sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
dc1997d0869bc6edf8cdedaf8152d1f31511cd17578ba15e0438d88700d4a27f | MATLAB | 5,768 | 163 | function varargout = SpineTurnover(varargin)
% SPINETURNOVER MATLAB code for SpineTurnover.fig
% SPINETURNOVER, by itself, creates a new SPINETURNOVER or raises the existing
% singleton*.
%
% H = SPINETURNOVER returns the handle to a new SPINETURNOVER or the handle to
% the existing singleton*.
%
% ... |
2e69f79d095e90687184c4a9765be49151020eb25d54fdd341a960f173e40ec4 | MATLAB | 5,772 | 177 | % plotproj() - plot projections of one or more ICA components along with
% the original data (returns the data plotted)
%
% Usage:
% >> [projdata] = plotproj(data,weights,compnums);
% >> [projdata] = plotproj(data,weights,compnums, ...
% title,limits,chanlist,channames,... |
e012b4260d1398e19d5bc5c54f983d4c19feffbeaf9c24f5b7679b6a8f1b4374 | MATLAB | 5,777 | 111 | function [score, scoreIndep, p] = compareAssignments(assigns1, assigns2, showTables)
% COMPAREASSIGNMENTS Computes a quality measure of the similarity between assignments.
%
% [score, scoreIfIndependent] = compareAssignments(assignments1, assignments2)
% The inputs, 'assignments1' and 'assignments2', must be two... |
d9d4dc2f0cbedd748c65ff38ca80662a50857db528057e4137d025ce4afbe778 | MATLAB | 5,781 | 155 | function bfsave(varargin)
% BFSAVE Save a 5D matrix into an OME-TIFF using Bio-Formats library
%
% bfsave(I, outputPath) writes the input 5D matrix into a new file
% specified by outputPath.
%
% bfsave(I, outputPath, dimensionOrder) specifies the dimension order of
% the input matrix. This value will be ign... |
597a865253c6221572795b6e0c58185859c7f7bab90ada7b50fd2d594f115496 | MATLAB | 5,797 | 110 | %% Step 3 Tiny Dancers: ERP analyses
clear all
clc
trial_mus=[];
trial_con=[];
trial_hpi=[];
trial_lpi=[];
% load names of all files '3m','6m','12m',
group={'adults'};
for g=1:length(group)
cd(['D:\MUSICOM_EEG\PROC\Step2_epochdata_mast\' group{g}]);
FileNames = {dir(['*' 'EPOCHS.mat']).name}... |
8cb9b0978edb6f320c14a62788f7ecce5f28bdf35fa400c506d4ea55d28d6101 | MATLAB | 5,801 | 163 | function Volume=polygon2voxel(FV,VolumeSize,mode,Yxz)
% This function POLYGON2VOXEL will convert a Triangulated Mesh into a
% Voxel Volume which will contain the discretized mesh. Discretization of a
% polygon is done by splitting/refining the face, until the longest edge
% is smaller than 0.5 voxels. Followed by ... |
cb643dedb1b4d1703743ee1385881ef08e8269dbe8e512424956a0f092864cb5 | MATLAB | 5,803 | 198 | function [vertices, faces, facevertexcdata, renderer, tags] = u3d_pre_patch(ax)
%U3D_PRE_PATCH Preprocess surface output to u3d.
%
% usage
% [vertices, faces, facevertexcdata] = U3D_PRE_PATCH
% [vertices, faces, facevertexcdata] = U3D_PRE_PATCH(h)
%
% optional input
% ax = axes object handle
%
% out... |
2378ffc5cec803d4633d73e9d9808d82d362a02c88a378b3eb0a3f8776f80eb6 | MATLAB | 5,806 | 166 | function [M, TF] = padcat(varargin)
% PADCAT - concatenate vectors with different lengths by padding with NaN
%
% M = PADCAT(V1, V2, V3, ..., VN) concatenates the vectors V1 through VN
% into one large matrix. All vectors should have the same orientation,
% that is, they are all row or column vectors. The vectors... |
c294ec935d2d8f216b17fae8b5cd2061d0deea87be1a0ba5b2634c016928208a | MATLAB | 5,808 | 148 | function CBIG_MSHBM_avg_profiles(seed_mesh,targ_mesh,out_dir,num_sub,num_sess)
% CBIG_MSHBM_avg_profiles(seed_mesh,targ_mesh,out_dir,num_sub,num_sess)
% This function will be used to average profiles across all the subjects
% and all the sessions. Please note that the profiles of sub-sessions will
% not be included. ... |
d64819b59ecc01acc6c2cec3cabd55923da03fa81e148d593d37a1925fb1b1a2 | MATLAB | 5,808 | 181 | function [ccg,x,y] = ShortTimeCCG(times1,times2,varargin)
%ShortTimeCCG - Time-varying auto/cross-correlograms of point processes.
%
% Determine how xcorrelograms vary in time, i.e. repeatedly compute xcorrelogram
% over successive short time windows.
%
% USAGE
%
% [ccg,bins,time] = ShortTimeCCG(times1,times2,<opt... |
8133f74a107c6c1552f5fa0c832ed21fa1d89114f862fcd633b82a9d9ba25f8b | MATLAB | 5,809 | 163 | function d = getdict
% Dictionary of NIFTI stuff
% _________________________________________________________________________
% Copyright (C) 2005-2013 Wellcome Trust Centre for Neuroimaging
%
% $Id: getdict.m 5759 2013-11-21 14:01:14Z guillaume $
persistent dict;
if ~isempty(dict)
d = dict;
return;
end
% Da... |
bf84d42cb0423dca2cd051b504abb22a6964924171ae039e178cd6299f03787a | MATLAB | 5,810 | 161 | % eeglab2fieldtrip() - do this ...
%
% Usage: >> data = eeglab2fieldtrip( EEG, fieldbox, transform );
%
% Inputs:
% EEG - [struct] EEGLAB structure
% fieldbox - ['preprocessing'|'freqanalysis'|'timelockanalysis'|'companalysis']
% transform - ['none'|'dipfit'] transform channel locations for DIPFIT
% ... |
2f8e85b05249c4a46dc2b53657df45f0d7c90457cf2ded8a1d93064a778a5236 | MATLAB | 5,812 | 131 | %% ODOR TASKS
% Calculate spectrogram - concatenated 6 subs
ts = lfp_odorTasks_combinedSubs;
sniffonset_conds = { sniffonsets_odorTasks_combinedSubs};
para = [];
para.freq = logspace( log10( 1), log10( 200), 100); % center frequencies for filtering
para.bandwidth = logspace( log10( 2), log10( 30), 100); % bandwidth of... |
cc6fddf363d43fa95d634f01ccce7b7d47c2a43544a323213a3f6c5e4255d39d | MATLAB | 5,813 | 152 | function cvx_global
%CVX_GLOBAL Create CVX's global internal data structure, if needed.
% CVX_GLOBAL creates a hidden structure CVX needs to do its work. It is
% harmless for the user to call it, but it is also useless to do so.
global cvx___
if isfield( cvx___, 'problems' ),
return
end
tstart = ... |
c67c4919c647938a292d8ef5651941e6917838af5058cda9a05dcd0d04ba936c | MATLAB | 5,819 | 114 | function [datac,datafit,Amps,freqs]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt,f0)
% fits significant sine waves to data (continuous data) using overlapping windows.
%
% Usage: [datac,datafit]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt)
%
% Inputs:
% Note that units of Fs, fpass have to be consistent.
... |
79b5730733b170dc8d3e13b4ee7ea70c03ed60ff89dd0b7934e1377dfea16ace | MATLAB | 5,820 | 176 | %
%
% Format: The prep_7 script extracts signature responses and saves them.
% These fields contain data tables:
% DAT.SIGNATURES.(signaturename).(data scaling).(similarity metric).by_condition
% DAT.SIGNATURES.(signaturename).(data scaling).(similarity metric).contrasts
%
% signaturenames is any of those from load_ima... |
47a19c7f26f5fd7914506165006046eacbce14352308e0d36fc574dd8ca6780f | MATLAB | 5,821 | 156 | % This version was derived from the original version by Pestilli and Caiafa.
% Copyright (2015), Franco Pestilli (Indiana Univ.) - Cesar F. Caiafa (CONICET)
% email: pestillifranco@gmail.com and ccaiafa@gmail.com
% https://github.com/francopestilli/life available under
% https://github.com/francopestilli/life/blob/mast... |
babc132a07207a2660ceee07ec130cf68783d3c4e3ff3c73ebc58375ef50394b | MATLAB | 5,821 | 163 | function borderResults = cvBorderClassifier(allROIs, randomBorders, nFolds)
% Batch-mode cross-validated SVM decoding
%
% Strategy:
% 1) Build per-segment, per-fold train/test datasets up front (including class balancing).
% 2) parfor over segments to fit/predict using the pre-extracted fold data.
%
% Inputs:
% a... |
c7ae7ee8a876d28a5b91cb2865f668e5cfc613e35e9d9daf4f1a2440558b4865 | MATLAB | 5,829 | 145 | % pop_loadeeg() - load a Neuroscan .EEG file (via a pop-up window if no
% arguments). Calls loadeeg().
%
% Usage:
% >> EEG = pop_loadeeg; % pop-up data entry window
% >> EEG = pop_loadeeg( filename, filepath, range_chan, range_trials, ...
% range_typeeeg, range_response, format); %... |
2f8fb91d7562e51056b366d60b75dd4667c534a346ea3fd17a800f6fe8ead1dd | MATLAB | 5,838 | 111 | function varargout = ea_normalize_schoenecker(options)
% This is a function that normalizes both a copy of transversal and coronal
% images into MNI-space. The goal was to make the procedure both robust and
% automatic, but still, it must be said that normalization results should
% be taken with much care because all r... |
8d8b152cf39ab1042561fe94fd25f731cf154b9d8af84e6777a5cdd61a30cc9b | MATLAB | 5,838 | 223 | function h = slice3i(resultfig, vol, I2X, slicedim, sliceidx, controlhandles)
% Display a slice from a volume in 3-D
% h = slice3(vol, I2X, slicedim, sliceidx, handle)
%
% Vol is either a scalar or RGB volume, e.g. N x M x K or N x M x K x 3.
% I2X is a transformation matrix from volume coordinates to xyz 3-D world
% c... |
9edfd72233a35c45d819291a8ebf622d490d4d86d99fbc70628dadfdc5f6db0f | MATLAB | 5,849 | 149 | function [ map,centers,occupancy,pos_loc,spk_loc ] = rate_map( varargin )
% RATE_MAP - Calculated the occupancy normalized rate map
%
% Calculates the N-dimensional occupancy normalized rate map. rate_amp
% uses the pass_index_parser inputs.
%
% [MAP,CENTERS,OCCUPANCY,POS_LOC,SPK_LOC] = RATE_MAP(POS_TS,POS,SPK_TS)
% [... |
fa2019e5fbe653b6c4448f4ed3957491def5c74dd801133b2ae06c9ce41e3227 | MATLAB | 5,853 | 185 | % matcorr() - Find matching rows in two matrices and their corrs.
% Uses the Hungarian (default), VAM, or maxcorr assignment methods.
% (Follow with matperm() to permute and sign x -> y).
%
% Usage: >> [corr,indx,indy,corrs] = matcorr(x,y,rmmean,method,weighting);
%
% Inputs:
% x = first i... |
ddf5d506daa2b6692295c91216c306a4c3e1128fc8a4a9cf38d8bf001611575c | MATLAB | 5,856 | 128 | % configure file for calculation of tensors
% DTI Configuration file
% BATCH system (Volkmar Glauche)
%
% File created by Susanne Schnell
function mapop = dti_cfg_mapop
% ---------------------------------------------------------------------
% filename1 name of probabilistic map 1
% ----------------------------------... |
1ef40f786c4d4b37e311fa057ad89e134ae1f204c268d2216d20da68b190aa70 | MATLAB | 5,860 | 208 | %% USER OPTIONS & VARIABLE DEFINITIONS
% -------------------------------------------------------------------------
% METRIC OPTION
mymetric = 'dotproduct'; % 'dotproduct' or 'cosine_sim'
% CONTROLLING FOR GROUP COVARIATE
group = [];
if isfield(DAT, 'BETWEENPERSON') && isfield(DAT.BETWEENPERSON, 'group')
group... |
dc6c70c42b1519648345923c5b90f51d9d2874728cc33f95a56fb3334ac0adae | MATLAB | 5,864 | 147 | function handles = dan_add_markings(handles, timeVec)
%
% Dump all the extra crap onto the screen such as bad epoch markings,
% notations, segments blah blah blah
%%
% Authors: Dan Denis
% Date: 2021-07-14
%% Mark bad epochs
epochIdx = str2double(get(handles.current_epoch_number, 'String'));
if handles.psg.ar.... |
e606e5d97a69a99badb45c7e0d953c0277feca09e16c80794b8804e1edda20c9 | MATLAB | 5,865 | 171 | function [SecondsAfterLightCycleStart_PerFile,SecondsAfterLightCycleStart] = TimeFromLightCycleStart(basepath,lightsonhours,lightsonminutes,lightsonseconds)
% Zeitgeber times of recording files... based on file names and/or metadata
% files.
% Inputs:
% - basepath - per buzcode standard, where all files for a given... |
b2bbb3c00c99cc5a7040fb7e1a514ce0d52cb97425e3aeb9d3ce26581695c286 | MATLAB | 5,872 | 109 | function Volume=polygon2voxel_double(FacesA,FacesB,FacesC,VerticesX,VerticesY,VerticesZ,VolumeSize,Wrap)
Vertices=[VerticesX(:) VerticesY(:) VerticesZ(:)]-1;
% List with all vertices coordinates of a face
FaceVertices=[Vertices(FacesA,:) Vertices(FacesB,:) Vertices(FacesC,:)];
Volume=false(VolumeSize);
Volume=Dr... |
c81f645bce0b997f1950689ed72176eb82fb58946a3c051f929c1d9e44465f7c | MATLAB | 5,874 | 149 | function CBIG_ArealMSHBM_avg_profiles(seed_mesh,targ_mesh,out_dir,num_sub,num_sess)
% CBIG_ArealMSHBM_avg_profiles(seed_mesh,targ_mesh,out_dir,num_sub,num_sess)
% This function will be used to average profiles across all the subjects
% and all the sessions. Please note that the profiles of sub-sessions will
% not be ... |
5b1a267bdec74ec6c7513dbed75c32a363bce8d3e930d73aaf6d13514ef0715d | MATLAB | 5,876 | 158 | function roi_table = dice_statistic_image_by_roi(imgA, imgB, roi_img, varargin)
% dice_statistic_image_by_roi Per-ROI Dice overlap between two statistic images.
%
% roi_table = dice_statistic_image_by_roi(imgA, imgB, roi_img)
% roi_table = dice_statistic_image_by_roi(imgA, imgB, roi_img, 'p_threshold', 0.01)
% r... |
a6bdedf713d712724d479f888759f754aba4bed7fa59dbb6f492e5c33f5fbcad | MATLAB | 5,876 | 160 | function timeBefAftEvent = timeBeforeAfterEvent(seqOfEvents,segmentMerge,segmentSplit,timeMerge,segmentContinuous,timeSplit,firstFrame )
% timeBeforeAfterEvent calculates the time before and after the event for
% the pairwsing of segments.
% timeBefAftEvent = timeBeforeAfterEvent(seqOfEvents,timeMerge,timeSplit )
%
... |
3af56f85512f98a1325b8e663186102b2e219609d6c6661e1666c58fe891ead6 | MATLAB | 5,877 | 138 | function bands = CoherenceBands(coherogram,frequencies,varargin)
%CoherenceBands - Determine running coherence in physiological bands.
%
% USAGE
%
% bands = CoherenceBands(coherogram,frequencies,<options>)
%
% coherogram coherogram obtained using <a href="matlab:help MTCoherogram">MTCoherogram</a>
% freq... |
903b1f4e87fe5208688264347aa6865b04b5629b75919b31ac8cd20d5ad861e1 | MATLAB | 5,878 | 231 | %test
function Errs = createjointLUTs(ten);
dirs = load('dwidirections.mat');
dirs = dirs.dirs128;
W = createWeightingScheme(ten);
W = diag(W);
orderMM = 8;
orderMS = 4;
alpha = 0;
%% model model
n = 25;
Dmin = -0.3;
Dmax = 6;
D1 = [Dmin Dmax];
D2 = [Dmin Dmax];
D3 = [Dmin Dmax];
l1 = (0:(n-1))/(n-1)*(D1(2)-D1(... |
e96237b26c97d9709234db4bdc87864025b65c38e3aaf5f459be259f29d671a9 | MATLAB | 5,879 | 225 | %% Create schematics of multiple FNPs
clear; clc;
loadparam;
% Number of FNPs
N_array = [10, 20, 50, 100];
max_N = max(N_array);
% Create tiledlayout figure
fig = figure;
fig.Position = [100, 100, 1400, 160];
set(gca,'Color','white')
% box on;
num_subcols = 9;
num_subcols_gap = 7;
t = tiledlayout(1, length(N_array)... |
859f1150a495ed63afc8ee7c7bc5e9d5d524c0023770cc3ca5fa8a926c798f9b | MATLAB | 5,885 | 110 | function SANDIinput = SANDI_batch_analysis(ProjectMainFolder, Delta, smalldelta, SNR)
% Main script to perform the SANDI analysis (on one or more datasets) using machine learning, as described in Palombo M. et al. Neuroimage 2020: https://doi.org/10.1016/j.neuroimage.2020.116835
% The code assumes that data are organ... |
a312a1cb196601d3e16af3e60e86ac31d3b2eacd267d34950976a0024af7be40 | MATLAB | 5,886 | 148 | function est = LaBGAScore_combat_fit(dat, batch, varargin)
% Fit ComBat harmonization parameters on a TRAINING set only
%
% :Usage:
% ::
% est = LaBGAScore_combat_fit(dat, batch)
% est = LaBGAScore_combat_fit(dat, batch, 'parametric', 1, 'ref', refLabel)
%
% :Inputs:
% **dat:** p x n data matrix (feature... |
cae90503235973d68c877da13cb7d034e810d717a6c44c8157515caaa3b521ae | MATLAB | 5,887 | 117 | function [g, c, tmp, m]=kMeansCluster(m,k,isRand)
% kMeansCluster - Simple k means clustering algorithm
% Author: Kardi Teknomo, Ph.D.
% ... |
77b06f63bc0633a8ed48447c0891bbc24427861b02bc65c99806a91206b79e02 | MATLAB | 5,888 | 165 | % surrogdistrib - Build surrogate distribution
%
% surrog = surrogdistrib(data, varargin);
%
% Inputs:
% data - [cell] data arrays for which to compute a surrogate
% distribution.
%
% Optional inputs:
% 'method' - ['bootstrap'|'perm'] use either 'bootstrap' or 'permutation'
% method. Bootstr... |
d3acdd32b3b6641d9101028da42922f5ce623dcddbd863965259728425640941 | MATLAB | 5,889 | 159 | function ArgStruct=parseArgs(args,ArgStruct,varargin)
% Helper function for parsing varargin.
%
%
% ArgStruct=parseArgs(varargin,ArgStruct[,FlagtypeParams[,Aliases]])
%
% * ArgStruct is the structure full of named arguments with default values.
% * Flagtype params is params that don't require a value. (the valu... |
3049682b51cec4ca74a2c5af512c4776b61f385cd0487cc553ea58c35d32f29b | MATLAB | 5,894 | 189 | function PlotBehavior(animal)
exp_dir=get_exp(animal);
stim_dir=[exp_dir 'stimuli\'];
load([stim_dir 'position.mat'])
position=downsample(position,25);
load([stim_dir 'running.mat'])
running=downsample(running,25);
load([stim_dir 'licking.mat'])
licking=downsample(licking,25);
load([stim_dir 'reward.mat'... |
471055c12e89c650767b97288bedb8616652e45fc5990fc88c8fb0646e9b0242 | MATLAB | 5,894 | 134 | function call_stampresp_v2(handles)
mainfig_pos = get(handles.mainfigure, 'Position');
clear trace_stamp_pool trace_num_all ttlabel_pool
for k = 1:length(handles.datafilename)
handles = loadtrace(handles, k);
if handles.plotRawdff == 0 && handles.plotBAPdff == 0 && handles.plotFiltdff == 0
handles.plotR... |
e0020102ca02a205959af8089a8b949f9d25933edbfe497cbb3ef91abe5eda6a | MATLAB | 5,895 | 147 | function colors = distinguishable_colors(n_colors,bg,func)
% DISTINGUISHABLE_COLORS: pick colors that are maximally perceptually distinct
%
% When plotting a set of lines, you may want to distinguish them by color.
% By default, Matlab chooses a small set of colors and cycles among them,
% and so if you have more ... |
2334babbcc939d81053d6ace0a77352ad467bd5389418ea379af52d680eab3c3 | MATLAB | 5,901 | 174 | function list = find(varargin)
% XMLTREE/FIND Find elements in a tree with specified characteristics
% FORMAT list = find(varargin)
%
% tree - XMLTree object
% xpath - string path with specific grammar (XPath)
% uid - lists of root uid's
% parameter/value - pair of pattern
% list - list of uid's of matched elements... |
47760ade3635b20b785a85e3838d30913dab46feaee0d2a1f949c347f0151a85 | MATLAB | 5,902 | 101 | function tractset = ea_discfibers_compat_statmetrics2statsettings(tractset)
if isnan(tractset.statmetric)
return
end
switch tractset.statmetric
case {'Two-Sample T-Tests / VTAs (Baldermann 2019) / PAM (OSS-DBS)'}
tractset.statsettings.stimulationmodel = 'VTA';
tractset.statsettings.efieldmetri... |
514a1dc8cbe3ab8daf3c4f70c9e6d3b2b677a17f07767145e1d630e45c5abc45 | MATLAB | 5,902 | 249 | function z = max( x, y, dim )
% Disciplined convex/geometric programming information:
% MAX is convex, log-log-convex, and nondecreasing in its first
% two arguments. Thus when used in disciplined convex programs,
% both arguments must be convex (or affine). In disciplined
% geometric prog... |
2f7ba1f903f5164a35ecbcc1e37a5e15961c79075dd4c5a46f03853f2b5d0213 | MATLAB | 5,903 | 114 | function AssemblyTemplates = assembly_patterns(SpikeCount,opts)
% Patterns = assembly_patterns(Activitymatrix,opts): extracts assembly patterns from the spike matrix.
%
% Description of inputs:
% Activitymatrix: spike matrix. Rows represent neurons, columns represent time bins. Thus, each element of the matr... |
748546b3de01d3ec31deab688ade76affd3264a4b3d8170e5f74d06359120d60 | MATLAB | 5,904 | 123 | function [lh_time_mat, rh_time_mat] = CBIG_hMRF_build_time_matrix(lh_fmri_fullpath_txt, rh_fmri_fullpath_txt, ...
mesh_type, lh_output_file, rh_output_file, censor_file_fullpath)
% CBIG_hMRF_build_time_matrix(lh_fmri_fullpath_txt, rh_fmri_fullpath_txt, mesh_type, lh_output_file, rh_output_file)
%
% This function ge... |
4e6196f952eb2a0ab01529f297981906de09c006ebd5417ac99b8a77f749a1da | MATLAB | 5,905 | 173 | function imData=bigread2(path_to_file,sframe,num2read)
%reads tiff files in Matlab bigger than 4GB, allows reading from sframe to sframe+num2read-1 frames of the tiff - in other words, you can read page 200-300 without rading in from page 1.
%based on a partial solution posted on Matlab Central (http://www.mathworks.co... |
57346611b2c88b4cdaf1dbb331cb81adead4fe64da7ed2dfae218b7323465d48 | MATLAB | 5,908 | 157 | function [spectrum,f,s] = MTSpectrum(lfp,varargin)
%MTSpectrum - Compute LFP spectrum by multi-taper estimation.
%
% The spectrum is computed as the average spectrogram, using the <a href="http://www.chronux.org">chronux</a> toolbox.
%
% USAGE
%
% [spectrum,f,s] = MTSpectrum(lfp,<options>)
%
% lfp w... |
f65540299b1f622893e449a8fad433c8ea22c3e746fb99545834e9ba5640128e | MATLAB | 5,910 | 111 | function [stat_img, fmri_dat, region_obj, region_table] = thresholded_fmri_data_from_pval_nii (fullpath_to_pval_nii, stat_vec, mask_obj, atlas_obj, p, p_type, stat_type, thr_type, k)
% thresholded_fmri_data_from_pval_nii Thresholded map and region table for a
% non-standard statistic, from a p-value NIfTI on disk.
%
%... |
abca335fff2ae5b8e7eca9c02824b31dd8fdb552390456025faed9688e52abf0 | MATLAB | 5,917 | 151 | function append_pdfs(varargin)
%APPEND_PDFS Appends/concatenates multiple PDF files
%
% Example:
% append_pdfs(outputFilename, inputFilename1, inputFilename2, ...)
% append_pdfs(outputFilename, inputFilenames_list{:})
% append_pdfs(outputFilename, inputFilenames_cell_or_string_array)
% append_pdfs output... |
17936332e63734c5cc1c7229e28567aae1f17cbe1265b912e62ce950ba3c28d6 | MATLAB | 5,918 | 248 | function z = min( x, y, dim )
% Disciplined convex/geometric programming information:
% MAX is convex, log-log-concave, and nondecreasing in its first
% two arguments. Thus when used in disciplined convex programs,
% both arguments must be concave (or affine). In disciplined
% geometric pro... |
cd44fa1600f61389a57319905fdd422b5183387963bedf5fc74e739cd026f928 | MATLAB | 5,919 | 206 | % Iterations over various initial NB-other cell size differences without
% delamination. Plotting success probability for each size difference
% shown in Figure 6.
% To speed up comment line 71 in
% SOP_multicell_LI_adapted_weighted_with_trigger_PerimSave.mat before
% running this script to avoid saving simulations... |
6c079c40367a1acb84470bd4273d89a251a4f3c80d904aec9333ef4f963f9382 | MATLAB | 5,920 | 145 | function move_betas_to_secondlvl(firstlvl_dir, datadir, operation, varargin)
% MOVE_BETAS_TO_SECONDLVL Move beta images to a second-level analysis directory.
%
% This function moves or creates symbolic links to beta images from a first-level
% analysis directory to a second-level analysis directory. It is designed to b... |
eb351e94afc741350c97f6c1ddc7e3ab193ad0273e007dedde790a78041bb635 | MATLAB | 5,920 | 194 | function [vertices, faces, facevertexcdata, renderer] = u3d_pre_surface(ax)
%U3D_PRE_SURFACE Preprocess surface output to u3d.
% U3D_PRE generates the input for the MESH_TO_LATEX function from
% Alexandre Gramfort from your surface-graphs. The surface graphs 3d-model can be
% displayed in u3d - format i... |
22b6c294f150a8ebceea9df6f9be2379a0727aa263d74695f7de363cb8018f67 | MATLAB | 5,921 | 189 | function this = freesurfer_read(filename)
% Low level reader of FreeSurfer file
% FORMAT this = freesurfer_read(filename)
% filename - FreeSurfer file
%
% Read ASCII triangle surface file and part of binary mgh file.
% See https://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats
%_______________________________________... |
5c8c2f37d8f2ab29a04e9be876f1d26da901473a5eecc191b16d009873ee636e | MATLAB | 5,921 | 130 | function [inds_of_sites_with_at_least_k_repeats min_num_repeats_all_sites num_repeats_matrix label_names_used] = find_sites_with_k_label_repetitions(the_labels, k, label_names_to_use)
% This function takes in labels in binned label format, and an integer k, and returns the indices for all sites (e.g. neurons)
% tha... |
41f0dd6e9b103d69accfcf4b0d4fce288d5b7542b29accfb6c613ff1db8e806d | MATLAB | 5,922 | 204 | function [trajectory,trajvector,estpoint]=ea_fit_line(centerline)
% This function fits a line to raw 3D data specified by centerline. It also
% exports a normalized vector between the fitted datapoints and the next
% expected point of the trajectory. The function uses robustmean by
% Developer "Jonas"
% (http://www.mat... |
cf4c357525be0af8ac41d1d90b5fc3e29257313a5799b05919b5ca1c8b8b4966 | MATLAB | 5,924 | 143 | function [SleepStateEpisodes] = StatesToEpisodes(SleepState,basePath)
% Takes a buzcode structure of sleep state data and imposes max and
% min durations and interruption criteria to make WAKE, NREM, REM Episodes,
% Packets, Microarousals and Microarusals in REM, as defined in
% Watson et al 2017. Returns the SleepSta... |
f60b08010bfb1ebcbd49c1f22c211b6d0cb067bed002e0db18509b80e9272a3a | MATLAB | 5,926 | 146 | % Name: Robert Kim
% Date: 09-01-2024
% Email: robert.f.kim@gmail.com
% fnc_time_bootstrap_cluster.m
% Description: Pointwise bootstrap CIs (like fnc_time_bootstrap.m) PLUS a
% cluster-based permutation test to control for multiple comparisons across
% time. Returns per-cluster p-values and a logical mask of timepoints... |
f40fd5172a70a602c592482905ff64aa0c756a8e81e1d7f00f97c0fa8625d2cb | MATLAB | 5,931 | 162 | %% Set the working directory
clear
cd('C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\Partage-QP\Dryad'); %<--------- change to local path
addpath(genpath(pwd))
chFigDir = 'Figures'; %<--------- relative path to output figure directory
%% Load data
db2Mat = xlsread('Input_Matrix.xlsx', 'C2:AJ25'); % ... |
e71bcbd1c582fb9f9d4387901db1b0a9afa0982988a449b68864fa3292b1b590 | MATLAB | 5,932 | 114 | function [datac,datafit,Amps,freqs]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt,f0)
% fits significant sine waves to data (continuous data) using overlapping windows.
%
% Usage: [datac,datafit]=rmlinesmovingwinc(data,movingwin,tau,params,p,plt)
%
% Inputs:
% Note that units of Fs, fpass have to be consis... |
49f7a0f99066bba648b31b5b0a4b333ef0d2a276b059885ee2f930d5967f45f9 | MATLAB | 5,933 | 133 | % std_changroup() - Create channel groups for plotting.
%
% Usage:
% >> STUDY = std_changroup(STUDY, ALLEEG);
% >> STUDY = std_changroup(STUDY, ALLEEG, chanlocs, 'interp');
% Inputs:
% ALLEEG - Top-level EEGLAB vector of loaded EEG structures for the dataset(s)
% ... |
f1e58eaa48e301027bb3e33534400ee2cd9c8aace5422f99dfe84331316d205f | MATLAB | 5,936 | 131 | function CBIG_visualize_factorComp_mixedAmyloid(subInfoFile, GMICVFile, K, GRP)
% CBIG_visualize_factorComp_mixedAmyloid(subInfoFile, GMICVFile, K, GRP)
% Colors
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
C_AP = 'r';
C_AN = 'g';
C_UK = 'b';
C_EDGE = 'k';
%-----... |
eaee5502caa6f84d38a00abbcbc8c4ed77aba5a557da273d85b7cf5c950abb9c | MATLAB | 5,937 | 115 | function [specEv_struct, TFRs, X] = spectralevents(eventBand, fVec, Fs, findMethod, vis, varargin)
% SPECTRALEVENTS Find and analyze transient spectral events in a
% time-series dataset. Spectral events are defined as local maxima above a
% power threshold of a specified band in the non-averaged time-frequency
% ... |
1e7072be5094f062b3a3bf15c0ef185873da1355e40bed7b5a246001c1b37341 | MATLAB | 5,940 | 211 | function [vert, face] = read_ply(fn)
% READ_PLY reads triangles, tetraheders or hexaheders from a Stanford *.ply file
%
% Use as
% [vert, face, prop, face_prop] = read_ply(filename)
%
% Documentation is provided on
% http://paulbourke.net/dataformats/ply/
% http://en.wikipedia.org/wiki/PLY_(file_format)
%
% See ... |
d729509a5118e5105f2021bd12d414042eb6a2937d81f17ebb93cec57a90f95a | MATLAB | 5,943 | 136 | function plotfluordirections(avgfluor,redtemps,ROIs,Xpix,Ypix,framerate)
%plot the data averaged for each ROI
%show the ROI?
fn=fieldnames(avgfluor);
[numROIs,triallength]=size(avgfluor.(fn{1}));
fig=figure('Position',[1 1 509 458]);
hold on;
subone=subplot(211);
subtwo=subplot(212);
fig2=figure('Position',[... |
56ca4dddb718dc5cf019462bedfcde843c21ad37c414c1bdf1b68d21c0d092ad | MATLAB | 5,948 | 193 | function pars = checkpars(pars,lponly) %#ok
% pars = checkpars(pars,lponly)
%
% CHECKPARS Fills in defaults for missing fields in "pars" structure.
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMa... |
4bfe7b9a3fa4f3d8ca2363ee8e404b2944fd71981d004fc036eb8ca94f1a05c1 | MATLAB | 5,950 | 165 | function bz_meta_extracted = bz_database_extract_meta(bz_datasets,j)
% Submit dataset to the Buzsakilab metadata-database
% v1.1
%
% INPUT
% bz_datasets
% structure with subfields named after the mySQL columns. The subfields has
% to have the right format for submitting to the database.
%
%
% By Peter Petersen
% peters... |
f56e62b5f68d2b9cd33976159ce534e297fd2a533e00b8392347e8b3f9599349 | MATLAB | 5,956 | 154 | function fix_lines(fname, fname2)
%FIX_LINES Improves the line style of eps files generated by print
%
% Examples:
% fix_lines fname
% fix_lines fname fname2
%
% This function improves the style of lines in eps files generated by
% MATLAB's print function, making them more similar to those seen on
% scree... |
9e25c1089e82f5de800430011662b4fb0b9c618d0629ffcdb2c4cce36b4247fd | MATLAB | 5,958 | 145 | function NPS_region_vals = plugin_extract_local_nps_region_vals(second_level_DAT_object, my_region)
%% Helper function to extract local NPS region values from DAT object
%
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published... |
e20ecd56fa5b3399fa0ead15be71f57d009239d952b1c4d2886178e0d6a3a498 | MATLAB | 5,968 | 208 | function [fig] = colormap_roi(mat, sorting, label, varargin)
% DESCRIPTION:
% Make figure of matrix, with option to sort by community label.
% * Note that if the matrix is already sorted (organized by labeled
% community, the sorting option should be set to 2 so it won't re-sort
% the same matrix.
% * ... |
de5e388d2f09653ef1d210d4f00412b48bf04f77d460cc7e8ce33c3cf467728f | MATLAB | 5,970 | 150 | %WAVELET 1D Wavelet transform with optional singificance testing
%
% [WAVE,PERIOD,SCALE,COI] = wavelet(Y,DT,PAD,DJ,S0,J1,MOTHER,PARAM)
%
% Computes the wavelet transform of the vector Y (length N),
% with sampling rate DT.
%
% By default, the Morlet wavelet (k0=6) is used.
% The wavelet basis is norm... |
98227185074f5a21c146671da4df0f9dc5309fc50e6e7085cc401276628650be | MATLAB | 5,980 | 119 | % Name: Robert Kim
% Date: 05-11-2023
% Email: robert.f.kim@gmail.com
% generate_trials.m
% Description: Generate synaptic-current trial data for a given trained
% two-layer one-modality (instr) RNN, optionally with a chosen lesion
% applied to the recurrent weight matrix. Saves a .mat file
% under <model_dir>/trials/ ... |
d80d1ca59657a4d63ddd68c8ab27e407ed35ef9c947b55052271394bbb86a14e | MATLAB | 5,982 | 175 | function bz_PreprocessSession(varargin)
% bz_PreprocessSession(varargin)
% Master function to run the basic pre-processing pipeline for an
% individual sessions. Is based on sessionsPipeline.m but in this case
% works on an individual session basis no in a folfer with multiple ones.
%
% INPUTS
% <o... |
2227bcd46a456b2787c39863dc57439cd832f1ffcd39934cd00dbeef5697966b | MATLAB | 5,987 | 178 | clc
clear
addpath 'C:\Users\Admin\AppData\Roaming\MathWorks\MATLAB Add-Ons\Functions\Shapiro-Wilk and Shapiro-Francia normality tests'
% Select an .xlsx file
[fileName, filePath] = uigetfile('*.xlsx', 'Select an .xlsx file');
if fileName == 0
error('No file selected');
end
fullFilePath = fullfile(filePath, fileNam... |
47334d188ebe2099c2864a00e6e5715cfb45ccbd8a72fa125209a218397b3eb7 | MATLAB | 5,991 | 167 | function [beta, intercept, alphaSel, lambdaSel, tuneInfo] = ...
selectENetHyperparams(XtrRaw, ytr, Ctr, cvIn, alphaGrid, lambdaGrid, rule, scaleMode)
% selectENetHyperparams Fold-averaged Elastic Net hyperparameter selection.
%
% [beta, intercept, alphaSel, lambdaSel, tuneInfo] = selectENetHyperparams( ...
% ... |
d2db9e037ded6ea48f7dbcf7cce0e279cd1cfffdc34f579ab8f58800e46241f3 | MATLAB | 5,991 | 152 | function output = resynthesise(x,fs,cfs,m,varargin)
%RESYNTHESISE Resynthesise a target from a time-frequency mask
%
% OUTPUT = IOSR.BSS.RESYNTHESISE(X,FS,CFS,M) takes an input vector X,
% sampled at FS Hz, and applies the time-frequency mask M. The mask M is
% a matrix, with one column for each frequency channe... |
9b86976a08345fb1ce96947585d94215ac0b5d01737490605867d02adef5e742 | MATLAB | 5,993 | 154 | function updateContents(folder)
%UPDATECONTENTS Create a Contents.m file including subdirectories
%
% IOSR.GENERAL.UPDATECONTENTS scans through the current directory, and
% its subdirectories, and builds a Contents file similar to Matlab's
% report-generated Contents.m files. Any existing Contents.m file will be... |
d39bbd2013a1e4aedbdb29f57b301295652eb23435cd71bf801cb35528eb13fe | MATLAB | 5,994 | 142 | function T = mvpa_reg_cov_benchmark_algorithms(mvpa_dat, fold_labels, varargin)
% mvpa_reg_cov_benchmark_algorithms Compare @predictive_model algorithms on one dataset.
%
% Re-runs the algorithm comparison under @predictive_model. The earlier
% comparison (cv_pcr 0.73, cv_pls 0.73, cv_svr 0.68) was measured with the
%... |
2ed4bff3df41ca84d6479f91c6de3c29d47e29fd3a84197ecc155550b885fab4 | MATLAB | 5,996 | 166 | function [R, t, iter_err, reg_pointqueary] = ...
ICP_point_reg(reg_points, reg_pointqueary, ops)
% This is an implementation of the Iterative Closest Point (ICP) algorithm.
% Arguments: pointcloud - 3 x n matrix of the x, y and z coordinates of data set 1
% pointqueary - 3 x m matrix of the x, y and z co... |
8fd2c5d9fa37f4338cc6c62f1fc8857160537b50696bdb4b60109b3099d6e2af | MATLAB | 5,997 | 164 | % written by Yiyuan Han, Essex BCI-NE Lab, 13/12/2019
% binary classification between two specific conditions
function [perfMat,numberType] = binaryClassTestMix(class1,class2,blockTagsAC,features,folderpath,nameTag,featureNum)
%% Extract the data in specific conditions
% These two classes should be modified according t... |
287c1cc1ad00f0777eb75ee27499d952e5f3fb656ca4e3abfbc39feaed493090 | MATLAB | 5,998 | 97 | function explorer = ea_unifiedmapping_compat_statmetrics2statsettings(explorer)
if isnan(explorer.statmetric)
return
end
switch explorer.statmetric
case {'Two-Sample T-Tests / VTAs (Baldermann 2019) / PAM (OSS-DBS)'}
explorer.statsettings.stimulationmodel = 'VTA';
explorer.statsettings.efieldm... |
0094be4de8d5057012631f314bee8c4100f63f482ca545db49fa74a8147b24e9 | MATLAB | 6,000 | 139 | function this = subsasgn(this, subs, A)
% Subscript assignment for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: subsasgn.m 6513 2015-08-05 17:52:13Z guillaume $
switch subs(1).type
c... |
e45f7ea24586bab51261760d24241b3d1b84b4f6d0f4f465aac57cc6f44e1040 | MATLAB | 6,002 | 155 | function display_result_progress(cv, results_to_display, display_progress)
% Displays the current mean and stdev when a single resample result is left out for different result types
% to give an idea whether the algorithm has converged to a stable decoding accuracy
% (these values could be used for stopping crite... |
576b029f12bc0b6716079b6f8b6ea3daf9beaddf7a675b4261dd8f884b2c6d12 | MATLAB | 6,006 | 155 | function [lat,coeff,rs,converge,yf] = latencyfit4AM(y,t,peak,fig)
%Fits a double Gaussian + cumulative Gaussian to neural data. latency is
%taken as the point at which the fit reaches 33% of its maximum.
%Input args:
%y = row vector of neural data, can be raw MUA or difference
%t = row vector of time in ms (same leng... |
22f2da99dd7239755f63efd9bbb407f43fa549f2c23fd4a7afd14b4b8be0bd53 | MATLAB | 6,007 | 115 | function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
% Multi-taper coherency - point process times
%
% Usage:
%
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
% Input:
% data1 (structure array of spike times with dimension trials... |
03f773583d803f752d5f172ff234cea8e5c13980189300d494bdd58dd30df163 | MATLAB | 6,010 | 184 | % Combined wire sizing and spacing
% Section 5.5, L. Vandenberghe, S. Boyd, and A. El Gamal
% "Optimizing dominant time constant in RC circuits"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 11/27/05
% Modified by Michael Grant - 3/8/06
%
% The problem is to determine the optimal sizes of interc... |
04d0f44b20a4ecba3e4cd8b59cdb678f1e5e8bf99c5cac15a655c535442ee1f2 | MATLAB | 6,011 | 198 | %%*****************************************************************
%% Examples of SQLP.
%%
%% this is an illustration on how to use our SQLP solvers
%% coded in sqlp.m
%%
%% feas = 1 if want feasible initial iterate
%% = 0 otherwise
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tu... |
114be03fde393b687ac6a4d3639be2391a786174b77be213ed75577acdedb0a0 | MATLAB | 6,021 | 131 | function [inds_of_sites_with_at_least_k_repeats min_num_repeats_all_sites num_repeats_matrix label_names_used] = find_sites_with_k_label_repetitions(the_labels, k, label_names_to_use)
% This function takes in labels in binned label format, and an integer k, and returns the indices for all sites (e.g. neurons)
% tha... |
7446ffc0ce389c55c5113bfa670d51324c819a865f3b3a6d933a3be6fb8b5cb7 | MATLAB | 6,022 | 167 | function cs_fmri_conseed_matrix_matrix(dfold,cname,sfile,outputfolder)
% ROI based fMRI connectivity matrix based on matrix type of connectome
tic
if ~exist('dfold','var')
dfold=''; % assume all data needed is stored here.
else
if ~strcmp(dfold(end),filesep)
dfold=[dfold,filesep];
end
end
disp(['... |
fc8c3f7b2f959274e06d3fc5589be8f7718b75a379d84bc9df19983f7e901ea1 | MATLAB | 6,022 | 132 | classdef mp4_video < VideoWriter
% Create mp4 video from figure window, like VideoWriter.
%
% Example for a moving circle:
% h = rectangle('Position', [0 0 1 1], 'Curvature', 1, 'FaceColor', 'k');
% axis equal; axis off; xlim([0 10]); ylim([0 10]); % set axis range
% vw = mp4_video('movingCircle.mp4', 4); ... |
052d6a557ea398da83b910019a8a3093913550ded87ba9afb7c70d374ef349bc | MATLAB | 6,023 | 211 | % Detect red and blue LEDs position in a video file and creates a 'led' file
%
% USAGE
%
% Process_DetectLED(videoFile,<options>)
%
% videoFile path to Basler video file, including the '.avi'
% extension or not
% <options> optional list of property-value pairs (see table be... |
b43d189824541346eff649516bf73b3243af89b29ce864ab3827b0e1b971922a | MATLAB | 6,027 | 125 | function ea_save_fibscore_model(obj, ExternalModelFile)
% this function is called from the GUI
% we want to define the model outside of cross-validation
if ~exist('patsel','var') % patsel can be supplied directly (in this case, obj.patientselection is ignored), e.g. for cross-validations.
patients... |
b65fde08d05216216b5a6fedc0ee76aeba7215166080e0f74d57f29efa0c4bbe | MATLAB | 6,034 | 140 | function [GridDim,dowarn] = LeG_determine_griddim(elec)
% DETERMINE_GRIDDIM uses the labels and positions of electrodes in elec to
% determine the dimensions of each set of electrodes (i.e., electrodes with
% the same string, but different numbers)
%
% use as:
% GridDim = determine_griddim(elec)
% where elec is a... |
1a17a8d076e3ed01193aec1791d208c3c5ad2922cd684af40410a69ceedee7cc | MATLAB | 6,037 | 132 | function hemi_full_label = CBIG_hMRF_merge_singular_parcels_on_one_hemi(hemi_full_corr,...
target_parcel_list, hemi_full_label, hemi_avg_mesh, hemi_mask)
% hemi_full_label = CBIG_hMRF_merge_singular_parcels_on_one_hemi(hemi_full_corr,...
% target_parcel_list, hemi_full_label, hemi_avg_mesh, hemi_mask)
%
% This func... |
523ba6b428c87802020bde835157166c1b1ecb974aa2eafd7e9a98cf8004f940 | MATLAB | 6,040 | 238 | function AUC = bootstrapOOB_ENet(X, Y, C, opts)
% bootstrapOOB_ENet Out-of-bag bootstrap AUC for one resample.
%
% AUC = bootstrapOOB_ENet(X, Y, C, opts)
%
% Draws one bootstrap sample of subjects WITH replacement, trains on it, and
% evaluates on the out-of-bag subjects. Repeated by the caller nBoot times to
% ... |
7d26bee7fc5a5e7e9a7d64d5a71156799c2736950f9f4c95f0d58a0a714a45d9 | MATLAB | 6,042 | 163 | function ea_dbsegment(input)
% Wrapper to run DBSegment pipeline
% Note: the additional options described on
% https://github.com/luxneuroimage/DBSegment are disabled and only the
% default ones used
input = GetFullPath(input);
if isfolder(input) % Input is subj folder in LeadDBS BIDS dataset
bids = BIDSFetcher(r... |
2b66a85124268c2d64797b323fa8baa06715ce988d9befad5336fc3cc53a7cc6 | MATLAB | 6,062 | 157 | %**************************************************************************
%
% This is a simple extension of the bar plot to include error bars. It
% is called in exactly the same way as bar but with an extra input
% parameter "errors" passed first.
%
% Parameters:
% errors - the errors to be plotted (extra... |
17ae4d2a5e66ca4de2a6ef50bdd311f18280f4eb199c36205ccd87c2d9578520 | MATLAB | 6,065 | 149 | % 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... |
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