sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
096b2d8340e67b47505c6f6e838007888082fca4221d22108dcf0eb1368459f5 | MATLAB | 3,342 | 83 | function L = symbchol()
% L = symbchol(X)
%
% SYMBCHOL Symbolic block sparse Cholesky factorization.
% L = symbchol(X) returns a structure L that can be used
% by the efficient block sparse Cholesky solver SPARCHOL.
% The fields in L have the followin... |
1006051aff764268cf2ef56a2a6e253f59bbb3b6a17fa3db0b268a25c0e621f7 | MATLAB | 3,342 | 84 | function ea_get_Eproj(tractset,vatlist)
% Comptute E-field metrics directly on fibers (optionally in native space).
% The results are stored as
% patient_folder/connectomes/connnectomeName/stim_ID/E_metrics.mat (values for all fibers in the connectome!)
% By Butenko and Roediger, konstantinmgtu@gmail.com
arguments
... |
479fbd3a5beac8b9387adc76bb4039861fff38f0e12c118a423754076900f1d0 | MATLAB | 3,342 | 48 | function [prams,results]=CBIG_gwMRF_graph_cut_clustering(varargin)
% This function performs MRF clustering using Graphcuts; modelling the data as VMF distributions.
% Results will be stored in the results struct. The used parameters will be saved in the prams struct.
% Input
%
% Possible parameter... |
167f380e9f35534a41d576b95c5dc6729f826cce369ee2e4ad50713e898c3f4a | MATLAB | 3,343 | 67 | function [S,f,Serr]=mtspectrumc(data,params)
% Multi-taper spectrum - continuous process
%
% Usage:
%
% [S,f,Serr]=mtspectrumc(data,params)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (in form samples x channels/trials) -- required
% params: structure with fields... |
b10c2567e1af471a89702d966be8249804bd21c6f97ef059f89c9453fb75c0e4 | MATLAB | 3,344 | 102 | function T=BoundaryCollapse3D(V,F,T,Options)
% This function performs 2D triangulation or 3D tessellation. Advantage
% above delaunay is that only returns the faces inside the object
%
% T=boundary_collapse_3d(V,F,T,options);
% V : Mx3 the vertices, with x,y,z coordinates
% F : Nx3 faces with ve... |
5884df7c8f3f695db7f8b145d02936b3f156d85a509144c6f3a924e0d100bd33 | MATLAB | 3,346 | 151 | function [cid, alpha, mu] = circ_clust(alpha, numclust, disp)
%
% [cid, alpha, mu] = circClust(alpha, numclust, disp)
% Performs a simple agglomerative clustering of angular data.
%
% Input:
% alpha sample of angles
% numclust number of clusters desired, default: 2
% disp show plot at each ste... |
a501edc382bfc5e421de8b9667c0e2f5d8534b64fcb28effc11e0039f119384f | MATLAB | 3,347 | 88 | % pop_writeeeg - write EEGLAB dataset to disk in EDF/GDF or BDF format
%
% pop_writeeeg( EEG ) % pops up a window
% pop_writeeeg( EEG, filename, 'key', 'val' )
%
% Inputs:
% EEG - EEGLAB dataset
% filename - [string] filename
%
% Optional keys (same as writeeeg):
% 'TYPE' - ['GDF'|'EDF'|'BDF'|'CFWB'... |
3239fc1b98b66eaa8e23cd73a1f615dad29426877c532625768c8311b9fb2f56 | MATLAB | 3,348 | 84 | function ea_get_Eproj(tractset,vatlist)
% Comptute E-field metrics directly on fibers (optionally in native space).
% The results are stored as
% patient_folder/connectomes/connnectomeName/stim_ID/E_metrics.mat (values for all fibers in the connectome!)
% By Butenko and Roediger, konstantinmgtu@gmail.com
arguments
... |
a0a8b6e502c223cd6a8ae50edff67a8045a7c8b333a2813c0654f14c976c5c1d | MATLAB | 3,349 | 97 | function[S,tau,tc] = staogram(data_spk,data_lfp,smp,plt,Tc,Tinc,Tw,w,D)
%
% staogram : calculates a moving window spike triggered ave %
% Usage:[S,tau,tc] = staogram(data_spk,data_lfp,smp,plt,Tc,Tinc,Tw,w,D)
%
% ******** INPUT *********
% Note that all times have to be consi... |
e2f612f25eaa72a47c005d57c88c8bf7cd647c7f42b9793f08fef95a47dc060e | MATLAB | 3,349 | 94 | function myPLS_plot_loadings_3D(var,var_name,signif_LC,pos_threshold,neg_threshold,save_opts)
%
% This function displays 3-dimensional loadings (e.g. volume) of all
% significant latent components (LCs). The loadings are constrained
% to a binary mask (e.g., DARTEL group template) and thresholded.
% Writes loadings o... |
22d83f68be0dd9417114c7453b8b76b78bdd7de31267995f68dee05b674532ee | MATLAB | 3,352 | 91 | function cell_array = CBIG_MMLDA_get_string_entry(spreadsheet, phase, rid, viscode, fieldnames, phase_match, viscode_match)
% cell_array = CBIG_MMLDA_get_string_entry(spreadsheet, phase, rid, viscode, fieldnames, phase_match)
%
% This function get string entries from ADNI spreadsheet.
%
% Input:
% - spreadsheet :... |
34f1c9d72e5555c4a1aa5c885c200a26150d462a658fee926b3913f384d13a04 | MATLAB | 3,355 | 115 | function PlotCCG(t,ccg,varargin)
%PlotCCG - Plot auto/cross-correlograms of point processes.
%
% USAGE
%
% PlotCCG(t,ccg)
%
% t time bins obtained using <a href="matlab:help CCG">CCG</a>
% ccg data obtained using <a href="matlab:help CCG">CCG</a>
% <options> optional... |
65091de79891aaa4269d277afe1b9b32e3affe504ea80ba0ecac1cef78e6090d | MATLAB | 3,355 | 74 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
177a9873d349513f4fed461392fb3fbec52552f7a014c7d6da25267fa3191d6b | MATLAB | 3,356 | 103 | % pop_firma() - Filter data using moving average FIR filter
%
% Usage:
% >> [EEG, com] = pop_firma(EEG); % pop-up window mode
% >> [EEG, com] = pop_firma(EEG, 'forder', order);
%
% Inputs:
% EEG - EEGLAB EEG structure
% 'forder' - scalar filter order. Mandatory even
%
% Outputs:
% EEG - filtered ... |
d48e40d8c8f589afb1e919d1fa12f99f4c8cfb9c73508cd2e4f3293febef2574 | MATLAB | 3,356 | 106 | % This main file imports data (WT or IFNAGRKO datasets),
% processes it (to approximate Gaussians from main body of log-normal distribution),
% estimates params, simulates the system (ODE and fluctuations) with fitted params,
% and plots the results for inspection
%% Add all folders to path
addpath(genpath(pwd)... |
e4ab07e3ff725cbeecf9fe2303ce83d8e86889c775ec4bb3fe521c0b6ca0c336 | MATLAB | 3,356 | 82 | function [rid_conv, rid_nonconv] = CBIG_find_conv_nonconv(rid_of_interest, years)
% [rid_conv, rid_nonconv] = CBIG_find_conv_nonconv(rid_of_interest, years)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
file_id = fopen('//share/users/imganalysis/yeolab/data/ADNI_me... |
f1e30c931d6734689986f28f96d43a93ec49741f8ceaf631345031dfac5a0601 | MATLAB | 3,356 | 130 | function [f,meanimt,meanim,meanref]=OIS_corr(fname,reference,section,meanim)
% Usage ... f=OIS_corr(OISfname,reference,section)
%
% reference - reference waveform for correlation
% section- sections of the timecourse to regress only in images!
% sections can be the image #s to use, in that case reference should
%... |
4c28d6b23bcdf3d95f50586e1c57c5b5b5fd1642c66da4c85d5e0ded7585faad | MATLAB | 3,357 | 93 | function removeNSxData(timestamps, filename)
%
% removeNSxData(timestamps, filename)
%
% This function removes chunks of data given in a 2-column timestamps
% variable from a NSx file and then saves it as another NSx. This is
% useful when removing useless data from the file to decrease the size of
% the NSx ... |
10d98126206405beca2159a2b690ef654f0710b2274c9ee1757f4b19ecb5a7e6 | MATLAB | 3,358 | 105 | function [Lx,Ly,corr_Lx_X,corr_Ly_Y,corr_Lx_Y,corr_Ly_X] = ...
myPLS_get_PLS_scores_loadings(X,Y,V,U,grouping,pls_opts)
% This function computes PLS scores & loadings.
% Individual-specific PLS scores are subjects' expression of imaging and
% behavior/design saliences (covariance patterns).
% Component-specific P... |
116730002361a0dacff136e6e0de65921debadd387bc7a21a654d494fb60cbc6 | MATLAB | 3,358 | 99 | %%*******************************************************************
%% HKMrhsfun: compute the right-hand side vector of the
%% Schur complement equation for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%***********... |
77005e15fca12dc51424af7cbfcdda511d56d7159ee1e3f29272e54a04e6f34f | MATLAB | 3,358 | 77 | function ea_predict_leave_one_out(uipatdirs,stimname,typemap,regressor,fdmri,dowhat)
if size(regressor,1)<size(regressor,2)
regressor=regressor';
end
if ~exist('fdmri','var')
fdmri.do='both'; % can be fmri, dmri or both
end
for pat=1:length(uipatdirs)
[~, subPrefix] = fileparts([uipatdir{pt}, '_']);
f... |
2dadadcbb5fc256fcaa8c893eb11ee547a82dc9081f0d6f657949be36cafd649 | MATLAB | 3,361 | 106 | function [ fields ] = bz_getPlaceFields1D(varargin)
% USAGE
%
%
% INPUTS
%
% ratemap MxNxD matrix where M is the number of cells, N is the number
% of trials, and D is the number of spatial bins
% minPeakRate minimum rate for peak of field [default: 1]
% minFieldWidth ... |
68b5eebae359c8d24535c915419f9bcf95e949a6a92e6c311dc6d1e1dba4aa89 | MATLAB | 3,361 | 91 | function [allTimestamps allSnippets allIndices] = findEventTimes(NEV, Channel, Units)
% Given a NEV file, an channel number, and a unit number this function
% will return indices corresponding to those spikes, timestamps
% corresponding to those spikes (optional), and snippets corresponding to
% those spikes (opt... |
a913d628768ade4ea583a35e8f967426e3348c8182981919f49f780ab7e12af4 | MATLAB | 3,362 | 122 | function T_S_C_p = CBIG_gender(subInfoFile, GMICVFile, K)
% T_S_C_p = CBIG_gender(subInfoFile, GMICVFile, K)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
T_S_C_p = cell(1, 4);
display('************* SEX *************');
fprintf('\n');
%------------------------... |
2be78172c9e340b824886398bf6a424e49d42782138dcb68299fc3a3c17ec29e | MATLAB | 3,363 | 84 | function SmoothY=fastsmooth(Y,w,type,ends)
% fastsmooth(Y,w,type,ends) smooths vector Y with smooth
% of width w. Version 3.0, October 2016.
% The argument "type" determines the smooth type:
% If type=1, rectangular (sliding-average or boxcar)
% If type=2, triangular (2 passes of sliding-average)
% If type=3, ... |
a1620b253172f16ce4f2fb70ace065c44572e59824d9c46736399b454314072e | MATLAB | 3,363 | 103 | function VRstatearraysNEW(animal, binsize)
%Create arrays with info about running times, lick starts/ends, reward
%starts/ends. The running times info is used by getruntimes to identify
%running bouts.
%LV analysis no longer uses this.
%Inputs/requirements: Animal ID, binsize (0.1 = 0.1 second bins), matfiles
... |
4b3394dff56a5d4731ad7928685ae2de936c1bb7f1719958cb699a1656870b7a | MATLAB | 3,365 | 64 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
05f74201fb75877cbf64ef55691b9e0c5c194d5e39cc98575663faf75aa5ba9d | MATLAB | 3,366 | 110 | % zica() - Z-transform of ICA activations; useful for studying component SNR
%
% Usage: >> [zact,basesd,maz,mazc,mazf] = zica(activations,frames,baseframes)
%
% Inputs:
% activations - activations matrix produced by runica()
% frames - frames per epoch {0|default -> length(activations)}
% baseframes - vect... |
0bf7596eda02f2b1e73a9273ef4140b2b5bea42842c63b881ee6a5271466aef7 | MATLAB | 3,370 | 81 | function fd = fluorAnalysis(f,flydata)
seconds = 30; % 40 for Exp2 slips; 67? for Exp4 real wind; 30 for everything else
sigma_a = 0.5; % across rows (smoothing over time)
sigma_b = 0.9; % across columns
per = 0.05;
frames = flydata(1).trllength;
green = [flydata.fluordata];
bgcorr = green([1,3:end],:) - g... |
6c6e786d2a00aec24ca450a84a55e92c1a225908c734a4c043360f90f44d9c6f | MATLAB | 3,370 | 113 | function [v]=arsim(w,A,C,n,ndisc)
%ARSIM Simulation of AR process.
%
% v=ARSIM(w,A,C,n) simulates n time steps of the AR(p) process
%
% v(k,:)' = w' + A1*v(k-1,:)' +...+ Ap*v(k-p,:)' + eta(k,:)',
%
% where A=[A1 ... Ap] is the coefficient matrix, and w is a vector of
% intercept terms that is included to allow... |
e2f46458f1f6c249b4c17b12bc1f244dc4e840b50bfc9bb9f5e29d877446fdaf | MATLAB | 3,370 | 83 | % eeg_timeinterp() - perform spline interpolation of a portion
% of data based on prior and post activity. See
% eeg_interp() for interpolation of bad channels.
%
% Usage:
% >> OUTEEG = eeg_timeinterp( INEEG, samples, 'key', 'val');
%
% Inputs:
% INEEG - input EEG structu... |
f6ebe268d192ed485fd822c37e6168f2fcb60132ac7638ecac58415d80645eb9 | MATLAB | 3,370 | 99 | % gradmap() - compute the gradient of an EEG spatial distribution.
%
% Usage:
% >> [gradX, gradY ] = gradmap( map, filename, draw )
%
% Inputs:
% map - level of activity (size: nbelectrodes x nbChannel)
% filename - filename (.loc file) countaining the coordinates
% of the electrodes, or arr... |
be4ce7fe6b70552db2346428023d7d40d12503c836285c5096364c6a6701ed18 | MATLAB | 3,371 | 151 | function [cid, alpha, mu] = circ_clust(alpha, numclust, disp)
%
% [cid, alpha, mu] = circClust(alpha, numclust, disp)
% Performs a simple agglomerative clustering of angular data.
%
% Input:
% alpha sample of angles
% numclust number of clusters desired, default: 2
% disp show plot at each ste... |
e81cd13a31a9961e0253aafb568f28d876d014c6b968bd2979b12e800da4caee | MATLAB | 3,372 | 106 | function lc=ea_handles2lc(handles)
% General settings (support both GUIDE and App Designer dropdowns)
parcellations = ea_lc_getdropdownitems(handles.parcellation);
parcVal = ea_lc_getdropdownvalue(handles.parcellation, parcellations);
lc.general.parcellation = parcellations{parcVal};
% Graph options:
lc.graph.struc_f... |
ca5beb88c4ffe75a56f11e58894fee0b862bce5b1c78cdb9e1547dd96489fdcc | MATLAB | 3,373 | 84 | function headdir = fixHeaddir(headdir)
plotIt = 0;
shortEpochThresh = 50;
bigDeviationThresh = 100;
maxChunkSize2flip = 200; % larger starts flipping inappropriate data, smaller might be okay. . .
if plotIt; hold off; plot(headdir(1:40000),'.b'); end
%%% PHASE 1:
% Drop all data points that deviate from the med... |
ebecb3c58be16f7586271be03d50a4b0d7b8e21406bdb5ec1217dc9f896fb30c | MATLAB | 3,374 | 81 | function [params,paramsFilePath] = getAnalysisParams(loadParam,varargin)
% getAnalysisParams loads parameters for compiling 2P data across animals
% (whether TRF map or response in contrast)
%
% INPUT:
% loadParam --> whether (1) or not (0) to load existing params
% varargin... |
318a8c3e1661950d817f9b5a0452e1415f947d633e0c03b294addfb50a8c6375 | MATLAB | 3,376 | 118 | function cvx_optval = norm( x, p )
% Disciplined convex programming information:
% NORM is convex, except when P<1, so an error will result if
% these non-convex "norms" are used within CVX expressions. NORM
% is nonmonotonic, so its input must be affine.
%
% Argument map
%
persistent remap1 rem... |
87852c328bf1c8be2f1835a4ffe23ab0f6b0bd7783fa6f2cc744a8b18567d817 | MATLAB | 3,376 | 75 | function [p, ADJ, NULL] = CBIG_ASDf_FCDiffAllSub_NBS(tThresh, id_asd_file, ...
id_con_file, sub_info_file, Nperm, output_name)
% [p, ADJ, NULL] = CBIG_ASDf_FCDiffAllSub_NBS(tThresh, id_asd_file,
% id_con_file, sub_info_file, Nperm, output_name)
%
% This function compares FC difference between all ASD and all control p... |
b99d9e9ac609e21e8439e1ca7ff0997b70141c1047f22f501ef2fed452b888b4 | MATLAB | 3,377 | 91 | function currPosition = moveToPosition(position, stepperHandle, panelHandle, encoderHandle, axisIdx, useEncoder)
%
% Function:
%
global isMotorStop
unitStep = fix(360/0.13*16);% pulses per mm
tolPulseNum = 2;
timeDelay = 10;%ms
valPtr = libpointer('int64Ptr', 0);
calllib('phidget21', 'CPhidgetStepper_getC... |
f18a26ad32319f7a4b0bbbfd02a101470494d182a038e616be9b3fa2abf115e6 | MATLAB | 3,377 | 101 | function normalized = NormalizeFields(fields,varargin)
%NormalizeFields - Normalize one or more firing fields in space and rate.
%
% For each field, interpolate space in [0..1] and normalize z values
% (typically, firing rates for place fields). Z values outside the fields
% should be set to zero (see example below... |
b75111021031825348f9add55afa7b8418be78a923bc7033b610d91cf9f68bca | MATLAB | 3,378 | 84 | ccc;
AREAs = {'AC', 'PFC'};
temp = dir("..\MAT Data\cwt result\Baseline\**\cwtres_*.mat");
SINGLEPATHs = unique({temp.folder})';
RAWDATAPATHs = cellfun(@(x) strrep(x, '\cwt result\Baseline\', '\pre (granger)\'), SINGLEPATHs, "UniformOutput", false);
GRANGERROOTPATHs = cellfun(@(x) strrep(x, '\cwt result\Baseline\', '\... |
bb814596b8c9cf6c5ef56b9d5a14950ccf5b8957c0b5e3d932e16f2b9192b35e | MATLAB | 3,380 | 89 | clear; clc;
%% Load and process experiment data
% data location
path_root = getenv('DECIDENET_PATH');
path_beh = fullfile(path_root, 'data/main_fmri_study/sourcedata/behavioral');
fname_beh = 'behavioral_data_clean_all.mat';
fname_meta = 'behavioral_data_clean_all.json';
% load behavioral and metadata
load(fullfile(p... |
033decd01d9c74d81a26c528f0c951a02524cdd88b8d85d5bdec8e05ff02f62f | MATLAB | 3,381 | 72 | function p_all = CBIG_MMLDA_characteristics_wrapper(out_dir)
% p_all = CBIG_MMLDA_characteristics_wrapper(out_dir)
%
% Wrapper function to perform GLM (and logistic regression fro binary variables)
% to compare AD subjects' characteristics (i.e., age, edu, sex, amyloid, apoe2)
% across factors.
%
% Input:
% - out_dir... |
8a524766e3f69e09d91143d00aa11d2666dfd3c52aa649aed774f9a0e0275d55 | MATLAB | 3,381 | 115 | function y = exp( x )
% Disciplined convex programming information:
% EXP(X) is convex and nondecreasing in X. When used in CVX
% expressions, X must be real. Typically, X must also be affine
% or convex; X can also be concave, but this produces a log-concave
% result with very limited ... |
062e6c27b87a99f32dd0b1eb1e2a46dc70363ec73c138e27a1fa677096e35c8b | MATLAB | 3,383 | 118 | function cvx_optpnt = rotated_lorentz( sx, dim, iscplx )
%ROTATED_LORENTZ Rotated real second-order cone.
% ROTATED_LORENTZ(N), where N is a positive integer, creates a column
% variable of length N and two scalar variables, and constrains them
% to lie in a rotated second-order cone. That is, given the declar... |
29953c5b6af5fe15066be61de340d560b417e866517f4ea807407a8aa7987161 | MATLAB | 3,383 | 92 | function [hObject, handles] = dan_edit_data_axes(hObject, handles)
% This function controls what happens when the mouse is clicked on the main
% gui window
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
%% Left click. Add a custom notation
if strcmp(get(handles.main_window , 'SelectionType'), 'normal')
c... |
6a47d045467d56c5cb06dfa6695e1b7fc014fff9cc530e822ed210723fa9f5f0 | MATLAB | 3,384 | 109 | %%*********************************************************************
%% norm_min: matrix 2-norm minimization problem
%%
%% (primal) minimize || B0 + x1*B1 + ... + xm*Bm ||_2
%%
%% (dual) maximize - Tr B0*Q
%% subject to Tr Bk*Q = 0, k=1,...,m
%% sum of singular values of Q is les... |
79e56982b8ce8cead599fbf7167dec0f2c1c134ede8b44dadfb8d49c8b387a43 | MATLAB | 3,384 | 141 | function [c2_idx] = dbscan2(x, varargin)
% dbscan2 - Clustering by two sequential DBSCANs. The first one is applied
% to the points in 'x'. The second one is applied to each cluster
% recognized by the first DBSCAN.
%
% After the second DBSCAN, a gaussian mixture classification is applied.
% The mean of each po... |
c426da21e8b4e0eba6595f0cd6116fbe6a90484485af4fafb68da29e117ec313 | MATLAB | 3,384 | 90 | function varargout = add(tree,uid,type,parameter)
% XMLTREE/ADD Method (add childs to elements of an XML Tree)
% FORMAT vararout = add(tree,uid,type,parameter)
%
% tree - XMLTree object
% uid - array of uid's
% type - 'element', 'chardata', 'cdata', 'pi' or 'comment'
% parameter - property name (a char... |
da7a56ee961ec9948b8d610528837dc539d4c6fbf58e521d125f39f3b61bb5b0 | MATLAB | 3,385 | 127 | function [gr,gi]=cgama(x,y,kf)
% [RealPartResult,ImaginaryPartResult]=cgama(RealPart,ImaginaryPart,1)
%
%This program is a direct conversion of the corresponding Fortran program in
%S. Zhang & J. Jin "Computation of Special Functions" (Wiley, 1996).
%online: http://iris-lee3.ece.uiuc.edu/~jjin/routines/routin... |
278553bfc58f241e994c9b64824172821495926aa7a8d5f02c844a0dec6cc7af | MATLAB | 3,387 | 76 | function [sv,sp,fm] = spsvd(data,params,mdkp)
% Space frequency SVD of input data - continuous processes
% Usage: [sv,sp,fm] = spsvd(data,params,mdkp)
% Inputs:
% data (data matrix in timexchannels form)-required
% params structure containing parameters - params has the
% following fields: ... |
032f2d4374abc073b2f84d906202d5da511b8950228a51d74f82ff90db7be4a8 | MATLAB | 3,388 | 69 | % sleepDanalyzer montage script.
% chanList. A list of channel names and (optionally) channel coordinates.
% This should be an EEGLAB chanlocs struct. Alternatively you can read in a
% .txt file using the readlocs function (EEGLAB). If you wish to
% differentiate channel types (e.g. EEG, EOG, etc.) make sure to use t... |
4021898bb4ccb3edf0e192026ae500d299fe023c428fc9598828d76a28bb8fd8 | MATLAB | 3,389 | 81 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
abf50b123b5556d7c894e425505d5fef0edd6a77ff1318e562b4fd03f323bab1 | MATLAB | 3,390 | 111 | function [output]= CNMF_noparpool(input, session);
%% load structure
foldername = input.foldername;
files = input.image;
listhdf5 = input.list;
ROI = input.ROI.file;
a = input.ROI.a;
FOV = input.param.FOV;
options = input.param.options;
tau = input.param.tau;
p = input.param.p;
merge_thr =input.param.merge_thr;
%Sess... |
b8e1e5b1401ede35b9269b9e295d697ada38f32375558540b06407c8072a5b23 | MATLAB | 3,393 | 89 | function [dtf,ctf]=SOFAhrtf2dtf(hrtf,varargin)
%SOFAHRTF2DTF converts HRTFs to DTFs (and CTFs)
% Usage: [dtf,ctf]=SOFAhrtf2dtf(hrtf)
% [dtf,ctf]=SOFAhrtf2dtf(hrtf,f1,f2)
%
% Input parameters:
% hrtf: SOFA object with SimpleFreeFieldHRIR convention
%
% Output arguments:
% dt... |
d42b56d391a60c61fb7e1ab19cb6913d00aea4ed7cae2f0eea481d6c269ccf13 | MATLAB | 3,394 | 88 | function angles = GetAngles(varargin)
%GetAngles - Get angles (from position samples).
%
% Angles are returned in radians (in [-pi,pi]). This function requires two
% or more LEDs (only the first two are used).
%
% USAGE
%
% angles = GetAngles(<options>)
%
% <options> optional list of property-value pairs... |
d6eb8ff56cf08439a1a1a331b94fe6cb35f0da00729047a3b40e31b689b125f1 | MATLAB | 3,395 | 77 | function ea_nc_segment(options)
%% neck-crop and segment MR-image
directory = [options.root,options.patientname,filesep];
matlabbatch{1}.spm.tools.preproc8.channel.vols = {[directory,options.prefs.prenii_unnormalized,',1']};
matlabbatch{1}.spm.tools.preproc8.channel.biasreg = 0.0001;
matlabbatch{1}.spm.tools.preproc8... |
41c5cdcd4a56875b0e7b9b1be68cf5acde87262dfe1a907e10ade7beb0ef3893 | MATLAB | 3,397 | 91 | function [id_keep, EB, reg] = CBIG_ASDf_CCA_genInputs(ind_scores, path_behav_scores, id_all, dx, regressors)
% [id_keep, EB, reg] = CBIG_ASDf_CCA_genInputs(ind_scores, path_behav_scores, id_all, dx, regressors)
%
% This function gets participants' IDs, exchangeability block (for permutation test
% controlling site) an... |
f4005d75f76adad413bbd4787a8314ae0f09827db02134faceaff934b52aa67d | MATLAB | 3,399 | 88 | function atlases=ea_atlasmajorcomponent(atlases,toclean)
% from specified component, only preserve largest component
for c=toclean
for side=1:2
% figure, patch(atlases.roi{c,side}.fv,'FaceColor','none')
fvsplit=splitFV(atlases.roi{c,side}.fv.faces,atlases.roi{c,side}.fv.vertices);
for comp=1:l... |
0d0f61a5274d5adbd9bf547254de527dc9269b3f51f9102c9c7d09dce5a3af5e | MATLAB | 3,400 | 106 | function plotKinematicDists(kinematics)
% Plots the mean within and between target distances at each time point
% across trials, then indicates at which time points these distributions
% are significantly different
% Params
mice = {'b8sSM5', 'b8sSM6', 'b8sSM7', 'b8sSM8', 'b8sSM9', 'b8sSM10'};
miceNames = {'mouse 1', '... |
35aec751cec3c9d0d5b7e45e2b3a92bae3564f3c687c1757d31d80066cc1fc7c | MATLAB | 3,401 | 80 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
7c6278d9942a85d53bed3d4295f592b923728f3e3f8151db1c9ca048cd636af5 | MATLAB | 3,402 | 180 | function trainmodel
%%
%scheme = evalin('base','scheme');
d1 = 0.5+(0:0.05:1)*2.5;
d2 = 0+(0:0.05:1)*3;
d3 = 0.15+(0:0.05:1)*2.5;
v = 0:0.05:1;
[D1 D2 D3 V] = ndgrid(d1,d2,d3,v);
nt = 10^5;
D1 = 0.5+rand(nt,1)*2.5;
D2 = 0.5+rand(nt,1)*2.5;
D3 = 0+sqrt(rand(nt,1))*2.5;
V = rand(nt,1)*1;
Vw = (1-V).*rand(nt,1)*0;
%idx =... |
758c021c5e8cc1177f7d26edc7d7dd40712ad984482102871f1f06b2f070755a | MATLAB | 3,404 | 133 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% We study the Direct Switch model with generic asocial behaviour
%
% We consider the best-of-n case
%
% We vary eta and we plot the difference between the asymptotic fraction of
% best option and second best option for a given eta with respect to the
% case best... |
7ed130339e47251f241b70654f521a0dc616bb6c420c92400582096cb15d3b94 | MATLAB | 3,404 | 92 | % This script sets up directory structure for new second-level analysis and
% copies in scripts from master 2nd-level script dir.
% Some scripts should be copied in and modified. Others can be run
% directly from the master scripts folder.
% Go to your new analysis folder and run this from within it.
% Note: type a_... |
2d627c11f1c6a0dbd1b26b02a85001c5b0947d93c9efe0112958df1fcc758b58 | MATLAB | 3,406 | 103 |
% Edit these two, and possibly the 3rd, before running
% -------------------------------------------------------
% Remember where the study's own setup put the results, so the call below can be
% checked against it (see the guard immediately after).
resultsdir_before_setup = '';
if exist('resultsdir','var'), resultsdi... |
44a5a64358a6548a0e44f2408847513cf033e1433961827dd49d882e69c62c12 | MATLAB | 3,406 | 96 | function scores = CBIG_MMLDA_get_num_entry(spreadsheet, phase, rid, viscode, fieldnames, phase_match, viscode_match)
% scores = CBIG_MMLDA_get_num_entry(spreadsheet, phase, rid, viscode, fieldnames, phase_match)
%
% This function get numeric entries from ADNI spreadsheet.
%
% Input:
% - spreadsheet : csv file fro... |
4a08a4a24684a7dd058b1de455453dd5f77a85f8db4528cef9ee45988f109c03 | MATLAB | 3,406 | 84 | ccc;
AREAs = {'AC', 'PFC'};
temp = dir("..\MAT Data\cwt result (ext)\Baseline\**\cwtres_*.mat");
SINGLEPATHs = unique({temp.folder})';
RAWDATAPATHs = cellfun(@(x) strrep(x, '\cwt result (ext)\Baseline\', '\pre (granger ext)\'), SINGLEPATHs, "UniformOutput", false);
GRANGERROOTPATHs = cellfun(@(x) strrep(x, '\cwt resul... |
a1c0fda8033d46aa3d8d917c1ce0b4d1663342554cc3126b06da5b8fd4b1e2b6 | MATLAB | 3,406 | 101 | function CBIG_pMFM_step6_SWSTD_state_Schaefer100()
% This function is used to conduct the statistical analysis corresponding
% to figure S8D and S8E in the paper.
%
% There is no input for this function as it can automatically get the
% output file from previous step.
% There is no output for this function as it will ... |
64763029f39fffd9ab85e42194e5668c81f37d0d7512283311f5e9141a5f0a9a | MATLAB | 3,407 | 66 | %% Canlab dataset basic usage
% Shows how to load a sample canlab_dataset object, extract variables, and
% make some plots.
% Instructions to include in help files as appropriate:
% -----------------------------------------------------------------------
%
% Before you start, the CANlab_Core_Tools must be added to your... |
10fc1494968e9daaf0fcf41fbae0cb07dca99914ff04c4bd6e574335d52c3e51 | MATLAB | 3,408 | 87 | function ea_export(options, clusterfunctionname)
% This function exports jobs created by the GUI of Lead-DBS. It is
% distributed within Lead-DBS toolbox (www.lead-dbs.org)
% __________________________________________________________________________________
% Copyright (C) 2016 Charite University Medicine Berlin, Movem... |
92b5d15ca35e5eb837850d90a673fbb47a0e47a92bd7038a5f5f2f0d3089d2e1 | MATLAB | 3,409 | 96 | classdef ButtonBox < uix.Box
%uix.ButtonBox Button box base class
%
% uix.ButtonBox is a base class for containers that lay out buttons.
% Copyright 2009-2015 The MathWorks, Inc.
% $Revision: 1165 $ $Date: 2015-12-06 03:09:17 -0500 (Sun, 06 Dec 2015) $
properties( Access = public, ... |
e542c5e610689942d21e0a0e5395e0700a46d56333f88afc412ac38577f2f3f2 | MATLAB | 3,410 | 102 | function [ ] = bz_RunAnalysis(analysisfunction,datasetfolder,varargin)
%bz_RunAnalysis(analysisfunction,datasetfolder) is a high level function that
%takes as its input an analysis function and returns the result of the
%analysis on multiple recordings
%
%INPUT
% analysisfunction A function name. The function sh... |
6eb52f77d399e211be30697f90b972f506b84b8ecd4a3616191c24c0aa77d7fe | MATLAB | 3,412 | 92 | function isom=ea_reformat_isomatrix(isom,M,options)
% this function tries to put the isomatrix provided into the correct format
% to be used by LEAD-DBS. The isomatrix is a matrix of values that can be
% displayed either at each active contact, each contact or in the spacings
% between contacts (e.g. for power-analyses... |
a704e9c038046734273197a892dabff5d52f52dc80b6e08efb4ec17e36ada88a | MATLAB | 3,412 | 93 | % fir1 bandpass filter implementation for rc files
% Base on firfilt2 (Hajime Hirase - 1998)
% Modification Lynn Hazan dec 2004: any offset can be used instead than an hard code offset of 2048 for 12 bit recordings
% (subtracts offset before filtering and adds offset before writing)
% function
% firfilter(inname,outna... |
56c2ed8fb425dc64e87d746853632ce3d935993796174589cb9022f2f8453b5b | MATLAB | 3,413 | 98 | function [Sc,Cmat,Ctot,Cvec,Cent,f]=CrossSpecMat(data,win,params)
%
%
% Multi-taper cross-spectral matrix - another routine, this one allows for multiple trials and channels
% but does not do confidence intervals. Also this routine always averages over trials - continuous process
%
% Usage:
%
% [Sc,Cmat,Ctot,C... |
500750c3f75cc0a2fca36256687c46708fc1e94a43bba1f026b858963c89d055 | MATLAB | 3,414 | 88 |
function data = loadmask(fn,threshold,ref,edges)
data = [];
if iscell(fn),
[fp fndum fext] = fileparts(fn{1});
else
[fp fndum fext] = fileparts(fn);
end;
if strcmp(fext(1:4),'.nii') || strcmp(fext(1:4),'.hdr'),
if size(... |
3b5c463f152303bb93953b9cbba70137e7368b1b9f07dff11d9b304429a91067 | MATLAB | 3,418 | 83 | function [p_spin, r_dist] = spin_test(map1, map2, varargin)
%
% Usage:
% [p_spin, r_dist] = spin_test(map1, map2, varargin)
%
% Description:
% Spin permutation (author: @saratheriver)
%
% Inputs:
% map1 (double array) - One of two map to be correlated
% map2 (double array) - The other map to be correlated
%
... |
ee7dff42625fcf11f28d455d51eefe3193bc5f2c4f40771b0fa6f37e9d1aa4cc | MATLAB | 3,418 | 97 | function P = paths()
%FNIRSPOWER.PATHS Return centralized, project-relative paths.
%
% P = fnirspower.paths()
%
% Description
% -----------
% This function defines the recommended repository and workspace layout
% used by the example scripts and convenience workflows. All paths are
% resolved relative to... |
ca007b5948e3c4b84b94422e658d0ea8fbe9eb2e9a45918953e08a3cf082c636 | MATLAB | 3,419 | 101 | % eeg_readoptions() - Read EEGLAB memory options file (eeg_options) into a
% structure variable (opt).
%
% Usage:
% [ header, opt ] = eeg_readoptions( filename, opt );
%
% Input:
% filename - [string] name of the option file
% opt - [struct] option structure containing backup values... |
8159c9781db532e6cabd54be54d57f3539bf8228a2f3d606ad6c3b8d1c318931 | MATLAB | 3,420 | 100 | function [h,U2] = WatsonU2Test(group1,group2,alpha)
%WatsonU2Test - Test if two samples (circular data) have different means / variances.
%
% This non-parametric test assumes the data comes from a continuous distribution.
%
% USAGE
%
% [h,U2] = WatsonU2Test(group1,group2,alpha)
%
% group1 angles in rad... |
ce8279177bf2c9724e5c91edb79f6cf81426f817b714d7fb452e241e50ce811b | MATLAB | 3,423 | 65 | function plotEulerDiagram(qMetric, param, qMetricNames,figHandle)
colorMtx = colors(14); % get 12 colorbling-friendly colors
colorMtx = [colorMtx(1:14, :, :), repmat(0.7, 14, 1)]; % make 70% transparent
colorMtx = colorMtx([1:2:end, 2:2:end], :); % shuffle colors to get more distinct pairs
if param.computeDistanceMe... |
29ef4379b826ee3dd8b81306a5c7c681566ef041ef593adacdd1bf2472fe8282 | MATLAB | 3,424 | 112 | function [In,pl] = ClusterPointsBoundaryOutBW(Data, ECells, ICells,m,b)
% function [In,pl] = ClusterPointsBoundaryOut(Data, IfPlot,nClusters)
%
% --This is from Anton's 'ClusterPoints.m'
% The only difference is that you can also output the boundary information (pl)
%
% Data is two column matrix of coordinates, IfPlo... |
88b6d09b729381bc39ffafd0078a3137c317607a3e231b701615cfa64d647904 | MATLAB | 3,424 | 97 | %%*******************************************************************
%% HSDNTrhsfun: compute the right-hand side vector of the
%% Schur complement equation for the NT direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*********... |
b7d4da4f6e159b6d426942f172ab6489446deab16e58c55da829b5e6fba13cdf | MATLAB | 3,424 | 93 | function ea_reconstruction2mni(options)
if ~isfield(options.subj, 'coreg')
options = ea_getptopts(fileparts(fileparts(options.subj.recon.recon)));
end
load(options.subj.recon.recon,'reco');
nii = ea_load_nii(options.subj.coreg.anat.preop.(options.subj.AnchorModality));
if ~isfield(options,'elspec')
options.... |
1b1654bfca9e01ab44f522f555e003bb0804357604a368f64255bbe099d0548d | MATLAB | 3,425 | 105 | function data = AFOFdata_struct2_5(inputdata, filenames)
% USE THIS FOR EXP2.5 SLIPS
% how it works:
% fly = AFOFdata_struct(data,filenames) where data and filenames are
% outputs from rotoball_importer()
for e = 1:length(inputdata)
for t = 1:length(inputdata{e}{1})
trial.filename = filenames{e};
... |
beea2e093780867f9d70d84e7d75c5660b7431b0352ea7d8352ccff9cf62f9fc | MATLAB | 3,425 | 80 | function handles = dendrite_regmater(handles, t_points, R_points, dendriteROI_mask)
handles.roimask = zeros(size(handles.im_norm));
im_norm = handles.im_norm;
scrsz = handles.scrsz;
pos_dend = round([scrsz(3)/6 20 scrsz(3)/3*2 scrsz(4)-100]);
[d1,d2] = size(im_norm);
if ~isempty(handles.size)
explinelength = s... |
58bf06ee01e44ced6772a6f7bbd6cae8df17081f74d8ac31a3209a00c2c69fb8 | MATLAB | 3,426 | 99 | % get holdout set for SVM contrasts, balanced across groups, 2nd-level batch scripts
% adapted from plugin_get_holdout_sets by @lukasvo76, March 2021
% hard-coded options
% 'fivefold_leave_whole_subject_out' : 5-fold cross-validation, leaving
% whole subject out (all images from subject across all conditions)
% 'leave... |
7d71f501fe405d79a9060696bb95f65fa9bda82fd5433aecaff63f6f32a1eb45 | MATLAB | 3,426 | 106 | function val = ft_getopt(opt, key, default, emptymeaningful)
% FT_GETOPT gets the value of a specified option from a configuration structure
% or from a cell-array with key-value pairs.
%
% Use as
% val = ft_getopt(s, key, default, emptymeaningful)
% where the input values are
% s = structure or cell... |
eb2c5d9fb64863a0d543c2848f2cbb836fc8949f18b7d00e94da3a1d7b0f73b5 | MATLAB | 3,426 | 97 | % [labels, start, stop, distance, speed] = CleverSys.load(filename, <sheet>)
% epochs = CleverSys.load(filename, <sheet>)
% Returns a list of event epochs generated by CleverSys.
%
% Example:
% filename = 'data\sequential events - frame.xlsx';
% sheet = 1;
% [labels, start, finish, distance, speed] = Clev... |
13c22832efa9c2a19158ce8a13c66784a2b359cc7a1b2b491941c68e6e5e46e8 | MATLAB | 3,427 | 111 | function [coords_mm,trajectory,markers,elmodel,manually_corrected,coords_acpc]=ea_load_reconstruction(varargin)
% [coords_mm,trajectory,markers,elmodel,manually_corrected,coords_acpc]=ea_load_reconstruction(varargin)
% __________________________________________________________________________________
% Copyright (C) ... |
720dfae14f3565f3581086596b867fe0af58b10e1314a84bae5f7f3622cf73c7 | MATLAB | 3,427 | 97 | %% RUN_VARIANCE_STEP
% Example driver for within-subject beta-variance estimation using
% fnirspower.pipeline.run_variance.
%
% This script:
% 1) sets up fnirspower and third-party paths
% 2) defines mesh / forward-model / layout inputs
% 3) builds an explicit SNIRF file list for the selected subjects
% ... |
ed37429aff9227451464b450e2a89f946b7a2d4eba6c3ed2d3dad51e68e0fb49 | MATLAB | 3,427 | 89 | function imData=read_file(path_to_file,sframe,num2read,options,im_info)
% Reads uncompressed multipage .tiff, .hdf5, .avi or .raw files
% Usage: my_data=read_file('path_to_data_file, start frame, num to read);
% INPUTS:
% path_to_file: location of file to be read
% sframe: first frame to read (... |
d56b3a76bc775f93904f3a594b1bae70865f7b54315d29cf237b236e17b44a62 | MATLAB | 3,428 | 109 | % readelp() - read electrode locations from an .elp (electrode positions)
% file as generated, for example, by a Polhemus tracking device
% Usage:
% >> [eloc, elocnames, X, Y, Z] = readelp(filename);
%
% Inputs:
% filename - name of the .elp file containing cartesian (XYZ) electrode
% loca... |
7128612d1315ee67db20bc59207ef7dccdee9c24b2fb3c27b4ca6533fb04ee9f | MATLAB | 3,429 | 101 | function bb_moments_raincloud(region_idx, parcellation, title)
%
% Usage:
% bb_moments_raincloud(region_idx, title)
%
% Description:
% Stratify regional data according to BigBrain statistical moments
% (authors: @caseypaquola, @saratheriver)
%
% Inputs:
% region_idx (double array) - vector of data.
% ... |
9c3363aeba293d145a9addbd01afe0a89db7326ee942ebd0dcaeb35a6a0c427e | MATLAB | 3,430 | 101 | function xcell = cellK(x,K)
% xcell = cellK(x,K)
%
% CELLK Stores SeDuMi cone K-vector in cell-array format.
%
% On output xcell.f and xcell.l are the free and >=0 components,
% xcell.q{k}, xcell.r{k} and xcell.s{k} contain the Lorentz,
% Rotated Lorentz, and PSD-components, resp.
% xcell.s{k} is a K.s(k) x K.s(k) mat... |
32dd4e30a11f7951818fcffda915a5c481baff68d65b480e8f37a97e91de6c0f | MATLAB | 3,431 | 58 | classdef Normalizer < uint8
enumeration
LINEAR_FIT (1) % linear fit 405 to 465, norm = (465-fit405)/fit405
NO_NOISE_SCALING (2) % same as LINEAR_FIT, but only 5s movmedian of 405 gets scakaled, noise not
ZSCORE_DEBLEACHED (3) % separately zscoring debleached 405 and 465 signa... |
bace56ad878af320fcbe2bf979e44000f90b0fd94714738d53b48a6587a57fa0 | MATLAB | 3,431 | 143 | function [fspec, fstem, fmt] = MRIfspec(fstring,checkdisk)
% [fspec fstem fmt] = MRIfspec(fstring,<checkdisk>)
%
% Determine the file specification (fspec), stem (fstem), and format
% (fmt) from the given file string.
%
% A specification is the name of a file as it could exist on disk. The
% specification has the form ... |
93de9259a0dc3a7c14a08ab7c58ce3c6538f297ba876bb45066db56bfbe6ab52 | MATLAB | 3,434 | 65 | function [bz_datasets,bz_datasets_excluded] = bz_database_submit_collection(database_name,Investigator,NYU_share_path)
% Submit datasets from a folder on the NYU sbare to the Buzsakilab metadata-database
% scans the directory tree for new sessions to add to the database.
% NYU_Share_Datasets / Investigator / Animal / ... |
4db204115163e3012ebe2af2fc7dd2f66f8f009a0b6dd09a78b4060f29ee39bb | MATLAB | 3,436 | 107 | function [ind,t0,s0] = crossing(S,t,level,imeth)
% CROSSING find the crossings of a given level of a signal
% ind = CROSSING(S) returns an index vector ind, the signal
% S crosses zero at ind or at between ind and ind+1
% [ind,t0] = CROSSING(S,t) additionally returns a time
% vector t0 of the zero crossings of ... |
f71fbe0afc9ae7d609e92cc1e75f297f73f8b1b1f518a0d643a915b537bcb084 | MATLAB | 3,436 | 67 | function [S,f,Serr]=mtspectrumc(data,params)
% Multi-taper spectrum - continuous process
%
% Usage:
%
% [S,f,Serr]=mtspectrumc(data,params)
% Input:
% Note units have to be consistent. See chronux.m for more information.
% data (in form samples x channels/trials) -- required
% params: structure wi... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.