sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
db6d7db0744e4e376569e702f42f54c5d63093c6bfcff3112316f54b9e40407b | MATLAB | 2,197 | 92 | function [inference] = tapas_vlinear_inference(inference, pars)
%%
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
if ~isfield(inference, 'estimate_method')
inference.estimate_method = @tapas_mcmc_blocked_estimate;
end
if ~isfield(inference, 'initialize_states')
inference.initialize_states = @tapas_linear... |
3ab294af899b3b673cb93da070fb2479f7b824499cf3a044cda9c0adf7b73e82 | MATLAB | 2,198 | 83 | function FigureS4(datadir, codedir)
%FigureS4 - Average trial initiation time in mixed blocks conditioned on
% the previous block
% datadir = directory of dataset
% codedir = director of code
%% Set up paths
s = pathsep;
pathStr = [s, path, s];
onPath = contains(pathStr,...
codedir, 'IgnoreCase', ispc);
if ~... |
6a19f583395fd805517d0f122d9912f62f75a210e7c26002fed7d7d6bf575e37 | MATLAB | 2,199 | 65 | %% [chi] = Wrapper_QSM_CFSL2(localField,mask,matrixSize,voxelSize,algorParam,headerAndExtraData)
%
% Input
% --------------
% localField : local field map (tissue fields), in Hz
% mask : signal mask
% matrixSize : size of the input image
% voxelSize : spatial resolution of each dimension of the data,... |
fa089b5072069ef80435158122f994ab339cab5bc4685fa05a527e858132d3bf | MATLAB | 2,199 | 54 | function truncated = TruncateIntervals(intervals, duration, flip)
%TruncateIntervals
%
% Sometimes it makes sense to limit the duration of the intervals you are
% analysing: for example, taking the first hour of slow wave sleep to
% score reactivation/replay. TruncateIntervals will truncate the inputted
% intervals f... |
d29b661a512771a1005c78ef84bb7ed3b5b09805e9df4f17d9dc59d8ca39d124 | MATLAB | 2,200 | 59 | %% function sphereKernel = SphereKernel(matrixSize,radius,voxelSize)
%
% Input
% --------------
% matrixSize : chi matrix size
% radius : radius of sphere, in mm
% voxelSize : voxel dimensions, in mm (1x3 vector); default = [1 1 1],
% i.e. radius is treated as being in voxe... |
fc715a8a3d470d7f69c033d34f88a8b8a42588d4b6cc71cc67df4b184de80643 | MATLAB | 2,200 | 75 | function fear_cueTrigReact_cond(basename,varargin)
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
param.binSize=0.02;
param.halfWindow=5;
param.targetHC=3;
param.varName='cueTrigReactCond';
param.saveFile=[basicMetaData.AnalysesName '-cu... |
31fd57638ae9d2a1cf3ba45e77ba4b118a6afd447d3bd751496f2b7805599488 | MATLAB | 2,201 | 59 | function [ T ] = getMultilevelThresholds(I, ttotal)
% OTSUREC Returns a set of thresholds for the input image using the multi-level
% otsu algorith.
%
% OTSUREC computes a set T of thresholds from the input image I employing the
% multi-level Otsu algorithm. The multi-level Otsu algorithm consists in
% fin... |
328a9ecdfac21ae2d9839d7328ac03cc031f5f0591723ad96ee5d851230779dd | MATLAB | 2,201 | 47 | function mask = select_this_atlas_subset(region)
run('set_library_paths.m');
addpath(SPM_PATH); % per spm docs, do not genpath it
addpath(genpath(CANLABTOOLS_PATH));
addpath(genpath(CANLABMASKS_PATH));
% this atlas is not implemented through CanlabCore/Neuroimaging_Pattern_Masks
% so we're just... |
4f2a7cf7a92bab27a13e6379336dc6ab7a83ad9e7498d47e2ed15dbd87134621 | MATLAB | 2,202 | 59 | % --------------------------------------------------------------------
function set_static_box_height_Callback(hObject, eventdata, handles)
% hObject handle to set_static_box_height (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see G... |
e005a7bb3602d29873621937095210332be87a7aca7c416f627c9e25a00775da | MATLAB | 2,202 | 75 | function cellid = fname2cellid(fname)
%FNAME2CELLID Convert filenames to cell IDs.
% CELLID = FNAME2CELLID(FILENAME) converts valid filenames into cellids
% or returns empty if it fails.
%
% Valid filenames
% (1) start with the default path or only include 'rat\session\unit.mat'
% (2) unit 1 of tetrode 1... |
2da8e29bdef0640baf2c1e97e90c2d5a0c1e343d412c30047ac5e37fd8e57f30 | MATLAB | 2,203 | 57 | function plotOptoHists(data)
% Plots histograms of contact times during optogenetic stimulation
% Requires data already concatenated across behavior files into a "data"
% struct
% Separate trials
trialsNormal = [data.success] == 1 & [data.optoProblem] == 0 & [data.optoTrial] == 0 & [data.grabTimeC] > [data.liftTimeC] ... |
9c6f478f31e88215bc4bfe34dde64492480bdd893040d94f4dbe13f196f084c1 | MATLAB | 2,203 | 49 | % EEG_CHANINDS - look up channel indices in a EEG structure. Function is obsolete.
% Use EEG_DECODECHAN instead.
%
% Usage:
% >> inds = eeg_chaninds(EEG, channames);
% Inputs:
% EEG - EEG structure containing a chanlocs substructure.
% the chanlocs structure may also be ... |
61f9327e84a49c4a121f83c053424cf8108dec297790f09f1c42847a536ec83f | MATLAB | 2,204 | 70 | function paths = config()
% CONFIG - Configuration file for SwitchBeta analysis
%
% Returns a structure containing all path information needed for the analysis.
%
% INSTRUCTIONS FOR SETUP:
% 1. Copy this file to config.m (which is git-ignored)
% 2. Edit the paths below to match your local system
% 3. Run config(... |
6d8d7f6c21f563fffc0414a29f4ee2a09c3dcab39e09bae7cb639ee01f942085 | MATLAB | 2,204 | 87 | function db_insert(tablename, s)
% DB_INSERT inserts a structure into a database table. Each field of
% the structure should correspond with one of the fields in the table.
%
% Use as
% db_insert(tablename, s)
%
% See also DB_OPEN, DB_SELECT, DB_SELECT_BLOB, DB_INSERT_BLOB, DB_CLOSE
% Copyright (C) 2007, Robert Oos... |
496676430fe23337a7f187bb8bf88dcf0981f27627ced5251e1497017cc22d24 | MATLAB | 2,205 | 54 | function TMSDeepTargetComp (t1dir,outdir,coord,roiradius,depthx)
%% example for input parameters
t1dir = 'E:\tt\wc1co3.nii' % the pathway of your c1co*.nii in MNI space
outdir= 'E:\tt' % folder saving associating results
coord = [-35.06 -8.97 79.47] % MNI coordinate
% this funciton was based... |
b03ca32c4d366e9d99e68e654ca569dc0e8215eab2727f103c89dbac877adec1 | MATLAB | 2,205 | 71 | function matlabbatch = tapas_physio_update_batch_with_spm_jobman(matlabbatch, ...
fileBatchM)
% loads existing matlabbatch into SPM Job manager and returns updated
% matlabbatch object (e.g., if created with old version and new fields
% were added to matlabbatch structure)
%
% matlabbatch = tapas_physio_updat... |
be80775222f4d85bbb78d67ab0c10a95113a19cbf147edfffab4f5d3bbd128ce | MATLAB | 2,205 | 59 | % prior distributions to be used for hyperparameters of Gaussian processes
% using infPrior.
% There are two different kinds of prior distributions: simple and composite:
%
% simple prior distributions:
%
% priorGauss - univariate Gaussian
% priorLaplace - univariate Laplace
% priorT ... |
e37e125940a045ace4454880c3c82b197c0fc5940364857f56e2a78c6a0db320 | MATLAB | 2,205 | 86 | function [gx_sym,gy_sym,gz_sym,u_sym,v_sym,w_sym]=symmetrize_vector(gx,gy,gz)
% This function symmetrize gradient vectors
%Shift the image if the first dimension is odd number
if mod(size(gx,1),2)==1
Shift=1;
if Shift
gx_old=gx; gy_old=gy; gz_old=gz;
NN=size(gx);
gx=zeros(NN(... |
0dc720b48ddc3c5f68e0ba0efe564711b3bb1703ec23622b895b90bde3f515e8 | MATLAB | 2,206 | 69 | %% inputNIFTIList = read_default_to_filelist(inputDir, filePattern)
%
% Input
% --------------
%
% Output
% --------------
%
% Description:
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 11 August 2021
% Date modified:
%
%
function [isLoadSuccessful, inputNIFTIList] = read_default_to_filelist(inputDi... |
8a8b047a7fa9e9e4a41135064947abc5594220646d940a90d7a4abfc68f20af2 | MATLAB | 2,206 | 62 | function glm_prfINITIALSCREENING(ppdir,runix)
% approach: assume HRF, average the 3 reps up front, fit all data, do supergrid.
% define
tr = 1;
% load data
data = {};
for p=1:length(runix)
a1 = load_untouch_nii(sprintf('%s/preprocessVER1/run%02d.nii',ppdir,runix(p)));
data{p} = single(a1.img);
end
clear a1;
% l... |
5abd0260672b1b78e16fab4c49d2d2abe8b327fa06d0e6efddb5bee7490c0cc4 | MATLAB | 2,208 | 69 | function [SW,w,CC,PLn] = small_worldness_RL_wu(A,R,L)
%SMALL_WORLDNESS_RL_WU Small-worldness
%
% [w,CC,PLi] = small_worldness_RL_wu(A,R,L);
%
% The value of small-worldness, w, is between -1 and 1. Values close to
% 0 have small-world properties; values close to 1 have random
% properties; values c... |
b8a883e1d8acbed26b91b25e31b64c3540a82d8cd86c44c215b5bf6b4c3eb7d6 | MATLAB | 2,208 | 91 | % op_takeaverages.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_takeaverages(in,index);
%
% DESCRIPTION:
% Extract the averages with indices corresponding to the 'index' input
% array.
%
% INPUTS:
% in = input data in matlab structure format.
% index = vector indicating the indices of the average... |
a9ba0734a1bc2f27c2516b819945d4d00b4fcfafe0cd9d50bb4e16e12259b845 | MATLAB | 2,209 | 69 | function violin(hA, Y, axLoc, color, alpha, mrkSz, mxStr, txtCol, fntSz, bw)
if isempty(hA)
hA = gca;
end
%% Calculate the kernel density
if axLoc(1) == 0
plotY = 1;
axLoc = axLoc(2);
else
plotY = 0;
axLoc = axLoc(1);
end
if nargin > 9
[f, u, ~] = ksdensity(Y, 'Bandwidth', bw);
else
[f, ... |
76be9f0b59326120c640d42a61e81627daba3fd1006b3e66fab26b04fb754f7c | MATLAB | 2,210 | 95 | function y = tapas_softmax_wld_sim(r, infStates, p)
% Simulates observations from a Boltzmann distribution with volatility as temperature
%
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2019 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of... |
486527575b0292ff504ea95fd77305ec9ab3e1ff35586f9aeb75486a649b93af | MATLAB | 2,211 | 59 | function MakeTableOfFunctions()
% MakeTableOfFunctions Outputs a csv summarizing INP_mops.txt
% ------------------------------------------------------------------------------
% Copyright (C) 2013-2026, Ben D. Fulcher <ben.d.fulcher@gmail.com>,
% <http://www.benfulcher.com>
%
% If you use this code for your research, pl... |
d8369dd338b37e10f8aa1ea7ec89be10c41b22e110e3ff90afb2636d0854e115 | MATLAB | 2,211 | 75 | function [w, state] = adam(w, state, grad, opts, lr)
%ADAM
% Adam solver for use with CNN_TRAIN and CNN_TRAIN_DAG
%
% See [Kingma et. al., 2014](http://arxiv.org/abs/1412.6980)
% | ([pdf](http://arxiv.org/pdf/1412.6980.pdf)).
%
% If called without any input argument, returns the default options
% structure.... |
26c2490d3e004e1d5eba9f3f97537f5f10b73d608ad6026f5c4876ba18fb530c | MATLAB | 2,213 | 62 | function id = defaultId(stack)
% DEFAULTID returns a string that can serve as warning or error identifier,
% for example 'FieldTip:ft_read_header:line345'.
%
% See also WARNING, ERROR, FT_NOTICE, FT_INFO, FT_DEBUG
% Copyright (C) 2017, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptool... |
b7eed09f57270c5018b25edf28958b0eed188d819b3ff67ba25e8f6f2ab1cbef | MATLAB | 2,214 | 76 | % function output = test_add_overlay(input)
% Test image overlay creation and plotting of 3D-RGB-image via montage
%
% output = test_add_overlay(input)
%
% IN
%
% OUT
%
% EXAMPLE
% test_add_overlay
%
% See also tapas_uniqc_add_overlay
% Author: Saskia Bollmann & Lars Kasper
% Created: 2014-11-25
% Copyright (... |
146f023677a05449b34d8ca8fb5c370e35479c9cf10e4f5dabe386596018803e | MATLAB | 2,218 | 62 | %% choose an arbitrary pupil trace
key.animal_id=8804;
key.session=1;
key.scan_idx=3;
%% fetch timestamps, fetch and filter pupil radius trace
r = fetchn(preprocess.EyeTrackingFrame & key,'major_r');
pupilTime = fetch1(preprocess.Eye & key,'eye_time');
% interpolate over undetected frames
rInterp = interp1(pupilTime... |
1af7bed66a0457c304bd8def80e2050f2b23d1471696dae294c7e625260cc267 | MATLAB | 2,218 | 79 | function vl_testnn(varargin)
%VL_TESTNN Run MatConvNet test suite
% VL_TESTNN('option', value, ...) takes the following options:
% `cpu`:: true
% Run the CPU tests.
%
% `gpu`:: false
% Run the GPU tests.
%
% `single`:: true
% Perform tests in single precision.
%
% `double`:: false
% Perform tests in do... |
ce0af48f253485525f636205c23707063ad7187765b64a224ab539e9591172b8 | MATLAB | 2,218 | 79 | function indic = meta_stochastic_mask_blobs(volInfo,cl)
% indic = meta_stochastic_mask_blobs(volInfo,cl)
%
% Shuffles blob locations (centers) for a study
% Makes a mask first and then returns
% indicator (indic) format for aggregation across studies
%
% Inputs:
% volInfo.xyzlist: list of all in-mask coordinates (e.g.,... |
251820d6b0ade450c2ba130df8967e8c627b091e6cfc3d7a86657db3052405c5 | MATLAB | 2,220 | 74 | function interactiveConductance3Droi(fa, mask, atlas, dim_size, potentials, dim, slice, max_limit)
% Interactive conductance map
%
% Author: Aina Frau-Pascual
% Conductance map
if dim==3
fa2 = squeeze(fa(:,:,slice));
mask0 = squeeze(mask(:,:,slice));
dimx_size = dim_size([1,2]);
atlas_slice = squeeze(... |
5cb1fb35df42dcc084925e51e885486a0c747ed7f469625c292f74254b3f9a32 | MATLAB | 2,220 | 59 | function [dataheat, ind_lim] = get_norm_rsc(spktr, norm_ind, nbins, prct_bounds)
% GET_NORM_RSC
% Syntax:
% [dataheat, ind_lim] = get_norm_rsc(spktr, norm_ind)
% [dataheat, ind_lim] = get_norm_rsc(spktr, norm_ind, nbins, prct_bounds)
% Description:
% Given neurons-by-time spike counts (spktr) and a per-neuron nor... |
03bb5b38d71c8837798613a0d6ed01709e840c666ba658db492f30479b5aee08 | MATLAB | 2,221 | 40 | function outputStruct = pairsProcessing(recordingData, recordingName, ...
singPulseRange, multPulseRange, show_plots)
disp("Processing singPulseRange")
mult = 0; calculateCurrent(recordingData, singPulseRange, mult, show_plots);
disp("Processing multPulseRange")
mult = 1; calculateCurrent(rec... |
56193357296237f2c12fb20b36054f5b3cdd755f3bb13475b42da034117c271f | MATLAB | 2,221 | 73 | function n2f=surfing_nodeidxs2faceidxs(f)
% finds the mapping from vertices to face indices.
%
% N2F=NODEIDXS2FACEIDXS(F)
% INPUT:
% F: Px3 node indices for P faces (base1)
% OUTPUT:
% N2F: QxR mapping matrix for Q nodes (Q==MAX(F(:))), if R is the
% maximum number of faces that contain a single n... |
3992cf656f597eaf4f4e8cee5fa4513d2320f4902c6db1fa7d77a8865de158f7 | MATLAB | 2,222 | 54 | function UKeywords = TS_WhatKeywords(whatData)
% TS_WhatKeywords Lists keywords contained in the specified HCTSA data file
% ------------------------------------------------------------------------------
% Copyright (C) 2013-2026, Ben D. Fulcher <ben.d.fulcher@gmail.com>,
% <http://www.benfulcher.com>
%
% If you use... |
732175c371b2ad30422c3d4ecc9bf1dd81089ced21b46075a0a85a2ebe6a22fe | MATLAB | 2,222 | 54 | % Regenerates the small-worldness ground-truth fixture used by
% test_pipeline_small_worldness.py. Unlike the other gen_*_reference.m
% scripts, this does NOT depend on a real MATLAB pipeline run's saved
% adjacency matrices (OutputData03Mar2026/ExperimentMatFiles isn't always
% present in every environment) — it build... |
e981b8b0ef9e2ccbe892de9ee2bceddcf9ee2870a9b39f8e244b69b05882279d | MATLAB | 2,222 | 67 | function results = analyze_simulation_results(s2, params, elapsed_time)
% ANALYZE_SIMULATION_RESULTS - Calculate simulation statistics
%
% H1 Line: Analyze spike data and compute network statistics
%
% Syntax:
% results = analyze_simulation_results(s2, params, elapsed_time)
%
% Description:
% Computes firing rates,... |
867a3638466b3d1b27786c851fe840180674f90070fc716a65507f3d4daa23dc | MATLAB | 2,223 | 72 | % generateSFTimeSeries - Generate stimulus time series from run info
% Converts SF indices into a vector of SF values.
% Blank periods are filled with a small value (0.0001) to avoid log(0) in logGauss.
%
% Syntax
% I = generateSFTimeSeries(p, t)
%
% Input Arguments
% p - structure containing ... |
17617f420667c83e5e0e59b258d138d94fcc0465975111e8fd7757efa9d5eb93 | MATLAB | 2,224 | 51 | %--------------------------------------------------------------------------
% voxelize.m script is used generate voxelized tif file from sparse points
%
%% Developed and maintained by Kannan Umadevi Venkataraju <kannanuv@cshl.edu>
%% do not distribute without permission.
%
% Usage
% nx=450; minx=0;maxx=450;ny=650;miny... |
410aa5fd1cd8d644da9dc5b4ac85f31dbce1fce99e0e74018c9f18c611650dd0 | MATLAB | 2,224 | 84 | function [BCMatrix, BCRHS] = boundaryCondition1D(BC)
% It creates the matrix of coefficient based on the BC structure provided
% by the user. It also generates the right hand side vector of the linear
% system of equations
%
% SYNOPSIS:
% [BCMatrix, BCRHS] = boundaryCondition1D(BC)
%
% PARAMETERS:
%
%
% RETURNS:
%
%
... |
6f5dc95983c8039bcd0b6a7472354ba869cf6e06ea6382b4f7d143e2fb111745 | MATLAB | 2,225 | 54 | function [nirs, qualityMatrices] = pruneWithQT(nirs, params, numChan)
% Applies the QT-NIRS algorithm to prune channels based on scalp coupling
% index (SCI) and power spectral power (PSP) thresholds. Ensures that both
% chromophore channels are consistently pruned if one is marked for
% removal.
% Check if pa... |
8e34ae3b7746d92bc12c49b0c2bd31dcbbeaccb2a277809fd048b8611bb13895 | MATLAB | 2,225 | 86 | function [m1gs] = GS_orth_1D(fname, rescale, show, oname)
%
% [A_orth] = GS_orth_1D(fname, rescale, show, oname);
%
% A function to perform Gram-Schmidt orthogonalization
% on 1D files.
%
% fname: Name of AFNI 1D file
% If nothing is specified, GUI file selector is used.
% Note that you can pass a m... |
c46089d690dc56439407224f164b6facdb78ed6baaeacc707b58db2d22426447 | MATLAB | 2,225 | 54 | function out = DN_PLeft(y, th)
% DN_PLeft Distance from the mean at which a given proportion of data are
% more distant.
%
% Measures the maximum distance from the mean at which a given fixed proportion,
% p, of the time-series data points are further.
% Normalizes by the standard deviation of the ti... |
f86caf65cb2964465090d1869fd611a9480572cef00a3e6d9a83a80c38259535 | MATLAB | 2,225 | 77 | function data = read_asa_msr(fn)
% READ_ASA_MSR reads EEG or MEG data from an ASA data file
% converting the units to uV or fT
% Copyright (C) 2002, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you ca... |
2de4922a00bde574b413cc309109f31c2ff8977396135341751955d327fb15ef | MATLAB | 2,226 | 71 | function [fh, this] = plot_regressors(this, module)
% Plots regressors
%
% G = MrGlm()
% G.plot_regressors(inputs)
%
% This is a method of class MrGlm.
%
% IN
% module which type of regressors shall be plotted
% 'realign' Realignment parameters.
% See also MrImage.re... |
e49b3edd005dcd46d905ea64df5cea17115c530397c9b8077609a158d8471430 | MATLAB | 2,226 | 58 | function [rez]=projection_2(rez,DATA)
M_clust = length(unique(rez.st(:,end)));
nt0 = rez.ops.nt0;
Nchan = rez.ops.Nchan;
batch = length(unique(rez.st(:,end-1)));
Nrank = 3;%default value for projection hard coded
[~,W, ~, ~,~] = SVD_template(single(rez.M_template/(rez.ops.bitmVolt*rez.ops.scaleproc)), Nrank,rez.ops.... |
305dc1224f21135725ec686db2fdc82b52f3a852cd6deafb7ba75fc67bf63787 | MATLAB | 2,227 | 87 | function [amsd_out] = amsd_detector(hsi_img,tgt_sigs,mask,n_dim_tgt,n_dim_bg)
%
%function [amsd_out] = amsd_detector(hsi_img,tgt_sigs,mask,n_dim_tgt,n_dim_bg)
%
% Adaptive Matched Subspace Detector
%
% ref:
% Hyperspectral subpixel target detection using the linear mixing model (article)
% Manolakis, D. and Siracusa... |
3b2ba51603fe987ba801d92cb066cbaa7679b3a3bc01c6c3ff75536298fe8058 | MATLAB | 2,228 | 66 | function export_Calls(loop_function, file_postfix, hObject, eventdata, handles)
% hObject handle to excel (see GCBO)
% This function xports selected call files to excel sheets with stats for each call
%% Select Files
% Select the files
[fname, fpath] = uigetfile([char(handles.data.settings.detectionfolder) '/*.mat'... |
7972f51610fe85bdaff91b28937b0d791ee378bf7af28f07c47caab00f08372d | MATLAB | 2,229 | 58 | function M = specialeuclideanfactory(n, k)
% Returns a manifold structure to optimize over the special Euclidean group
%
% function M = specialeuclideanfactory(n)
% function M = specialeuclideanfactory(n, k)
%
% The special Euclidean group (the manifold of rigid transformations):
% This is a product manifold of the ro... |
b186cab4f198d5a98f6d794e7331ba286079e766525f86447716d16aaed749f5 | MATLAB | 2,229 | 69 | function plotMP2RAGEproperties(MP2RAGE, HG)
% Don't plot anything if the user has closed the figure
if nargin<2
HG = gcf;
set(HG, 'Name','MP2RAGEproperties');
end
if ~isgraphics(HG)
return
end
% define signal and noise function as in the paper
Signalres = @(x1,x2) x1.*x2./((x2.^2+x1.^2));
noiseres = @(... |
44d14b8c3e2a190ccadec38956419a3baccb0c11e8ed0af4da7fda549ff104a7 | MATLAB | 2,230 | 87 | function [LocalMinIndex, BasinGraph, AdjacentList] = mfunc_LocalMin(nodeNumber, E)
% Find local minimum points
% Get vector list
vectorList = mfunc_VectorList(nodeNumber);
% Calculate vector index (See mfunc_VectorIndex())
[vectorIndex EnergyIndex] = mfunc_VectorIndex(vectorList);
% Calculate local minimum ... |
57f3549762c6c7ec32f046937c79624cd76222960b4c5253a475f205a9c20075 | MATLAB | 2,230 | 58 | %VL_NNBNORM CNN batch normalisation.
% Y = VL_NNBNORM(X,G,B) applies batch normalization to the input
% X. Batch normalization is defined as:
%
% Y(i,j,k,t) = G(k) * (X(i,j,k,t) - mu(k)) / sigma(k) + B(k)
%
% where:
%
% mu(k) = mean_ijt X(i,j,k,t),
% sigma2(k) = mean_ijt (X(i,j,k,t) - mu(k))^2,
% ... |
b2c2a804b69529066c1ea1e8cc7ea0573710d6c725e0652068e8743eddface56 | MATLAB | 2,230 | 91 | function h_line=signalplot(S)
%function h_line=signalplot(S)
%
%PURPOSE
%
%To plot several signals, e.g., estimated sources into the same
%graphic axis; a simplified alternative to MATLAB's native subplot
%command.
%
%EXAMPLE OF BASIC USE
%
%Get the "best" estimated sources from Icasso result struct sR and
%plot them... |
984a62b3e8fecfc9f9189bc0da50b0bf35fb1fe10dca0954aed4748fed499e72 | MATLAB | 2,231 | 48 | function tapas_ph_binary_plotTraj(r)
% Plots trajectories estimated by tapas_fitModel for the tapas_rw_binary perceptual model
% Usage: est = tapas_fitModel(responses, inputs); tapas_rw_binary_plotTraj(est);
%
% --------------------------------------------------------------------------------------------------
% Copyri... |
41a7d3d3bbb5a05731261f43f04b971e8198a471447d1d4b8dc1ded049e77880 | MATLAB | 2,232 | 59 | function propIncreased = computeTrialProportion(all_spike_times_s, allStimTimes, poststim_window_s, baseline_window_s)
% COMPUTETRIALPROPORTION Proportion of trials with more post-stim than pre-stim spikes.
%
% For a single electrode, this function:
% 1. For each stimulus trial, counts spikes in the pre-stim and post-s... |
667ed2f3ca0bdb1e9848c4ae27d301150b1463352bee2211c4e4ab2322fd4fb1 | MATLAB | 2,232 | 50 | % TUTORIAL - Bring up the ICA / electrophysiology toolbox tutorial
% in a browser window (see docopt.m in the toolbox dir).
% Tutorial URL: http://www.sccn.ucsd.edu/tutorial/
% Download: See http://www.sccn.ucsd.edu/ica.html
%
% Authors: Scott Makeig & Tzyy-Ping Jung, SCCN/INC/UCS... |
c496ff3dfa63c333448b0850ed7aa8b2526f91b798671051a0111b6892e4efa1 | MATLAB | 2,232 | 41 | function [HeadMotion FD_Jenkinson FD_VanDijk FD_Power]=HMCal(RPDir,MeanFunDir)
RP = load(RPDir) ;
% [path aname b] = fileparts(RPDir)
MaxRP = max(abs(RP));
MaxRP(4:6) = MaxRP(4:6)*180/pi;
MeanRP = mean(abs(RP));
MeanRP(4:6) = MeanRP(4:6)*180/pi;
%Calculate FD Van Dijk... |
e49b851e1702973ed54fed73e23026f56bec8f5502a0158d2be13c87d8c90504 | MATLAB | 2,232 | 70 | [data4 timeEP] = load_open_ephys_data_faster('\*.spikes');
NumSpikes = 4; % indicate the number of diff cells from the particular electrode
Tfile= FindFiles('TTp113.0n0*.t64');
r= LoadSpikes(Tfile);
RawData = zeros(40 +3, 4*NumSpikes);
InterpFactor = 20; %interpolation factor
for i = 1:NumSpikes
for k = 1:4
data = ... |
0b5460c67c284e7532de2dacf7d50a73dd85c0db8122974e456c7956c06ce7fa | MATLAB | 2,233 | 75 | %{
Copyright (c) 2024 Axion BioSystems, Inc.
Contact: support@axion-biosystems.com
All Rights Reserved
%}
classdef Waveform < matlab.mixin.Heterogeneous
%WAVEFORM Container for single dimensional recorded sample data
%
% Channel: Source Location of the waveform
%
% Start: Tim... |
5f1e426154708ffc09ae55f63faf23a3dd06f1eb1cda39579312a84cc66564bf | MATLAB | 2,233 | 51 | function [ floatVAXF ] = uint32le_to_VAXF( uint32le )
%UINT32LE_TO_VAXF Converts from IEEE-LE (UINT32) to VAXF (single precision)
% This function takes a raw 32bit unsigned integer (little endian)
% and converts it into the equivalent floating point number it represents
% in the VAXF file format for floating point n... |
3ad1b618d7987164a59534bc0228d95d0bb3d2534181190de2851916709d85a4 | MATLAB | 2,234 | 70 | function [vol] = read_ctf_hdm(filename)
% READ_CTF_HDM reads the head volume conductor model from a *.hdm file
%
% vol = read_ctf_hdm(filename)
% Copyright (C) 2003, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free... |
79cbe868dba0a7a2bdc8bd6f37da038a4d083cd13c3f34b04d85bf02dddc3ed6 | MATLAB | 2,234 | 69 | function [M, Mx, My] = diffusionTerm2D(D)
% This function uses the central difference scheme to discretize a 2D
% diffusion term in the form \grad . (D \grad \phi) where u is a face vactor
% It also returns the x and y parts of the matrix of coefficient.
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
%... |
d4fa6e6961e0e37f62c0d82d9c6443373919c2e34f02418f555353e3e06f202c | MATLAB | 2,234 | 76 | function cost = plotprofile(problem, x, d, t)
% Plot the cost function along a geodesic or a retraction path.
%
% function plotprofile(problem)
% function plotprofile(problem, x)
% function plotprofile(problem, x, d)
% function plotprofile(problem, x, d, t)
% function plotprofile(problem, x, [], t)
% function plotprofi... |
f5839bb24605355c6574290a2c70470785f2cb1b8d2d5ff13d4abed5c92f91b5 | MATLAB | 2,234 | 53 | %{
# all directional drift trials for the scan
-> preprocess.Sync
---
ndirections : tinyint # number of directions
%}
classdef Directional < dj.Computed
properties
keySource = preprocess.Sync & (vis.Trial*vis.Monet & 'speed>0' & 'trial_idx between first_trial and la... |
4808cd4eaeeb359428c7bc912dd7a942f45fe9b3ee5a0140fa7260eea72481f4 | MATLAB | 2,235 | 68 | function ImportFromXBAT(hObject, eventdata, handles)
[fname, fpath] = uigetfile('*.mat','multiselect','on','Select X-BAT logs');
if isnumeric(fpath); return; end
[outpath] = uigetdir(handles.data.settings.detectionfolder,'Select Output Folder');
if isnumeric(outpath); return; end
if ischar(fname)
fname = {fname};... |
0fa378b8b440b44594f428b4e689319f5c04d9be98197a5542026615bf046479 | MATLAB | 2,236 | 50 | function [pval,norm_zscore] = get_episode_signif(raw_trace,this_eventonset_frames,this_eventoffset_frames,shuf_frame_range)
% determine whether each cell’s activity was significantly correlated with a behavior
% ZZ 2022
% Ref: Paquelet et al, Neuron, 2022.
num_shuff = 1000;
if isempty(this_eventonset_frames)||isem... |
77175c2b03151ae93588567b3bc205b2f597d171d5ddda9a1f1af65159271309 | MATLAB | 2,237 | 62 | function otherImage = compute_mask(this, varargin)
% transforms image into binary mask with pixels >= threshold set to 1
% 0 for all other pixels
%
% Y = MrImage()
% Y.compute_mask('ParameterName', ParameterValue)
%
% IN
% varargin 'ParameterName', 'ParameterValue'-pairs for the following
% prope... |
78325088af41c2145cc3e02d6f63c0464d5a5089e51b5569fdd10c781a0f1bca | MATLAB | 2,238 | 56 | function [lp,dlp] = priorTMulti(mu,s2,nu,x)
% Multivariate Laplace hyperparameter prior distribution.
% Compute log-likelihood and its derivative or draw a random sample.
% The prior distribution is parameterized as:
%
% p(x) = ( 1 + r2/(nu-2) )^(-(nu+D)/2) / Z, where
% Z = gamma(nu/2) * sqrt(det(pi*(nu-2)*s2))... |
b58529af15322ae8d7c8499aa0be413fbb12957e1ccf3b03dce8b66e07848396 | MATLAB | 2,238 | 52 | function osp_updateMMSpecsOvWindow(gui)
%% osp_updateSpecsOvWindow
% This function updates the specs overview tab.
%
%
% USAGE:
% osp_updateSpecsOvWindow(gui);
%
% INPUT:
% gui = gui class containing all handles and the MRSCont
%
%
% AUTHORS:
% Dr. Helge Zoellner (Johns... |
d50fd079e1de1849a202a0f6347791150d679fc150d394eb95621e984361d92e | MATLAB | 2,239 | 73 | % op_phaseCrCho.m
% Georg Oeltzschner, Johns Hopkins University 2019.
%
% USAGE:
% [out,phaseShift]=op_phaseCrCho(in, suppressPlot);
%
% DESCRIPTION:
% This function fits two Lorentzians to the Cr and Cho peaks, and optimizes
% the phase of the input spectrum based on Cr/Cho.
%
% If data with multiple averages is sup... |
de4810d9bd98bd906dedd7c76e3b38adc26dcefb6e130033845e9737093b2764 | MATLAB | 2,239 | 73 | % Bang et al (2020) Private-public mappings in human prefrontal cortex
%
% Reproduces Figure 3C
%
% Visualises ROI contrast estimates under GLM1 and performs associated
% statistical test
%
% Note that contrast estimate for "signalled vs hidden" (SvH) context is not
% shown in Figure 3C but is included here
%
% Statis... |
257f704424c4cefeb1748ba2ff758b506955a40ddcd3e6f4600f4eede417e36d | MATLAB | 2,240 | 58 | function [Wrr, Wrf, degree_params] = load_indegree_connectivity(options, params)
% LOAD_INDEGREE_CONNECTIVITY - Load connectivity with degree information
%
% H1 Line: Load connectivity matrices with heterogeneous degrees
%
% Syntax:
% [Wrr, Wrf, degree_params] = load_indegree_connectivity(options, params)
%
% Descrip... |
f2e6b791271c03ee37e186c9fbbf2b86eacebff1aaf883f412b58b19286b9fea | MATLAB | 2,240 | 58 | function out = DN_CustomSkewness(y, whatSkew)
% DN_CustomSkewness Custom skewness measures
%
% Compute the Pearson or Bowley skewness
%
% ---INPUTS:
% y, the input time series
%
% whatSkew, the skewness measure to calculate, either 'pearson' or 'bowley'
%
% cf. https://mathworld.wolfram.com/PearsonsSkewnessCoeffici... |
fcfb0cf7af12727f4d3da5058e48aa3453caac060265812a9323ad389b31fb5a | MATLAB | 2,240 | 69 | % Preprocessing of fmri time series
%
% This script performs slice timing correction, fieldmap undistortion and
% realignment of an array of fmri time series. Realignment can be done
% across multiple time series. Note that the same slice timing and fieldmap
% parameters are assumed for all time series. So, it makes m... |
863d31402f6db94105d456b60f26a163953b1cbc8b04d5c6db59478a2dac71cb | MATLAB | 2,241 | 73 | function [gx,gy,gz,mag]=compute_grads_local(img)
%Neighbourhood for connected components
%6 or 18 or 26
Ngh=6;
%Pad edges to account for excessive cropping of full image
img_new=zeros(size(img)+2);
img_new(2:end-1,2:end-1,2:end-1)=img;
img=img_new;
ind=find(img);
fprintf('%d voxels in mask\n',length(i... |
6738ae72aff391fca52093219ee033f9e179e654bdef6066d5ded56ee8989b01 | MATLAB | 2,243 | 68 | function L = compute_slice_leakage(this, dy, dz)
% Computes slice leakage as cross-correlation between this image and a FOV
% and slice-shifted copy
%
% Y = MrDataNd()
% L = Y.compute_slice_leakage(dy, dz)
%
% This is a method of class MrDataNd.
%
% IN
% dy [1, nShifts], FOV shift(s) in number of pixels in y (ph... |
339ec12c7486323a771463ac179922f143c9e4a8a2d21e4a8ed505a339019421 | MATLAB | 2,244 | 55 | function [ensmat_in,enscells_in,raster,frates] = generate_data(N,T,nens,ncellsperens,fr,timesperens,show_plot)
% Generate a synthetical raster with pre-defined ensembles.
% INPUT:
% N : <integer> with the number of neurons in the population.
% T: <integer> with the number of total frames.
% nens: <integer> with t... |
7c4e95bc0965059d7c0b52ab454a974c41a87d6e889f6a5d8d20231edbbee8dd | MATLAB | 2,244 | 96 | function y = tapas_softmax_mu3_wld_sim(r, infStates, p)
% Simulates observations from a Boltzmann distribution with volatility as temperature
%
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2017-2019 Christoph Mathys, TNU, UZH & ETHZ
%
% This file i... |
564121fc709fbfb3dd45050e509590ea5c8fa9b617b504ab5bb5748d02006aac | MATLAB | 2,245 | 70 | function [rez]=merge_temp(rez,Threshold)
%Variable initialization
SF = rez.ops.fs; %sampling frequency to convert from sampling rate to second
Nclusters = length(unique(rez.st(:,3))); %Number of initial clusters from kilosort
NG_clus = Nclusters; %Number of clusters
nt0 ... |
5c57c1f37a4c7d05eefc92cd77f521e970fe4c0d311128cc576d636aa9df77ba | MATLAB | 2,245 | 54 | % compute abscissas and weight factors for Gaussian-Hermite quadrature
%
% CALL: [x,w] = gauher(N)
%
% x = base points (abscissas)
% w = weight factors
% N = number of base points (abscissas) (integrates an up to (2N-1)th order
% polynomial exactly)
%
% p(x)=exp(-x^2/2)/sqrt(2*pi), a =-Inf, b = Inf
%
% Th... |
2a9fa3c03f7dd6081fe0ddcbb95913748e5f5ddd70de632ceecc76dcd1120a99 | MATLAB | 2,246 | 61 | function Show_RVT_Peak(R,fg),
for (icol = 1:1:length(R)),
figure(fg); clf
set (fg, 'KeyPressFcn', @afni_fig_interface);
subplot(211);
plot (R(icol).t, real(R(icol).X),'g'); hold on
if (~isempty(R(icol).RVT)),
subplot (211);
plot (R(icol).tmidprd,...
... |
2f484acee382ad80840b91601cc27ca045d7b759339036497f580c9f0a2e92e6 | MATLAB | 2,246 | 94 | %% === compare timings for MULT
% number of repeats (to increase measurement accuracy)
R = 10;
% what sizes of (square) matrices do we want measure? (log spacing)
nn = unique(round(exp(linspace(log(4),log(100),10))));
% number of different sizes to try
N = length(nn);
% size of the output C, in Megabyte... |
533200edfeb4fe34e255d6c90dd691dd95f31e067bd6f338b50a9cb1157963f0 | MATLAB | 2,246 | 78 | % op_getSNR.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [SNR]=op_getSNR(in,NAAppmmin,NAAppmmax,noiseppmmin,noiseppmmax);
%
% DESCRIPTION:
% Find the SNR of the NAA peak in a spectrum.
%
% INPUTS:
% in = input data in matlab structure format
% NAAppmmin = min of frequncy range in which to searc... |
edcd34c3b98c6822e3390b932843f4ac95919c68cee2124717177123e5f2694f | MATLAB | 2,246 | 81 | function [vertex,face,normal, uv, sphparam] = read_mesh(file)
% read_mesh - read data from OFF, PLY, SMF or WRL file.
%
% [vertex,face] = read_mesh(filename);
% [vertex,face] = read_mesh; % open a dialog box
%
% 'vertex' is a 'nb.vert x 3' array specifying the position of the vertices.
% 'face' is a 'nb.f... |
4f0069f756267a1a3eea43d2698fba18154b097df361cf41afa05bad2a6f2204 | MATLAB | 2,247 | 54 | function y = BF_PreProcess(y,preProcessHow)
% BF_PreProcess Preprocess a time series, y
% ------------------------------------------------------------------------------
% Copyright (C) 2013-2026, Ben D. Fulcher <ben.d.fulcher@gmail.com>,
% <http://www.benfulcher.com>
%
% If you use this code for your research, pleas... |
abe13d5e63d4b917d1b7c5e4988158bc85aa581eef816dce6288a6e673ee09c6 | MATLAB | 2,247 | 53 | function signal = clean_drifts(signal,transition,attenuation)
% Removes drifts from the data using a forward-backward high-pass filter.
% Signal = clean_drifts(Signal,Transition)
%
% This removes drifts from the data using a forward-backward (non-causal) filter.
% NOTE: If you are doing directed information flow analys... |
6ca6a2a49dbee8563f8cc2bee8cf99061868cba561e7836e2d3ef7abf0c89ff1 | MATLAB | 2,248 | 46 | clear all
close all
%%
data_path='path_to_the_dataset';
load(fullfile(data_path,'data_ccg_nCRF.mat'));
%% scatter plot of BO modulation index vs CCG asymmetry
figure('Color',[1 1 1],'Position',[100,100,450,300]);
scatter(ccg_BO_sig.Asymmetry,ccg_BO_sig.MI_BO,10,'black','Marker','o','LineWidth',1);hold on
mdl=fitlm(cc... |
86dea00b0414db8e276144ecd90d0b736d6719cb484bd3064a3d70ec40a02973 | MATLAB | 2,249 | 67 | clc;
clear;
addpath('C:\work\code\download\cifti-matlab-master');
bag_res_file = 'C:\Users\lihon\Desktop\abcd_study\pnc\vis_v2_r400_ro1\bag_cen_K3_regional_r400.mat';
bag_res = load(bag_res_file);
bag_p2 = bag_res.bag_mat(bag_res.st_idx==2, :);
bag_p3 = bag_res.bag_mat(bag_res.st_idx==3, :);
num_r = size(bag_p2, 2... |
1c3e4151b8dd8cbff2d9adecee29e2ecc590013bdcd033403e05cc6f5632c75e | MATLAB | 2,250 | 67 | function b=surfing_cluster_borders(cl,nbrs)
% Finds the borders of clusters, useful for visualization
%
% B=SURFING_CLUSTER_BORDERS(CL,NBRS)
%
% INPUT:
% CL Px1 cluster indices for P clusters; CL{K} are indices of
% cluster K. Typically this is the output of SURFING_CLUSTERIZE
% NBRS KxN neigb... |
1514598637eb802bbb6dc96e2942fb45b670df3ccbf97c5b529e675bda3a6fcb | MATLAB | 2,251 | 71 | function [cst X] = test03(n, m)
% function [cst X] = test03(n, m)
% All intputs are optional.
%
% Crude attempt at spreading m points over the (n-1) sphere to test the
% oblique manifold implementation. Based on April 13, 2012 notes:
%
% Maximize sum |xi-xj|^2 over all (i, j) pairs is equivalent to
% Minimize sum xi'*x... |
772873f15575ac958e35396566bcfce03d83639deb3ecbe19de8b2a1fce1453b | MATLAB | 2,252 | 61 | clear all
close all
clc
exp_root = 'C:\Users\User\Documents\fMRI_EXP\';
more_code = fullfile(exp_root, 'cells_data_muller');
data_folder = fullfile(more_code, 'wetransfer_neil-s-data_2023-09-25_1057');
addpath(genpath(more_code));
addpath(genpath(data_folder));
place_cells_rats = [4, 6, 7, 8];
num_place_rats = length... |
7b56e1c4d27d3d819a57ff0525c191e6e6da51314d003664f20dcc1c9343b74f | MATLAB | 2,252 | 77 | function [b, tau, er] = regress_wt_vs_rew(A, nback, plotarg, cond)
%regress waittime against rewards, a la Wang/Uchida 2013.
%also fits exponential. Adapted from regress_latency_vs_rew
%inputs: A struct. If you give it the S struct, will convert it to A struct.
%nback specifies number of previous trials to regress.
%av... |
8933a516b9690fea623875ebcbb7ce2c5dba12be98df02fed3d479909c1fb3a4 | MATLAB | 2,252 | 88 | function Test_synchronization
n = 3;
m = 10;
A = randn(m, n)
SOn = rotationsfactory(n);
B = A*SOn.rand()+.1*randn(m, n)
C = A*SOn.rand()+.1*randn(m, n)
% Create the problem structure.
manifold = rotationsfactory(n, 2);
problem.M = manifold;
% Define the problem cost function and its gradient.
problem.cost = @cost;
... |
b7f1504a1811cb36c226853aa845628bcf38474704a78bc3b911e546c4db1911 | MATLAB | 2,252 | 63 | % Main script for resampling subject-specific supragranular and
% infragranular SANDI surface overlays to the fsaverage surface
% using FreeSurfer mri_surf2surf
%
% Reference:
% Lee H, ..., Huang S, Communications Biology, 2026
%
% Requirements:
% - FreeSurfer installed and configured
% - FreeSurfer recon-all completed... |
f2448554d92e255d1838d064835e1532ebdcc2ff32b0469fb46ef082a7e0d26f | MATLAB | 2,252 | 67 | function [clustAssign] = GetARTwarpClusters(LineData, net, settings)
% Return clusters from existing ARTwarp2 model after training
h = waitbar(0,'Initializing');
%% Standardize all data, determine scaling factor for shape distance
CallLengths = zscore(cellfun(@length,(LineData)));
CallLengthsMean = mean(cellfun(@leng... |
50be600a5e40f57468d08e8233bf8c7e3a89ecca437465409613f384252941e1 | MATLAB | 2,254 | 72 |
function [nLL, nLL_Trial] =...
lognNLL_latency_secondhalf(params, lat2fit, ratTrial,...
mdl, likparams)
%lognNLL_latency_secondhalf - calculate nLL of model parameters given data
% INPUTS:
% params - model parameters
% lat2fit - data to compare model outputs to
% ratTrial - rat beahvioral data
% mdl - ... |
0040afc5602879c1b04f916fd4ce6f841ece4ae03ec58b2278e95a0636a22340 | MATLAB | 2,256 | 59 | %VL_NNBNORM CNN batch normalisation.
% Y = VL_NNBNORM(X,G,B) applies batch normalization to the input
% X. Batch normalization is defined as:
%
% Y(i,j,k,t) = G(k) * (X(i,j,k,t) - mu(k)) / sigma(k) + B(k)
%
% where:
%
% mu(k) = mean_ijt X(i,j,k,t),
% sigma2(k) = mean_ijt (X(i,j,k,t) - mu(k))^2,
% ... |
90412173e6467c5805eea543408a62af52b7dd22e768b72bd13e64aea0805904 | MATLAB | 2,256 | 58 | function survive = prune(bfile, pval_vec, pval_thresh, r2_thresh)
% Args:
% bfile: plink bfile prefix (N SNPs and M samples). All chromosomes in corresponding bim file must be int.
% pval_vec: array of p-values, size(pval_vec) = N, the order of SNPs must correspond to the order in bfile.
% pval_thr... |
d5811a55e8077846814828e6aff8aea0a57610ab44a456a408a59ac45ceaa373 | MATLAB | 2,257 | 75 | % (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
function opt = getOptionSearchlight()
% returns a structure that contains the options chosen by the user to run
% decoding with cosmo-mvpa.
if nargin < 1
opt = [];
end
% suject to run in each group
opt.subjects = {'001','002','003','004','005','0... |
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