eba4187efa2b | MATLAB | 6,342 | 167 | classdef (Abstract) dirichletdiags
% Utilities to compute and test values for dirichletdiags
%
% COMMON TASKS
%
% 1. Given an expected state lifetime, what dirichletdiags should I use?
%
% dirichletdiags.get(0.2,100,11) <- 0.2s expected lifetime, 100Hz sampling rate, K=11
%
% 2. Given a value for dirichletdiags, wh... |
f3f133cf6dd33834ff93eb83faf64b702d0a7c6fa03bcfc156966f1271a42bc7 | MATLAB | 6,376 | 255 | function spike_info = spike_information(data, data_win, parm)
% spike_information of extracted window data
% spike_info = spike_information(data, data_win, parm)
%
% --- spike info for extracted window
% spike_info.spike_num(n) = spike number of n-th window
% spike_info.spike_time{n} = spike onset time of n-th... |
c44273919adb6a467d93b0229c20306f32ef708405e754f4af7192876d2a137c | MATLAB | 6,381 | 155 | %Copyright © 2021- Sampsa Pursiainen & GPU-ToRRe-3D Development Team
%See: https://github.com/sampsapursiainen/GPU-Torre-3D
load([torre_dir '/system_data/signal_configuration.mat']);
load([torre_dir '/system_data/mesh_1.mat']);
load([torre_dir '/system_data/system_data_1.mat']);
load([torre_dir '/system_data/nodes_1.... |
e6eb6f8724c62dbe159974d3479195fd3f79879bdb055e7b124c3b9d11ed3908 | MATLAB | 6,394 | 110 | function [ensemble_performance] = calculate_ensemble_performance_with_threshold(params, ensemble_nodes, log_likelihood_by_frame, data_index, threshold_reference)
num_udf = params.num_udf;
dataset = [params.x_train; params.x_valid; params.x_test];
true_labels = dataset(data_index, end-num_udf+1:end)'; % hardcode beca... |
593a16f7cbaf164880ba1ac3bde737c100cd4925fa843afe28032f1c032e9cf9 | MATLAB | 6,410 | 149 | %% Result 1 : Long-Range Connections Enhance Object Recognition in Shallow Networks (Figure 2)
%% Generate dataset
if ~exist('IMAGE_mod')
tic
disp('generating modified MNIST ...(~ 30 sec)')
[IMAGE_mod,LABEL_mod] = fun_generate_mMNIST(numTrain_mod);
toc
end
%% Show dataset
ind_img = 3;
di... |
1e1f40e1b342808c3089043357e550e96277370749e87fdf7b920c4fa4c49506 | MATLAB | 6,431 | 133 | %% Result 1 : Long-Range Connections Enhance Object Recognition in Shallow Networks (Figure 2)
% ============================================================================================================
%% Add LRC vs Add Layers (Figure 2g)
disp('================================================================='... |
56fd1bb723b1efd2d2b10960b41e8deb78153b471884def23f76cc6c3cd2ac8b | MATLAB | 6,439 | 185 | function [I,dist_vec] = zef_point_in_compartment(zef,reuna_p,reuna_t,nodes,varargin)
if isempty(zef)
zef = evalin('base','zef');
end
if eval('exist(''zef'')')
if eval('isfield(zef,''meshing_threshold'')')
meshing_threshold = eval('zef.meshing_threshold');
else
meshing_threshold = 0.5;
... |
29b0ccb49d4cd67751b056a5e33079fef7c35038e3849b3b2902fed712bb220d | MATLAB | 6,446 | 155 | function A = generateNewRandomRingMatrix(N, d, gamma, includeSelf, undirected, allowSelf, ensureConnected)
%% Generate a new ring network, which is rewired subject to a given probability
%
% Inputs
% - N - network size
% - d - in-degree
% - gamma - probability of rewiring each link after the regular network is co... |
bd355c5e8607fe67dbeeba806b6398eb5fafa645e601255559e4f1f93ff6804a | MATLAB | 6,456 | 210 | function [meas_data,roi_source_pos,dip_ori,amp_all,n_multiple_sources,roi_specs] = zef_find_source_ROI(zef,varargin)
allow_overlapping_ROIs = true;
if nargin>1
if islogical(varargin{1})
allow_overlapping_ROIs = varargin{1};
end
end
%get variables
noise_level = zef.synth_source_ROI(1,17);
s_p = zef.s... |
1385b0b1ac2fbae5395b100df49025ff2253c158be8b30361ab20f4bf26640be | MATLAB | 6,459 | 123 | function zef = zef_exp_app_start(zef)
if isfield(zef,'EXP')
if isfield(zef.EXP,'app')
return;
end
end
zef.EXP.app = exp_app;
if ~isfield(zef.EXP,'parameters')
zef.EXP.parameters = [];
end
%Script piece for either loading values from zef structure or
%substitute them there if the app is launched firs... |
77331a58cab72642c1d6ec439d7453b9a70e01b1cb99e41e70351f78b41ff25e | MATLAB | 6,478 | 117 | %Copyright © 2018- Joonas Lahtinen, Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
%This is script for opening advanced GMM plot options.
if isfield(zef.GMM.apps,'PlotOpt')
if isvalid(zef.GMM.apps.PlotOpt)
eval(zef.GMM.apps.PlotOpt.UIFigure.CloseRequest... |
7805a9b28523e04e675150f5748ddbebecbab3d2afe69ba514b4b18b1b7542d9 | MATLAB | 6,495 | 205 | function M = realphasefactory(n, z0, zmax)
% Returns a manifold struct to optimize over phases of fft's of real signals
%
% function M = realphasefactory(n)
% function M = realphasefactory(n, z0)
% function M = realphasefactory(n, z0, zmax)
%
% If x is a real vector of length n, then y = fft(x) is a complex vector
% wh... |
88787e4e03ab43391c72df77fec93efa019d474b3fc541e1839c98e91b02d152 | MATLAB | 6,500 | 92 | function zef = zef_open_dataBank(zef)
zef.dataBank.app=zef_dataBank_app;
zef = zef_dataBank_init(zef);
%intitial values
if ~isfield(zef.dataBank, 'folder')
zef.dataBank.save2disk='Off';
else
if ~isfield(zef.dataBank, 'save2disk')
zef.dataBank.save2disk='Off';
end
zef.dataBank.app.DataFolder.... |
8a3195fbc45b689835ee8c48d44fa50f822c186024bb131b995bc24b5b3ecece | MATLAB | 6,511 | 189 | function [control_infor, output_infor, time_infor, r_end] = func_reservoir_validate(traj_type, bridge_type, time_infor, ...
input_infor, res_infor, start_info, properties, dim_in, dim_out, Wout, r_end, dt, plot_movie, save_rend, ...
failure, blur, traj_frequency)
%% read parameters
% save_rend = 0 means, the robot ... |
f55d4ddeaa20b12c462ca1abfde7bf4dbec37c66109cf2cba8a647e8b61b39f1 | MATLAB | 6,515 | 144 |
%--------------------------------------------------------------------------------
% adder.m
%
% This demo is included in
% Triple equivalence for the emergence of biological intelligence
% Takuya Isomura
%
% The MATLAB scripts are available at
% https://github.com/takuyaisomura/reverse_engineering
%
% Copyright (C) 20... |
b4256cd783e1850ffb5620d13ba48448801d246dce7eed60ebb72d641bacbd5a | MATLAB | 6,519 | 211 | function M = fixedrankfactory_2factors_subspace_projection(m, n, k)
% Manifold of m-by-n matrices of rank k with two factor quotient geometry.
%
% function M = fixedrankfactory_2factors_subspace_projection(m, n, k)
%
% A point X on the manifold is represented as a structure with two
% fields: L and R. The matrix L (mxk... |
84e6633bb5d0da6ee6c335112ed6b8ff9f8801a085e1fbd2a8b3f47985d88f4e | MATLAB | 6,533 | 195 | classdef IASInverter < inverse.CommonInverseParameters & dynamicprops
%
% IASInverter
%
% A class which defines the properties needed by the IAS inversion method,
% and the method itself.
%
properties
%
%This defines the post-hoc weighting used with the Bayesian model
... |
d438179c133328a66145d8418b829a5dfd0d8366cad12f37137173761917815e | MATLAB | 6,536 | 109 | function process_files_cox(suffix, reg_exp, test)
addpath(genpath('/home/mfromano/spm/spm12/'));
BASE_DIR = ['/data2/MRI_PET_DATA/processed_images_final' suffix filesep];
if nargin > 2 && test
MRI_folder_old = [BASE_DIR 'ADNI_MRI_NACC_recenter' suffix filesep];
else
MRI_folder_old = [BASE_DIR 'ADNI_MRI_nii_rece... |
e6fd812417dfa23c1346135317bcdca01a138c98693b21e82eb4298158b0b2e8 | MATLAB | 6,566 | 169 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function [z,reconstruction_information] = exp_em_iteration(void)
h = zef_waitbar(0,1,['EM MAP iteration.']);
hyper_type = evalin('base','zef.exp_em_hyper_type');
n_ias_map_iter = evalin('base','zef.in... |
212c842e1d036f6d852c1c55f79d6a78bb76e2894897003520597bb48686aaa5 | MATLAB | 6,580 | 208 | function [z_vec, self] = invert(self, f, L, procFile, source_direction_mode, source_positions, opts)
%
% invert
%
% Builds a reconstruction of source dipoles from a given lead field with
% the selected beamforming method.
%
% Inputs:
%
% - self
%
% An instance of Beamforme... |
150e3dd7a31467d921e90be92f2c3cdc8dffbbbf8b90e3670fc812a520d834c9 | MATLAB | 6,603 | 216 | function M = obliquecomplexfactory(n, m, transposed)
% Returns a manifold struct defining complex matrices w/ unit-norm columns.
%
% function M = obliquecomplexfactory(n, m)
% function M = obliquecomplexfactory(n, m, transposed)
%
% Oblique manifold: deals with complex matrices of size n x m such that
% each column has... |
25e189d1b007f952298950f09bbc587250e4a35d60d99571fc37053c0cbbdd8c | MATLAB | 6,607 | 248 | function run_VL_haemodynamic
% VL scheme - DCM haemodynamic model example
%
% Hidden states (x):
% 1. S - vasoactive signal
% 2. logf - log rCBF
% 3. logv - log venous blood volume
% 4. logq - log dHb
%
% Parameters (P):
% 1. log_transit - haemodynamic transit rate (Hz)
% 2. log_decay - decay rate of vasoactive si... |
f4176eea668a062e55dc99dfc53e600d0280f3f0bcb111879467513916c347a1 | MATLAB | 6,617 | 185 | %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
function [x, theta] = zef_gibbs_sampler_step(L, y, x, theta, theta0, beta, std_lhood, hypermodel, decay_val_hyperprior, nbins_hyperprior, source_direction_mode)
%One-dimensional sampling resolution.
i... |
c53c3b50411b874560f57e37a867588fd399c16e7a89c0f066efdd79ab90ba42 | MATLAB | 6,664 | 210 | % AUC Area under ROC
%
% [dblAUC,Aci,Ase,pAuc] = getAuc(vecTP,vecFP,alpha,flag,nboot,varargin);
%
% INPUTS
% vecTP - True positive values
% vecFP - True negative values
%
% OPTIONAL
% alpha - level for confidence intervals (eg., enter 0.05 if you want 95% CIs)
% fla... |
892bd1a44506be567ad5d2683c9dd98d7a10d9d5288ea321079c67ae3a2af4a4 | MATLAB | 6,672 | 205 | % clearvars -except SS
function subject_struct=excel_parsing_personalized(filename)
% filename = 'S01';
sheet = 1;
xlRange = 'B2:G2';
demograph_xl = xlsread([filename],sheet,xlRange);
demographics.Age=demograph_xl(1);
%% sex
if demograph_xl(2)==1
demographics.Gender='male';
elseif demograph_xl(2)==2
... |
c4714965440100868e42747193746b5d83df49b49ce04304e44025a9ea90bc3f | MATLAB | 6,675 | 197 | function [stensil, signs, source_moments, source_directions, source_locations, n_of_adj_tetra] = zef_fi_dipoles( ...
nodes ...
, ...
tetrahedra ...
, ...
brain_ind ...
)
% zef_fi_dipoles: generates the information related to face-intersecting
% dipoles in the tet... |
534cc774bd31d8074711af97a73aaf34a4f0f06a55d16685188490ecf7d33c68 | MATLAB | 6,687 | 114 | function process_files_cox_unused(suffix, reg_exp)
addpath(genpath('/home/mfromano/spm/spm12/'));
BASE_DIR = ['/data2/MRI_PET_DATA/processed_images_final' suffix filesep];
MRI_folder_old = [BASE_DIR 'ADNI_MRI_nii_recenter' suffix filesep];
disp(MRI_folder_old)
if nargin < 2
reg_exp = '^([0-9]+_mri_I[0-9]+).*\.nii$... |
c232c25c6b1902c6c5d68cebdbb528bcac49e0aa66d009ffa845e3a43b91bea3 | MATLAB | 6,698 | 121 | function [ensemble_performance] = calculate_ensemble_performance(params, ensemble_nodes, log_likelihood_by_frame, data_index)
num_udf = params.num_udf;
dataset = [params.x_train; params.x_valid; params.x_test];
true_labels = dataset(data_index, end-num_udf+1:end)';
log_likelihood_by_frame = log_likelihood_by_frame(:,... |
f77e9a162ecb7edc967bc7a19734a0657878a75281646dd4ea67432480495274 | MATLAB | 6,700 | 220 | function load_model(app)
% function load model
filename = app.file_model;
update_log(app, 'Parsing the Model File');
% load params file first
try
params = load(filename,'params');
params = params.params; % ends up nested
params = convert_paths_to_absolute(params);
app.params = params;
app.ParamsL... |
a8a5ffd7466bb0b052e32681d165a4c3605e7beeb9aba975cb52e685eab1256b | MATLAB | 6,703 | 207 | % -------------------------------------------------------
%
% synthesize_P_QRST_timeSeries.m - This script synthesizes a simulated
% P wave and a QRST segment to a full hearbeat and extends it to a 10s
% time series
%
% Ver. 1.0.0
%
% Created: Claudia Nagel (13.10.2022)
% Last modified: ... |
1581bd10ea7dd33093b1e30bb4b687e9ac918b6500bcb46ffd2d0b0dc49729ab | MATLAB | 6,723 | 290 | function data = generate_spike_signal(parm, spike_time)
% ----- Poisson spike signal generation
% data = generate_spike_signal(parm, spike_time)
% ----- Time of Poisson spike
% spike_time = time of spike onset [sec] (Nspike x 1)
% ----- spike generation setting
% parm.tau = [onset time; decay time] [se... |
09d7a639179c969850e74f41153ba8e7fde08a822f3cc85717b8468c4718e13a | MATLAB | 6,724 | 198 | function [z_vec, self] = invert(self, f, L, procFile, source_direction_mode, source_positions, opts)
%
% invert
%
% Builds a reconstruction of source dipoles from a given lead field with
% the IAS RAMUS method.
%
% Inputs:
%
% - self
%
% An instance of RAMUSInverter with t... |
4142c829b377db294299df8bc27a39b60602f9fa420c513d2f93786b342ea1d3 | MATLAB | 6,725 | 183 | function [cellCoeffs,matX,cellFunctions,vecLinCoeffs,vecLinCoeffFunctions] = gnmfit(matX,vecY,cellCoeffs0,varargin)
%gnmfit Fits a generalized non-linear model where predictors are
% related to parameter values through non-linear functions.
%
%[cellCoeffs,matXwithBias,cellFunctions,vecLinCoeffs,vecLinCoeffFunction... |
49761aa6fbd6ba4e6793a93f688665535b192cbb422c2328abb5975491c8a4d2 | MATLAB | 6,729 | 164 | label_ind = uint32(label_ind);
if isequal(labeling_flag,1)
%***********************************************************
%Initialize labeling.
%***********************************************************
[node_labels,distance_vec] = zef_solid_angle_labeling(zef, label_ind, nodes, h);
I = find(sum... |
6a94ba76256187c254eadf61cae743d89902b512c8aed7723c42be59ebfcf6ab | MATLAB | 6,733 | 221 | function clusters = ez_clusterstat_time(cond1,cond2,reps,t)
%ez_clusterstat_time Cluster-based statistical test for paired data; Maris and Oostenveld (2007)
%clusters = ez_clusterstat_time(cond1,cond2,reps,t)
%
%Inputs:
%cond1 and cond2: 2d matrices with dimensions [trials, time]
% Any missing data should be conv... |
c4c564e38949902955c75ec6e398f0089196b4392be2c6e2aeb6363bd5bc0e72 | MATLAB | 6,736 | 183 | function [matC, dblMSE, intRankT, sSuppOut] = doRdRankReg(matX, matY, varargin)
%doRdRankReg Performed reduced rank multivariate regression.
% [matC, dblMSE, intRankT, sSuppOut] = doRdRankReg(matX, matY)
% Finds the reduced rank regression using a full rank assumption. X
% is a n-by-r matrix, and Y is a n-by-... |
35ba086eb66d6ebd5e5e1937d23af6c4067048092a7291e7284494182d74ccb4 | MATLAB | 6,754 | 249 | function [Model,data] = estimate_multispike_step(...
Model,Data,Spike_state)
% Estimate multispike state
% [Model,data] = estimate_multispike_step(...
% Model,Data,Spike_state)
% --- Model parameters (input: fixed parameter)
% Model.tau
% --- Model parameters (input/output: updated parameter)
% Mo... |
9c73713dac09ffcf4b179042aa46c642b13f0e79c4f0c1744bbea6fadc77648e | MATLAB | 6,764 | 182 | function [sPupil,imPupil,imReflection,imBW,imGrey] = getPupil(gMatVid,gMatFilt,sglReflT,sglPupilT,objSE,vecPrevLoc,vecPupilT,sET)
%getPupil Detects pupil in image using GPU-accelerated image processing
%syntax: [sPupil,imPupil,imReflection,imBW,imGrey] = getPupil(gMatVid,gMatFilt,sglReflT,sglPupilT,objSE,vecPrevLoc,v... |
481d02486f3c6b1ffb28189cb2bc1f78dbd14dc1412a73194b1bd1ab36c17371 | MATLAB | 6,773 | 184 | function tests = hmmtest (Gamma,T,Tsubject,Y,options,hmm)
% Statistical testing to differenciate between groups according to how much
% time they spend on the different states, or how quickly they switch between states.
% For statistical testing on how the probability of the states is modulated
% by a stimulus, time p... |
9232b54baa40dc61216570be1f29654b5043217535f4497781f86b104ea8630d | MATLAB | 6,793 | 195 | function [opt, spindle, stats, fh] = sw_run_spindle_LFP(varargin)
% [spindle] = sw_run_spindle_LFP(dat, opt)
% top level function to perform event detection
% inputs:
% dat - data input which can be either
% a) string with path/file.dat or
% b) a data structure with the follo... |
eb3c6d8fd3d1ae03f22f1ce701c77a36bbac9b836bafd1c74fdaeb4d6115e831 | MATLAB | 6,804 | 180 | %% For all patient-specific VTAs
function fingerprint_all_sessions(varargin) %path, pat, assessment
% Reads and concatenates each HCP subjects session
% computes the correlation between the mean activity of voxels included
% in the each VTA and all the non-VTA voxels
% averages and z transforms the results... |
a324b7d268c55696f9fd99c61809c4052f04334773a425e330c1263c3d26e64d | MATLAB | 6,807 | 140 | function A = generateNewRandomMatrix(N, p, allowSelf, undirected, ensureConnected, ensureALinkForEachNode)
%%
% Generate a new Erdos-Renyi random matrix
%
% Inputs
% - N - network size
% - p - connection probability
% - allowSelf - whether to allow self-connections
% - undirected - whether to make the matrix ... |
e654163e78b7ec553dda4a02bd504dd5ab957b328f1cfcbc66dfae315743091e | MATLAB | 6,828 | 215 | function result = lgcpregress(n,k,kernel)
%{
LGCPREGRESS Log-Gaussian Cox Process regression
RESULT = lgcpregress(N,K,KERNEL) infers log-rates from binned visit
counts K and spike counts N using kernel KERNEL returned by
MAKEGRIDCELLKERNEL(L,P,V), where L is the size of the L×L 2D spatial
grid, P is the grid-... |
7f74992bbaa9db48aaebd751e9c72720697167b4c36faae9afd76b37f0083cf0 | MATLAB | 6,844 | 191 | function d = estoi(x, y, fs_signal)
% d = estoi(x, y, fs_signal) returns the output of the extended short-time
% objective intelligibility (ESTOI) predictor.
%
% Implementation of the Extended Short-Time Objective
% Intelligibility (ESTOI) predictor, described in Jesper Jensen and
% Cees H. Taal, "An Algorithm for ... |
bff5dcbd01d12978fbeef290d8a9a504a619d6ba7107f4cb1aca31f252fae16a | MATLAB | 6,850 | 191 | function d = estoi(x, y, fs_signal)
% d = estoi(x, y, fs_signal) returns the output of the extended short-time
% objective intelligibility (ESTOI) predictor.
%
% Implementation of the Extended Short-Time Objective
% Intelligibility (ESTOI) predictor, described in Jesper Jensen and
% Cees H. Taal, "An Algorithm fo... |
9f1794e5134a68fd9d9f610df21e0f1b0bfc9e3fafad679c0e9ad1a20243e445 | MATLAB | 6,853 | 260 | % Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_folder is... |
5112a5dcb6f8b5d3cf793f7b4ebd9d0f298473e15e5d4beacf670aeef0daab4c | MATLAB | 6,898 | 117 | function zef = zef_downsample_surfaces(zef)
if nargin == 0
zef = evalin('base','zef');
end
zef.h = zef_waitbar(0,1,'Resampling surfaces.');
zef.temp_time = now;
relative_resolution_vec = zef_find_relative_resolution(zef);
zef.number_of_compartments = length(zef.compartment_tags);
active_compartment_ind = 0;
for ... |
6e98a4fea5bcce6271c65cb4c7866c18d79d5dd30056211c9ddf8dd625e85f52 | MATLAB | 6,919 | 256 | %
% disturbance = 1.00;
% measurement_noise = 0.00;
% try for only the first one and then only the second one
% then try them together
% then try uncertainty
time_today = datestr(now, 'mmddyyyy');
%% only disturbance
measurement_noise = 0.00;
% disturbance_set = exp(linspace(log(0.01), log(10), 20));
disturbance_se... |
a26c638a0ae2e2e71b3bbe520c04b99bf3454d8339f6e96444af12e2eee8ea91 | MATLAB | 6,964 | 202 | %% Nat Comms Ictogenesis Figure S5
clear
load('20230127_PooledData.mat');
% Set up binning ranges
ephistbins = 1:15;
ephistedges = (1:16) - 0.5;
rshistbins = 0:7;
rshistedges = ([0:7, 9]) - 0.5;
EXP5HZ = "B30_P5F5_";
EXP10HZ = "B30_P5F10_";
EXP20HZ = "B30_P5F20_";
sz = struct();
sz.stim... |
a76d0ecdaf1848b58dc197585dcf1bd9cda3a899ac3157c8b43e0ffaa9114c28 | MATLAB | 6,965 | 215 | function M = fixedrankfactory_2factors(m, n, k)
% Manifold of m-by-n matrices of rank k with balanced quotient geometry.
%
% function M = fixedrankfactory_2factors(m, n, k)
%
% The first-order geometry follows the balanced quotient geometry described
% in the paper,
% "Linear regression under fixed-rank constraints: ... |
afd337e3c64a70db1eda707c0c503085fbfa4dd5ec4c811ca7a7a401904e1e7d | MATLAB | 6,966 | 307 | function zef = zef_nse_tool_init(zef)
if not(isfield(zef,'nse_field'))
zef.nse_field = struct;
end
if not(isfield(zef,'inv_time_1'))
zef.nse_field.inv_time_1 = 0;
end
if not(isfield(zef,'inv_time_2'))
zef.nse_field.inv_time_2 = 0;
end
if not(isfield(zef,'inv_time_3'))
zef.nse_field.inv_time_3 = 0;
e... |
04bd5c15e4c32c9c1480d9672242fd5c4ac9219b3fbed44b6d289f52265a3969 | MATLAB | 6,981 | 162 | classdef ParModelCollection
properties
%Properties & Definitions
models; % individual models in collection
x_train; % training dataset
x_valid; % validation dataset
x_test; % test dataset
end
methods
function self = ParModelCollection(models, param... |
9e4f1274e7f3de19cb25341480fe7a6928d18fed728e666c6999d419f86b51fe | MATLAB | 6,991 | 162 | classdef SingleModelOptimization
properties
%Properties & Definitions
models; % individual models in collection
x_train; % training dataset
x_valid; % validation dataset
x_test; % test dataset
end
methods
function self = SingleModelOptimization(mod... |
35bac191da7d582fa7c26f0b57d0d50a66e1afd1929f1aabc40f6e6aff29fbe5 | MATLAB | 7,035 | 114 | % NLX2MATTS Imports data from Neuralynx NTS files to Matlab variables.
%
% [TimeStamps, Header] = Nlx2MatTS( Filename, FieldSelection, ExtractHeader,
% ExtractMode, ModeArray );
%
% Version 6.0.0
%
% Requires MATLAB R2012b (8.0) or newer
%
%
% INPUT ARGUMENTS:
% FileName: String... |
16793ae38fb69ac3b00b184631fdbac8629f1725202bd4b33dc571ed366a3d59 | MATLAB | 7,043 | 150 | function A = generateNewRandomFixedDMatrix(N, p, allowSelf, undirected, ensureConnected)
%% Generate a new random matrix with a fixed indegree for each node
%
% Inputs
% - N - network size
% - p - connection probability
% - allowSelf - whether to allow self-connections
% - undirected - whether to make the matri... |
59af0ee52413a631f5f0e8f59aed9d5d208fcf8c4bf358fadf37dd8ef9516701 | MATLAB | 7,053 | 116 | %Copyright © 2018- Joonas Lahtinen, Sampsa Pursiainen & ZI Development Team
%See: https://github.com/sampsapursiainen/zeffiro_interface
%This is script for opening advanced GM modeling options.
if isfield(zef.GMM.apps,'ModelingOpt')
if isvalid(zef.GMM.apps.ModelingOpt)
eval(zef.GMM.apps.ModelingOpt.UIFigu... |
b2808c011b995de51f10344706b3f997ad1eca8481f40aef516b7e17ea340775 | MATLAB | 7,069 | 203 | function [cv_acc,acc,meanGenPlot,AUC,LL] = standard_classification(X,Y,T,options,binsize)
% Determine the cross validated accuracy of a classification type on brain
% data X with mutually exclusive classes Y
%
% INPUT
% X: Brain data, (total time by regions) or (time by trials by regions)
% Y: Stimulus, (total time by ... |
5cd133c9ba5b72bbdaeb4eb5249de97102d4178886aae088935c598367fd88b1 | MATLAB | 7,116 | 200 | function M = multinomialdoublystochasticfactory(n)
% Manifold of n-by-n doubly-stochastic matrices with positive entries.
%
% function M = multinomialdoublystochasticfactory(n)
%
% M is a Manopt manifold structure to optimize over the set of n-by-n
% matrices with (strictly) positive entries and such that the entries o... |
a59e37163e862a39d095e7a637fc34621db8c302f06756835bf714573d203e50 | MATLAB | 7,119 | 216 | function M = elliptopefactory(n, k)
% Manifold of n-by-n psd matrices of rank k with unit diagonal elements.
%
% function M = elliptopefactory(n, k)
%
% A point X on the manifold is parameterized as YY^T where Y is a matrix of
% size nxk. As such, X is symmetric, positive semidefinite. We restrict to
% full-rank Y's, s... |
e77d8441e1b8679bc22504a87d4b955b4f49502b00948cd39883417314ebb1f7 | MATLAB | 7,120 | 127 | function plot_ensemble_coordinates_structure_style_2(app)
cla(app.ensemble_coordinates);
app.ensemble_coordinates.NextPlot = 'replacechildren';
% 1
udf_id = app.StimulusEditField.Value;
neuron_id = app.HighlightedEnsNode.Value;
% 1
rois = app.rois;
num_rois = size(rois.xpix, 1);
best_model = app.best_model;
edge_mat ... |
49b05b7cb2b8d241a0c5abab8248c73ec620fdedda20ce72185874363417ed10 | MATLAB | 7,121 | 272 | function [ ...
surface_triangles, ...
surface_nodes, ...
tetra_ind, ...
tetra_ind_global, ...
tetra_ind_diff, ...
node_ind, ...
node_pair, ...
face_ind] = zef_surface_mesh(tetra, nodes, I, gpu_mode)
% TODO Documentation
%
% The basic idea is that this function returns the surface triang... |
c8ebcd118a9d055af71673dd7c0dceb9d12957f13fcc4003c21ff1321c1758b2 | MATLAB | 7,124 | 258 | % Copyright © 2018- Sampsa Pursiainen & ZI Development Team
% See: https://github.com/sampsapursiainen/zeffiro_interface
%
% TODO Documentation
%
% This function decomposes a given set of nodes and tetrahedra (degrees of
% freedom or DOF) into
%
% Input:
%
% - nodes
%
% The nodes that make up a finite element mesh.
%... |
9f21fe4ad33fdd21d1ae42523127f6ca82346601596fab800b2dd9044d1fda4a | MATLAB | 7,160 | 187 | function [vecSpikeCh,vecSpikeT,intTotT] = DP_DetectSpikesInBinaryFile(strFilename,sP,vecChanMap)
%DP_DetectSpikesInBinaryFile Detect spike times in binary (SpikeGLX) file
% [vecSpikeCh,vecSpikeT,intTotT] = DP_DetectSpikesInBinaryFile(strFile,sP,vecChanMap)
%
%Note: vecSpikeT is in sample numbers, not in seconds. ... |
3f1f6dad5fdda0701ba78ddc927b5151a1f46e80dd3cc4f7a8d88059338ce72c | MATLAB | 7,172 | 200 | function [assignment,cost] = munkres(costMat)
% MUNKRES Munkres (Hungarian) Algorithm for Linear Assignment Problem.
%
% [ASSIGN,COST] = munkres(COSTMAT) returns the optimal column indices,
% ASSIGN assigned to each row and the minimum COST based on the assignment
% problem represented by the COSTMAT, where the... |
46a97f7366f8511c7c777e9980415f537a32ad801dea4fd84f5d1e8f0d52ad52 | MATLAB | 7,181 | 145 | function [mu,sig,alpha,beta] = fit_eeg_distribution(X,min_clean_fraction,max_dropout_fraction,quants,step_sizes,beta)
% Estimate the mean and standard deviation of clean EEG from contaminated data.
% [Mu,Sigma,Alpha,Beta] = fit_eeg_distribution(X,MinCleanFraction,MaxDropoutFraction,FitQuantiles,StepSizes,ShapeRange)
... |
a1645d7ba37eb123eddd04cee9c267ebac1cacde138697e8d637483ee5942a89 | MATLAB | 7,207 | 189 | %% initialize
clear; clc;
currentPath = pwd;
cd ../temp
load('tempFileForAnalysis.mat');
cd(pathBIDS);
cd derivatives
pathDeriv = pwd;
cd(pathDeriv);
cd('spm-preproc'); % For saving preprocessed file from SPM
pathPrepFile = pwd;
prepSubjFolders = dir('sub*');
cd(pathDeriv);
cd('behavior');
pathBehav = pwd;
load('be... |
08e50754174a694e9e7fe784d933a5e21c34310cb6dcabfaf52328c7d600bb0b | MATLAB | 7,220 | 232 | %% Copyright © 2025- Joonas Lahtinen and Alexandra Koulouri
classdef GroupLassoInverter < inverse.CommonInverseParameters & dynamicprops
%
% GroupLassoInverter
%
% A class which defines the properties needed by the GroupLasso inversion method,
% and the method itself.
%
properties
... |
3d66951b702c66ec7cdbb77948e654f1ad7f49e3704d3c311f8ddfe687563d9d | MATLAB | 7,223 | 207 | function wssize(varargin)
% WSSIZE Display in the command window the size of the variables in the workspace using KB, MB and GB
%
% WSSIZE Display preserving the order of the workspace pane using mixed units
%
% WSSIZE arg or WSSIZE('arg') One argument syntax
% WSSIZE arg1 arg2 or WSSIZE('arg1','arg2') Two ar... |
66de83548588a77d3c38d25fc7d9a2b5f5cee43189c0bb4eaec1a88e64b5932b | MATLAB | 7,241 | 143 | function signal = clean_channels(signal,min_corr,ignored_quantile,window_len,max_broken_time,linenoise_aware)
% Remove channels with abnormal data from a continuous data set.
% Signal = clean_channels(Signal,MinCorrelation,IgnoredQuantile,WindowLength,MaxBrokenTime,LineNoiseAware)
%
% This is an automated artifact reje... |
f93042796d740fe9abf19a5c02d164fb85a2293f10b0c7c3a3825e66304d8105 | MATLAB | 7,257 | 191 | %% initialize
clear; clc;
currentPath = pwd;
cd ../temp
load('tempFileForAnalysis.mat');
cd(pathBIDS);
cd derivatives
pathDeriv = pwd;
cd(pathDeriv);
cd('spm-preproc'); % For saving preprocessed file from SPM
pathPrepFile = pwd;
prepSubjFolders = dir('sub*');
cd(pathDeriv);
cd('behavior');
pathBehav = pwd;
load('be... |
3fd3d8ac5700c542d0c0239d9155f0f27c4c31537849da28b553eabeeba22afa | MATLAB | 7,277 | 122 | function zef = find_synthetic_source(zef)
if nargin == 0
zef = evalin('base', 'zef');
end
zef.find_synth_source = find_synthetic_source_app;
zef.synth_source_init = cell(16,2);
%Initial names of the parameters:
zef.synth_source_init{1,1} = 'x position';
zef.synth_source_init{2,1} = 'y position';
zef.synth_source_i... |
1f6aabae292ed87eb06b79401109afe200e45582ea7fe804ac446f4b3214b9d5 | MATLAB | 7,298 | 240 | function tests = specttest(sp_fit,Nperm,within_state,relative)
%
% From a multitaper or MAR estimation of the states spectra (per subject),
% or from a spectral factorisation as returned by spectdecompose,
% this function performs, for each state and frequency component (or bin),
% statistical testing (via permutati... |
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