sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7ed11fbc0e1e9a20933b19ef0dece68f947fe677885526a4f04c12d756081135 | MATLAB | 4,902 | 113 | function plot4fit(Age,Data_rremain,fitresult,name,ylabelname,pvalue,rsq)
N=0;
pwhile = pvalue;
if(pvalue>0)
while(pwhile<1)
pwhile = pwhile*10;
N=N+1;
end
pstr = num2str(pwhile);
if(length(pstr)<3)
pstr = pstr;
else
pstr = pstr(1:3);
end
pstr = ['p = ',pstr, ' x 10^{\bf\fontsize{28}-' num2str(N)... |
0d4d04219b4664b980b04850725a492ca12da1ef0aced57e9df191ac2219f691 | MATLAB | 4,905 | 128 | function [MRSCont] = osp_LoadDICOM(MRSCont)
%% [MRSCont] = osp_LoadDICOM(MRSCont)
% This function reads raw (but coil-combined) data from DICOM files
% produced by Siemens sequences (*.dcm or *.ima).
%
% USAGE:
% [MRSCont] = osp_LoadDICOM(MRSCont);
%
% INPUTS:
% MRSCont = Osprey MRS data contain... |
d00c539c3820685ceb95aeca08db46d798ad820a7fb80837bfe6eb55f32a56eb | MATLAB | 4,905 | 105 | %Axon analysis and quantification code associated with Gutman-Wei et al.,
%2025 - function to calculate tracing statistics with a grid overlaid
%Generates quantification of length, branchpoints, and endpoints in each
%grid for cell input, as well as convex hulls at each level specified. The
%location of grid vertices a... |
c179352c1bbc37edd9cbe6d0e8452a93cd0b03fbf7534fb150fa714a4195616c | MATLAB | 4,907 | 140 | %% This file is used to crop regions for two-color STORM analysis
clear all;
close all;
clc;
binpath = '\\E1-054867\Jinyu\20250324 b3_AF647 CHC_CF583R\Analysis'; %%%%%%% path that you saved your png and bin files
mkdir([binpath '\diat_regions']);
ipath=[binpath '\diat_regions\'];
filename = dir(fullfile(strcat([binpat... |
c0edaf63f01f39eb8fe46f03318292dfde0492d4f10eeeba62c07d14a7df9073 | MATLAB | 4,909 | 120 | %{
trippy.RF (computed) # receptive fields from the trippy stimulus
-> rf.Sync
-> pre.Spikes
-----
nbins : smallint # temporal bins
bin_size : float # (ms) temporal bin size
degrees_x : float # degrees along x
degrees_y... |
c289c2407e141b4aa9b9354e8965dfb936f87ad3baa91ab4247927085bf8bcf2 | MATLAB | 4,910 | 158 | function [hdr,data]=read(filename)
machineformat='ieee-le';
ind=findstr(filename,'.');
if ~isempty(ind)
fileprefix=filename(1:ind-1);
else
fileprefix=filename;
end
if exist(strcat(fileprefix,'.hdr'),'file') & exist(strcat(fileprefix,'.img'),'file')
type=0;
hdr_filename=strcat(filepre... |
0c9309c78eafe90db94f2327b46037296ed76af11ebea49ae5b85f0e51f10bd2 | MATLAB | 4,911 | 165 | function plot_fig3h_right(datadir)
% Plot dopamine AUC at the reward cue (0-0.5 s) vs -delta trial initiation
% time, averaged across rats. N = 10 rats.
%
% INPUTS
% datadir: file path of data downloaded from Zenodo. Link to download can
% be found in README.
fname = fullfile(datadir, 'data-published/deltaITI_vs_AUC_S... |
5b8c3574c1503fce4d8b63eb89bb1480a06819544b1ff76f0fc4b73519f14f4b | MATLAB | 4,912 | 134 | function out = MF_hmm_Fit(y, trainp, numStates, randomSeed)
% MF_hmm_Fit Fits a Hidden Markov Model to sequential data.
%
% Actually highly stochastic, so for reproducible results helps to reset the
% random seed...
%
% ---INPUTS:
% y, the input time series
% trainp, the proportion of data to train on, 0 < trainp < ... |
631fe532747da840c12ab378b271b0604bdd18f61de2cde52dd1411399ecfb36 | MATLAB | 4,916 | 140 | %% get_set_bfr_lbv(h,mode,input)
%
% Input
% --------------
% h : structure contains all handles of SEPIA
% mode : 'set' - extract information from GUI to config file
% 'get' - extract information from config file to GUI
% input : if mode is 'set' then input should be fid
% ... |
77717ac5b0f48d06a213be00e090bc3f88c510ad73b00477725b501d584dda32 | MATLAB | 4,923 | 133 | function [delta_rats, E2_rats, ratlist_elisa] =...
Estradiol_vs_DeltaInit_bystage(SerumTable, SerumBehData, detrend_arg)
%relate change in estradiol expression to change in delta initiation times, ie "behavioral sensitivity" (pro -
%di) only for sessions with blood samples
%calculates mean concentration for repeate... |
940e51922471775ae961d55d375198727eeeb1e625ea90c95acf5c9980f83309 | MATLAB | 4,925 | 144 | function res = permutation_null_coexp(img_data, geneset, expressions, gene_symbols)
% PERMUTATION_NULL_COEXP(IMG_DATA, GENESET) performs permutation testing to examine
% whether imaging profiles associate with gene expression profiles, based
% on the null-coexpression model (where random genes with similar
% coexpressi... |
443a5fdf6e4897b09323e3890a55c971f5040c11b232aa68aad8bdb7595d7c8b | MATLAB | 4,927 | 120 | % Analyse behvioural responses
%
% For all those subjects where they have been recorded, calculate responses
% to the task.
clear;
clc;
warning('off');
% % add spm to the path
% initiate bidspm
% Initialize report
% Start a new report
report = {'subject','run','trial_type','keyPress','response_type'};
reportExtr... |
dce085bcd059f2f56258595e24cf0b5172f119a1c6adc22e43eb832bc88c7a31 | MATLAB | 4,928 | 108 | function [masterlist,alignlist,pairedlist,grouplist,STRlist] = modelKernelLists()
%a running list of all kernel names used in the models. These lists
%dictate how kernels are plotted and used in most of the analysis
%script. if you make a typo in your kernel, it could get missed!
%
%naming convention is Java style: no ... |
131676618b3cae5b5fa1b4c93ab6935cf72435f8add7cc6aea76bc1046bb3ddd | MATLAB | 4,929 | 99 | %{
pre.ScanCheck (imported) # average frame before image corrections
-> pre.ScanInfo
-> pre.Channel
---
avg_frame : longblob # raw average frame
min_intensity : int # min value in movie
max_intensity : int ... |
d19c9ee5edd0efc839b843ae4382e6238ed9c0ce0ae48a65af8ee681a410c757 | MATLAB | 4,931 | 153 | function [ all_metrics, all_suma, all_subjects, active_hdm_class ] = nmri_load_metrics( all_subjects, metric_txt, freq, params )
% [ all_metrics, all_suma, all_subjects, active_hdm_class ] = nmri_load_metrics( all_subjects, metric_txt, freq, params )
% will load a specific connectivity netric (or power/normalized pow... |
c5dc6418226f526b82e41a3c3d313fbd2a25eefd92805b902553f75d5a7ee7ae | MATLAB | 4,932 | 151 | % this is a one-off to create a really nice big figure.
% goal: fsaverage. all sessions, all subjects. mean and R2 (from onoff)
% NOTE: this was all achieved BEFORE we reset the cvnlookup cache. thus, the annotations have to be updated too.
%% %%%%% Map various 1mm volume results to subject surfaces and then to fsave... |
4b6339b8eeb301f4694ded4db819dea1f1fe92626c974435cc3b33ce359361da | MATLAB | 4,933 | 117 | % Analyse behvioural responses
%
% For all those subjects where they have been recorded, calculate responses
% to the task.
clear;
clc;
warning('off');
% % add spm to the path
% initiate bidspm
% Initialize report
% Start a new report
report = {'subject','run','trial_type','keyPress','response_type'};
reportExtr... |
1c49af2aa1bfa0209c839dac42a82b78df77a1ff23e9f63b36dff5982e79630c | MATLAB | 4,934 | 93 | % The goal here is to generate basic surface visualizations
% relevant to the NSD dataset.
%% DEFINE
% name color range color map threshold outname
atlasesMASTER = { ...
{'curvature' [] [] 1000 []} ...
{'Kastner2015' [0 25] ... |
2667587bf23d22fa7c6001bb2c39fb6528ad3b0741635d1f9a276c042d4ca07a | MATLAB | 4,936 | 180 |
%% Prepare workspace
clear all;
close all;
clc;
commandwindow;
% Grab date
t.the_date = string(datetime('now', 'Format', 'yyyyMMdd'));
t.the_time = string(datetime('now', 'Format', 'HHmm'));
% Generate unique seed for rng
rng('shuffle');
t.my_rng_seed = rng;
%% Input device name
p.device_string = 'Apple Internal ... |
c64aff20bcf8916f64536762cf684240df251f8d3059fb8cc4361cb2eac89849 | MATLAB | 4,936 | 139 | function [recov_params,results] = parameterRecovery_happy_model_responsibility_redux(mtx,params,noiseLevel,Nrep,displayFlag)
% mtx are input regressors
%assumes that each row of the cell array is a different subject
%% Settings
constant = NaN; % has always been like that
rptfit = 5; % repeat N times jittering ... |
185ae176ea5dc401ad86c9e714c38d0125b3ba5cd2784976bdd56bba9468c67b | MATLAB | 4,937 | 144 | function coactPaper_tableS02()
close all
height=9.6;
fontsize=6;
fh=initFig('width',18.6,'height',height,'font','Arial','fontsize',fontsize);
panel_01(7)
drawnow()
print(fh,sprintf('~/Dropbox/FearAnalyses/paper/figure/tableS02_%s.pdf',datestr(now,'yyyymmdd')),'-dpdf','-painters','-r300')
end
function panel_01(fs)
o... |
21a1e292c63f7a5377c84cc63992c318ce392ddf6fa8d65d6d0aece6d86beee0 | MATLAB | 4,938 | 113 | function [varargout] = likNegBinom(link, hyp, y, mu, s2, inf, i)
% likNegBinom - Negative binomial likelihood function for count data y.
% The expression for the likelihood is
% likNegBinom(f) = 1/Z * mu^y / (r+mu)^(r+y), Z = G(y+1)*G(r)/(r^r*G(y+r))
% with G(t)=gamma(t)=(t-1)!, mean=mu and variance=mu*(mu+r)/r, wh... |
f6ce2b72986ffcd5bc38fcf88ad11082ac1c485fb213623a208879b4f95a04a6 | MATLAB | 4,939 | 117 | % Analyse behvioural responses
%
% For all those subjects where they have been recorded, calculate responses
% to the task.
clear;
clc;
warning('off');
% % add spm to the path
% initiate bidspm
% Initialize report
% Start a new report
report = {'subject','run','trial_type','keyPress','response_type'};
reportExtr... |
104885ff5d0ec40edc647d915865a12c4f88b5fd78e3b29374608ed333b5c8bf | MATLAB | 4,940 | 176 | function [ subject, data ] = nmri_artifactrejection_reviewICA(subject, data, params)
%[ subject, data ] = nmri_artifactrejection(subject, data, params)
%
% This is an interactive function to review and reject the ICA components
%
%
% subject = subject structure, see nmri_read_subject
% could be a... |
7cb7b81d093e2f6e43ea4b7c2f52b467c34f6a41bf2694382e8590e9551985fb | MATLAB | 4,940 | 171 | function fear_spkModulationByMoving_ShBase(basename,varargin)
% basename='~/data/Fear/triple/hoegaarden181115/hoegaarden181115';
%%
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName)
%%
param.sesIdx=2;
param.tBinSize=0.02;
param.nIte=500;
par... |
37dcf28e0096c985ef9d55206747b52e0d3853ae31c1100454b6d7dc6e76282f | MATLAB | 4,942 | 144 | % READLOCSOLD - Read electrode locations file in style of TOPOPLOT or HEADPLOT.
% Output channel information is ordered by channel numbers.
%
% Usage: >> [nums labels th r x y] = readlocsold(locfile);% {default, polar 2-D}
% >> [nums labels th r x y] = readlocsold(locfile,'polar'); % 2-D
% ... |
af2955656421f94be9886ba8ee7ef5c661cd06aa8d1f7540cce7ae11fce8cef9 | MATLAB | 4,942 | 157 | function [Rlatt,Rrp,ind_rp,eff,met] = latmio_und_v2(R,ITERATIONS,D,metric, plotIterations)
%LATMIO_UND_V2 Lattice with preserved degree distribution
%
% [Rlatt,Rrp,ind_rp,eff,met] = latmio_und_v2(R,ITERATIONS,D,metric);
%
% This function "latticizes" an undirected network, while preserving the
% degree... |
c317744a31cea70e4944eb240cd0313a0841accd033622305a144e47f619e82a | MATLAB | 4,942 | 152 | function run_permuvartest2_examples
%RUN_PERMUVARTEST2_EXAMPLES Run two-sample permutation F-test examples.
% Generates random multivariate data for 2 "independent" samples X and Y.
% Each sample has 20 variables, each with a standard deviation of 1,
% except for the first 10 variables of Y which have a standard... |
186d79a4b84a508df46eea46005a5d62d7b30b3c55bd5ae15f3b05db02ef253f | MATLAB | 4,943 | 138 | % EEG_MERGELOCS - merge channel structure while preserving channel
% order
%
% >> mergedlocs = eeg_mergelocs(loc1, loc2, loc3, ...);
%
% Inputs:
% loc1 - EEGLAB channel location structure
% loc2 - second EEGLAB channel location structure
%
% Output:
% mergedlocs - merged cha... |
358ad818ef85ba1555aaa9a71706822d044f2dabc07935f27b7f3dbc2b05276f | MATLAB | 4,943 | 120 | function figureRDMs(RDMs, userOptions, localOptions)
% figureRDMs(RDMs, userOptions[, localOptions])
%
% figureInterleavedRDMs is a function which accepts a multidimensional struct of
% RDMs, puts them into a 1D struct, and then shows them.
%
% RDMs --- A struct of RDMs.
% All RDMs in here will... |
6246aab6a81bfd96f1decb89c118ae3e9f63653c87ffb2db6d919d3f06da7097 | MATLAB | 4,944 | 122 | function plotBrainTopo_trialsData(params, trialsData)
% plots trialsData onto brain topology (slices or 3D model)
% trialsData =
% info: [1x1 struct]
% xVals: [1025x1 double] ~ 1D: time, in [s]
% yVals: [1025x110x2 double] ~ 3D: time x channels x classes
% yErrs: [1025x110x2 double] ~ 3D:... |
a4874901f46c4ccedd608703856166f8ef89cc43246216ff6b6b8da5ace7f31d | MATLAB | 4,945 | 146 | % GETKEYVAL - get variable value from a 'key', 'val' sequence string.
%
% Usage:
% >> val = getkeyval( keyvalstr, varname, mode, defaultval);
%
% Inputs:
% keyvalstr - string containing 'key', 'val' arguments
% varname - string for the name of the variable or index
% of the ... |
0f6f3cd74e8c7bd230d24ecfefea7ad369cadcb209a33c60ecd017b3d85004d9 | MATLAB | 4,947 | 173 | function RGB = HSLuv_to_RGB(varargin)
%{
RGB = HSLuv_to_RGB(HSV)
Returns RGB values for an n by 3 matrix of [H, S, L] values.
RGB = HSLuv_to_RGB(n)
Returns n columns of RGB values for a pastel colormap.
RGB = HSLuv_to_RGB([n], 'H',H, 'S',S, 'L',L)
Returns n columns of RGB values for linearly spaced value... |
083d9f6b4e0da70511a518616f188cc54d8d560aad38cb817562df07b61b1dd8 | MATLAB | 4,950 | 165 | function fear_icaCoactTrigWaveletCueRet_optShift(basename,varargin)
% basename='~/data/Fear/triple/karmeliet190901/karmeliet190901';
load([basename '.basicMetaData.mat'])
fprintf('%s start %s with data of %s\n',datestr(now),mfilename,basicMetaData.SessionName);
load([basicMetaData.AnalysesName '-nremWaveletPow.mat'])
... |
76887d3f9a8b6c76b92870e31e7dee586017f20618d9169435be7d4a9c70f302 | MATLAB | 4,953 | 129 | function [colormap]=cbrewer(ctype, cname, ncol, interp_method)
%
% CBREWER - This function produces a colorbrewer table (rgb data) for a
% given type, name and number of colors of the colorbrewer tables.
% For more information on 'colorbrewer', please visit
% http://colorbrewer2.org/
%
% The tables were generated fr... |
8df83f8e16d781b01677b9108ccfda524a9a0e7ebd150ff0ae8ef85d414fa76e | MATLAB | 4,954 | 144 | function axislabel_rotation(~,ax)
% This function rotates x, y and z labels to the direction of their
% corresponding axes when a rotate operation has finished. So that labels
% will be parallel to axes.
% The function is used as an 'ActionPostCallback', which is a callback
% function of a rotate3d object.
% I... |
9ec512c34df89ba7db155a4b6837d41a8bbf5936d2771a4a013d9b3c9b315801 | MATLAB | 4,954 | 87 | % Script from Tor Wager's canlab github to compare an image to a "neural
% signature", a multivariate predictive pattern, for example for guilt
% ("Guilt-Related Brain Signature", or GRBS, from Yu, Koban et al., CerCor
% 2020) or reward ("A neural signature for reward", Speer et al.,
% Neuroimage 2023).
%% Set up dire... |
edb29704f42ab1dfb31d52184f9292176b1b426160b84bccfecd2de5a7243fe1 | MATLAB | 4,955 | 136 | function ch2roi_plot_allFreq(GRUP, groupInfo)
% groups channels into defined ROIs (anatomic areas), averages & plots
% FIG:
% - subplots = freqBands x ROIs
% - 1 subplot: time x clz
% based on the following criteria:
% - selected anatomical areas (groups)
% - selected freq. band
% - significance (difference ... |
47db11da47ffea4ae5e0cb51cb311f37e641ac5a96f88b070bc924f85dc05759 | MATLAB | 4,957 | 173 | function [B1, B2, B1iti, B2iti,...
dwt1, dwt2, diti1, diti2,...
pcatch1, pcatch2, pvio_iti1, pvio_iti2] =...
macro_regress_overtraining_V2(nsess, ratList, Sdir)
%this version compares early sessions in training stage 9 from the S
%struct, instead of the A struct, which has already been curated. cmc
%11/16/... |
ed93ac19f47b7fef0bffe6f3e22b76040df4a9979d537e73b14648067748213e | MATLAB | 4,959 | 114 | function filePath = BF_WriteTempFile(dataVector,whatPrecision)
% BF_WriteTempFile Write a temporary file in the system temporary directory
%
% All ~26 TISEAN-based master operation instances for a given time series
% call this with the SAME z-scored data, x_z (computed once per time series
% in TS_CalculateFeatureVec... |
68584b0de5ff47274ef0eabaa1393e9a3170d315c0811045e83e24838786aeff | MATLAB | 4,962 | 137 | % TRANSFORMCOORDS - Select nazion and inion in anatomical MRI images.
%
% Usage:
% mewcoords = transformcoords(coords, rotate, scale, center, reverse);
%
% Inputs:
% coords - array of 3-D coordinates (3 by N or N by 3)
% rotate - [pitch roll yaw] rotate in 3-D using pitch (x plane),
% roll (y... |
2220b6f1c128339b73eb16d9df6a7d4a4f62eb320d3326500cd29a6f3778f759 | MATLAB | 4,963 | 123 | function out = MD_hrv_classic(y)
% MD_hrv_classic Classic heart rate variability (HRV) statistics.
%
% Typically assumes an NN/RR time series in units of seconds.
%
% ---INPUTS:
% y, the input time series.
%
% Includes:
% (i) pNNx
% cf. "The pNNx files: re-examining a widely used heart rate variability
% ... |
338fb7c6fe3cb090f662c74a56f19f0ecfb875ede26dacb2b4a2103d2a2e25ea | MATLAB | 4,964 | 147 | % pop_dipfit_gridsearch() - scan all ICA components with a single dipole
% on a regular grid spanning the whole brain. Any dipoles that explains
% a component with a too large relative residual variance is removed.
%
% Usage:
% >> EEGOUT = pop_dipfit_gridsearch( EEGIN ); % pop up interactive window
% >> EEGOU... |
fbd63136cad8dc26bc7915c172e664e0ca8bcff7f99f17b63cba9692da430ead | MATLAB | 4,964 | 188 | function [dt1,dt2,travel,index] = FitCCG(t,ccg,varargin)
%FitCCG - Fit dampened sinewave to the cross-correlogram of a pair of theta-modulated cells.
%
% USAGE
%
% [dt1,dt2,travel,index] = FitCCG(t,ccg,<options>)
%
% t time bins
% ccg cross-correlogram
% <options> optional lis... |
34aceaf13757ebef1279552ba83c5e9a9a4e1c194dba0f55b0d7cf7c9e1836b1 | MATLAB | 4,967 | 144 |
models = {'alexnet','flynet'};
do_bootstrap = false;
for m = 1:length(models)
%% get some information about file structure and number of subjects
t = readtable(['naturalistic_betas.' models{m} '.only_sc.csv']);
yhat = table2array(readtable(['naturalistic_pred.' models{m} '.only_sc.csv'])); %alexn... |
2f5d3e93b2d6b04307a3a4bb9f511ff6dbdee11ae0a418b299c3ebdab6c74538 | MATLAB | 4,968 | 147 | function [output,status] = plugin_urlwrite(urlChar,location,method,params)
% URLWRITE Save the contents of a URL to a file.
% URLWRITE(URL,FILENAME) saves the contents of a URL to a file. FILENAME
% can specify the complete path to a file. If it is just the name, it will
% be created in the current directory.... |
4fbaf19a06c86988f2b97fa17c0056bb747e77ed35414cb0c4d545e0142e27dc | MATLAB | 4,968 | 186 | function hdr = load_nifti(niftifile,hdronly)
% hdr = load_nifti(niftifile,hdronly)
%
% Loads nifti header and volume. The volume is stored
% in hdr.vol. Columns and rows are not swapped.
%
% Handles compressed nifti (nii.gz) by issuing a unix command to
% uncompress the file to a temporary file, which is then deleted.
... |
6e870726924b3853b088448713e1f0444839e1684c9536808f27a735a2956850 | MATLAB | 4,968 | 114 | %% TestUnwrapMatrixPhantom - Tier 2 synthetic-phantom phase-unwrapping method regression matrix
%
% Mirrors TestQSMMatrixPhantom.m: runs the one-stop SEPIA pipeline on the
% synthetic phantom once per phase-unwrapping method in methodUnwrapName
% (sepia_universal_variables.m) AND per matrix size (the same 5 odd/even
% ... |
dfc4742d70a638afe82bae1019cdba301ed0c92a20fb9787f2cd18f2244d4c36 | MATLAB | 4,968 | 130 | % ¶¨Òå״̬תÒƺ¯Êý£¬ÓÃÓÚÉú³ÉеĺòÑ¡½â
function [ElementNew, sensorNew, update_sign] = UpdateLocationNew(sim_vol,Element,sensor,kgrid)
Pitch = Element.Pitch;
Kerf = Element.Kerf;
ElementLength = Element.ElementLength;
ElementNew = Element;
CoorList = Element.CoorList;
CoorSubList = Element.CoorSubList;
PitchVoxelNum =... |
0022028e55812de2febef3d6a71b9fe939fd7e66630e6789875568d65be3bc2b | MATLAB | 4,969 | 130 | function [MRSCont] = osp_LoadRDA(MRSCont)
%% [MRSCont] = osp_LoadRDA(MRSCont)
% This function reads raw (but coil-combined) data from RDA files
% produced by Siemens sequences (*.rda).
%
% USAGE:
% [MRSCont] = osp_LoadRDA(MRSCont);
%
% INPUTS:
% MRSCont = Osprey MRS data container.
%
% OUTPUTS... |
cef6ad705cf1e6dee05c66f19aa35c4187ae16061f78d73a5189564fd0114d1a | MATLAB | 4,972 | 108 | function varargout = binaryGP(hyper, approx, covfunc, lik, x, y, xstar)
% Approximate binary Gaussian Process classification. Two modes are possible:
% training or testing: if no test cases are supplied, then the approximate
% negative log marginal likelihood and its partial derivatives wrt the
% hyperparameters is co... |
41254413526e3454ce791048d490a430fc1ff11691232001374d05da20a07036 | MATLAB | 4,974 | 101 | % MAKEHELPFILES - generate function help pages
%
% Usage:
% >> makehelpfiles(list);
%
% Input:
% 'folder' - [string] folder name to process
% 'outputfile' - [string] file in which to write the help
% 'title' - [string] title for the help
%
% Author: Arnaud Delorme, UCSD, 2013
%
% Example: Generate EE... |
9d58fcc1b4140e398b1989cf96c3936d2e0f3ccdbf0b87fd08e32ca09df447b5 | MATLAB | 4,974 | 160 | %GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path
% is stored for future reference.
%
% Once ... |
b21a4f4f0fc7dd1b7ba0f324734215321a6cd3b67ddfcf75650fff2431ad9f4b | MATLAB | 4,974 | 145 | function cl = threshold_pa_overall(OUT,varargin)
% cl = threshold_pa_overall(OUT,[task level name])
%
% if no opt. argument, works with overall pa and pa_overall.img
% Otherwise, restricts analysis to specified task level only
%
% saves output struture OUT in STATS_VARS.mat
% saves cl structure to file
%
% called by db... |
62a216f153ce6f82712c8bde60a8e251a4f9a60bc26a63ac04d42d397807a5b2 | MATLAB | 4,975 | 167 | % LOGSPEC - plot mean log power spectra of submitted data on loglog scale
% using PLOTDATA or PLOTTOPO formats
%
% Usage:
% >> [spectra,freqs] = logspec(data,frames,srate);
% >> [spectra,freqs] = logspec(data,frames,srate,'title',...
% [loHz-hiHz],'chan_locs... |
93229cf45deb13318aebc21d5498cffc63408ba072015a415e7a8dd0007ff806 | MATLAB | 4,977 | 136 | %PLUGIN_MOVEPATH- Given a path to a plugin folder, this function will
% put the plugin at the bottom of the path.
%
% Usage:
% plugin_movepath('x','begin'); % Put plugin 'x' at the top of the path
% plugin_movepath('x','end'); % Put plugin 'x' at the bottom of t... |
447e83cad0dfe58b1f2eeb765e4a1f935ffd7136069d8e176f05d3e67fc26bf3 | MATLAB | 4,980 | 97 | %% load libraries
run('set_library_paths.m');
addpath(SPM_PATH); % per spm docs, do not genpath it
addpath(genpath(CANLABTOOLS_PATH));
%% VARIABLES THAT MUST BE DEFINED BEFORE THE SCRIPT IS SOURCED
% This script is designed to estimate predicted-observed correlations
% for a _combined_ encoding model pre-fit on a give... |
164cb01247263623178d752414fde7c2cc5b75d225dd243ed92ff567a398bacd | MATLAB | 4,982 | 162 | function [Burst SpikeBurstNumber] = BurstDetectISIn(Spike, N, ISI_N)
% ISI_N burst detector
% © Douglas Bakkum, 2013
%
% [Burst SpikeBurstNumber] = burstDetectISIn( Spike, N, ISI_N)
%
% 'Spike' is a structure with members:
% Spike.T Vector of spike times [sec]
% Spike.C (optional) Vector of spike channe... |
131e4a6ee97dab6b82c836354607a460722944e7c06ad0ed2be130b8f91114b4 | MATLAB | 4,984 | 133 | % pop_firwsord() - Estimate windowed sinc filter order depending on
% window type and requested transition band width
%
% Usage:
% >> [m, dev] = pop_firwsord; % pop-up window mode
% >> m = pop_firwsord(wtype, fs, df);
% >> m = pop_firwsord('kaiser', fs, df, dev);
%
% Inputs:
% wtype - char arra... |
7fcc6dbc0912f96ee1a4d96c76397d061aa9b280acb6ff01b7fd1cffe03340b4 | MATLAB | 4,984 | 128 | function spectra = computeSpectra(params, trials)
% computes spectra for each trial using STFT
% trials =
% data: [3073x125x500 double]
% time: [3073x1 double]
% sessTime: [3073x500 double]
% labels: [1x500 double]
% sessNumber: [1x500 double]
% (c) Jiri, May16
display('Computin... |
326d0a7a138fd84d4554afb85ccb8a4e19abffb46bb241ed07faff70caa79d80 | MATLAB | 4,985 | 154 | % CHANGEUNITS - Takes one or more points in one axes and gives its position
% in another axes. Useful for drawing lines between
% sbplots (see SBPLOT).
%
% Usage: >> newpoint(s) = changeunits(point(s),curaxhandle,newaxhandle)
%
% Inputs:
% point(s) - two-column vector of curre... |
cd4c630262e5ca6c08912fb98f2cd59edf3ce98930b9db3270d165397dbaa7d9 | MATLAB | 4,990 | 111 | function parcel_data = moment_age_model(moment_metric, age_metric, ...
input_table, uparc, total_num_parcels, valid_parcels, fdr_correction, thickness)
%--------------------------------------------------------------------------
% performs parcel-wise linear models: moment_metric ~ age_metric + sex (+ thickness)
%
%... |
49f38703df0681b94e43e10e33a038cb8fcd4813a77c937a066f24bf8280a94b | MATLAB | 4,991 | 138 | function tapas_hgf_ar1_binary_mab_plotTraj(r)
% Plots the estimated or generated trajectories for the binary HGF perceptual model for multi-armed
% bandit situations.
%
% Usage example: est = tapas_fitModel(responses, inputs); tapas_hgf_binary_plotTraj(est);
%
% --------------------------------------------------------... |
4e0658499d6935e0b26531dc2786f4c715a3fa6dd1f5806cb09cc6eebafbab8c | MATLAB | 4,991 | 137 | function plotEigenvalueGrid_4x3(toi, eigenvalue, behavior, a, b, c, outputFolder)
% One figure: 4 rows x 3 cols.
% Cols = Groups [NIG, FCG, CAUG]. Rows = [E1C1; E2C1; E1C2; E2C2].
% Each axes shows mean±SEM time courses for the 3 ages (as shades of the group color).
% Requires: shadedErrorBar.
% ---- configurati... |
eaa31e2e07e6925a7ce16d603e0e33f19bd085856c5fed00d1c29cf4d57ce226 | MATLAB | 4,993 | 154 | %% [chi] = Wrapper_QSM_QSMnet(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 dat... |
61413c14c01842bccdc6b7c1e18db7e8c799f12cecbee4e2e592195c4079b39d | MATLAB | 4,996 | 100 | function significantResults = posthoclme(data, behavior, a, g, toi)
data = permute(data, [1 3 2 4]);
uniqueAges = unique(behavior.Age);
uniqueGroups = unique(behavior.Group);
significantResults = struct();
significantResults.Age = cell(size(data, 2), size(data, 3));
significantResults.Group = cell(size(data... |
08c1b07a3beb74d532ad64fba4f4a0a29209e7324eaa805b00f6d1ee1eb7855c | MATLAB | 5,001 | 148 | function physio = tapas_physio_save_batch_mat_script(fileBatchM, pathOutput, ...
doRemoveEmptyDefaults, doUpdateInputFileBatchM)
% Saves .m-matlabbatch-file as .mat and as spm-independent matlab-script
%
% physio = tapas_physio_save_batch_mat_script(fileBatchM)
%
% IN
% fileBatchM either .m-file of batch j... |
61e3df8a3def46a5332a2b4ac803a8bc19bfa428d30681fd52c8766b654be779 | MATLAB | 5,005 | 142 | function tapas_hgf_binary_mab_plotTraj(r)
% Plots the estimated or generated trajectories for the binary HGF perceptual model for multi-armed
% bandit situations.
%
% Usage example: est = tapas_fitModel(responses, inputs); tapas_hgf_binary_plotTraj(est);
%
% ------------------------------------------------------------... |
aee76f5f47afad0a3a848eca9c37b68c347998e28a09342db6e5234c8bda5df5 | MATLAB | 5,008 | 129 | % EEG_MULTIEEGPLOT - Produce an EEGPLOT of a the average of an epoched dataset
% (with optional pre-labelling of specific trials).
% Usage:
% >> eeg_multieegplot( data,trialrej, elecrej, ...
% 'key1', value, 'key2', value ... );
% Inputs:
% data - input data (... |
c2ec15725b2d7fe4884e3765ba2860da7f8131be16c92808b2271f8747112a60 | MATLAB | 5,009 | 134 | %EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, dest, crop, append, gray, quality)
%
% This function converts an eps file to pdf f... |
41a69d7a8f7e8423a0af14d299846f4c7978b45eb4e8f6c3ce4f41a1893f92d8 | MATLAB | 5,011 | 166 | % PROMAX - perform Promax oblique rotation after orthogonal Varimax
% rotation of the rows of the input data. A method for
% linear decomposition by "rotating to simple structure."
% Usage:
% >> [R] = promax(data,ncomps);
% >> [R,V] = promax(data,ncomps,maxit);
%
% Inputs:
% ... |
46e749e70152e1d843fe9ae0a996852012ddf135858641e3e341e9f78566625c | MATLAB | 5,012 | 126 | % dipfit_nonlinear() - perform nonlinear dipole fit on one of the components
% to improve the initial dipole model. Only selected dipoles
% will be fitted.
%
% Usage:
% >> EEGOUT = dipfit_nonlinear( EEGIN, optarg)
%
% Author: Robert Oostenveld, SMI/FCDC, Nijmegen 2003
% Tha... |
683930356b4a941fa861c155131ef8c08cc516c5d84e6b8fc38ea42004ea15fa | MATLAB | 5,012 | 162 | function [session_cnm,merged_ROIs] = merge_cnm_rois(session_cnm,dmin,merge_thr,deconv_options)
%% modified from merge_neuron_dist_corr but simplified
% - find pairs of ROIs that have highly-correlated activity (corr >merge_thr), and
% - are close to each other (dist<dmin)
% ZZ 2022
merge_thr_abs_raw = 0.65; % for ... |
13c38554f7322a0bfe29c28baf19441dfbb1413d8d05878603c40d1243f52a5c | MATLAB | 5,013 | 94 | function [M P V] = smc_oopsi(F,V,P)
% this function runs the SMC-EM on a fluorescence time-series, and outputs the inferred
% distributions and parameter estimates
%
% Inputs
% F: fluorescence time series
% V: structure of stuff necessary to run smc-em code
% P: structure of initial parameter estimates
%
% Outputs
% M:... |
d3d1db120c85bc9723cd875250690378a2631127be03f5d53589d89ef178d8e2 | MATLAB | 5,015 | 126 | % Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.335901v1
% Rubén Herzog October 2020
clear;clc;close all;
%% Parameters for raster
T = 500; %Number of frames
fr = 0.15; %Fir... |
14047b16b94f78170ed5d58b77ced498150d2192514505d58e65578cb8c335e1 | MATLAB | 5,016 | 103 | function ProcessData_ExtendedData9(datadir, savedir, codedir)
%ProcessData_ExtendedData9 - Process raw data saved under datadir such that it can be plotted by PlotExtendedData9.
% INPUTS:
% datadir - Local directory where 'Golden_Nature/RawData_ExtendedData9.mat' from Zenodo was saved
% codedir - Local directory wh... |
dc03032ad15ec309dde84269c7b79c80931af8aaa5ebbde92ea6f797136c8865 | MATLAB | 5,016 | 127 | %% %%%%%%%% Perform prf analysis
% NOTE: we want to use the vanilla analyzePRF, so we do this and check our version
rmpath(genpath('/home/stone/kendrick/code/analyzePRF/'));
which analyzePRF -all
% using parpool?
parpool(16);
parpool(12);
parpool(8);
% do the FULL analysis [possibly farm out to different machines!]
... |
e3971fcbbca1852ccdf8121c4e5cd9cccb3a164a083e9d4d711f6e7e78fe41d3 | MATLAB | 5,017 | 174 | function Meta_Study_Table(DB,varargin)
% function Meta_Study_Table(DB,['study'])
%
% Prints text table of all independent contrasts for export
%
% looks for Study or study field in DB (also takes clusters, cl)
% determines length, and looks for other fields of the same length
% uses specified fields in a particular ord... |
19a8316657482f2f658803bddf94634e8280a95a603050fe2fc93183758e101f | MATLAB | 5,018 | 121 | function [G,Sig]=crossvalIPM(B,partition,conditionVec,X)
% function [G,Sigma]=crossvalIPM(Y,partition,conditionVec,X);
% Calculates the crossvalidated inner product matrix (IPM) between activation patterns
% (estimated beta weights) from the first level analysis. The IPM is calculated
% by using data across partition... |
1d2ac05865e2a5e8987f8501d6e4f083e84acbd6abc0e3ce6155b615e7efaf95 | MATLAB | 5,018 | 135 | function PlotColorMap(data,dimm,opt)
%PlotColorMap - Plot a color map.
%
% Plot a color map (e.g. the firing field of a place cell).
%
% USAGE
%
% PlotColorMap(data,dimm,<options>)
%
% data data
% dimm optional luminance map
% <options> optional list of property-value pairs (see ... |
54e717f0d7a9db39bceb63f310683427ed1cb888c3a76215e6a4206428589467 | MATLAB | 5,018 | 129 | function fixationTargets = setFixationTargets(cfg)
%
% fixationTargets = setFixationTargets(cfg)
%
% Set fixation targets in a matrix of ``nbBlocks`` by ``nbEventsPerBlock`` with some rules:
%
% - if there are 2 targets per block we make sure that they are at least 2 events apart
% - targets... |
d6a1d52938174e2350703967168111d6a3eb2bbded1226ba77749ef5ed8cab6f | MATLAB | 5,018 | 136 | function ch2roi_plot_allFreq_subjMean(GRUP, groupInfo)
% groups channels into defined ROIs (anatomic areas), averages & plots
% FIG:
% - subplots = freqBands x ROIs
% - 1 subplot: time x clz
% based on the following criteria:
% - selected anatomical areas (groups)
% - selected freq. band
% - significance (di... |
24b9c4cb91a05073f06718fdbad315f9ef6b47950b7c26034c8225578b591ba2 | MATLAB | 5,021 | 253 | function ignore = ignorefields(purpose)
% IGNOREFIELDS returns a list of fields that can be present in the cfg structure that
% should be ignored at various places in the code, e.g. for provenance, history,
% size-checking, etc.
switch purpose
case 'appendtimelock'
ignore = {
'cfg'
'dimord'
'... |
f82230b5648e126f1dbecca6c9fb5357a8c067a2a3dac9d59fc820db2d698bce | MATLAB | 5,024 | 177 | function [err, ErrMessage] = WriteBrikHEAD (FileName, Info)
%
% [err, ErrMessage] = WriteBrikHEAD (FnameHEAD, Info)
%
%Purpose:
% Create the header file for an AFNI Brik
%
%
%Input Parameters:
% FnameHEAD the name of the header file
% Info, a structure detailed in function BrikInfo
%
%Output Parameters:
% err... |
f678409db459ac4b2488b6ef0bfc20c4f57269cff10d710035674cb4a26f2dff | MATLAB | 5,026 | 122 | function [plotStat, flattenedCortex] = flattenCortex ()
addpath ('/usr/local/netgpu/fluoMouseBrain/scripts/utils/')
%imFlattenCortexLine = imreadstack('ORL_ARA_v2.3_bi_cortexFlattenLines.tif');
% generated using extractCorticalLayers.m
imFlattenCortexLine = imreadstack('/home/kannanuv/workspace/code/cortexFlatten/ORL_... |
fd2fcf01c3191427a78a83844a1667fe862ade90370d1813844f8242efaa9535 | MATLAB | 5,026 | 138 | function foundHandles = find(obj, nameClass, varargin)
% Finds all (handle) object properties whose class and property
% values match given values
%
% foundHandles = obj.find(nameClass, 'PropertyName',
% 'PropertyValue', ...)
%
%
% IN
% nameClass string with class name (default: MrCo... |
44c57bd611f6082dd2a3860b7715ad1ba5f9a6483c37c64f428ff9666b56b74b | MATLAB | 5,027 | 130 | function ft_hmri(file_t1w, file_pdw, file_b0, file_b1, pathHMRI_defaults, ...
pathHMRI_b1_defaults)
% hMRI processing
%
% ft_hmri(file_t1w, file_pdw, file_b0, file_b1, pathHMRI_defaults, ...
% pathHMRI_b1_defaults)
%
% Inputs:
% file_t1w - cell array of multi-echo t1w data set.
% file_pdw ... |
4e186a2f5af1513efab60278c782ee19398eb7ba2d9a0c3618191487b56f3dd2 | MATLAB | 5,028 | 134 | function newTarget = ReplaceWithGoodies
% Function sorts through SelectedVectors to use library of top scoring
% vectors to replace poorly scoring vectors instead of randomly generated
% replacement vectors.
global numFact run lastGoodies numDose scoreProxThresh intraVarAlgo interVarAlgo
global SelectedV... |
0b519893466ecd23de72ea4b9fa04272d4792c149848ffd63dfe52dbe4c3c2bf | MATLAB | 5,030 | 136 | function [adjM, adjMci] = adjM_thr_parallel(spikeTimes, method, lag_ms, tail, fs,...
duration_s, rep_num)
% This function generates synthetic spike times from original
% events and randomizes them using circular shift. All synthetic data is
% created from existing events.
%
% It then averages the functional connect... |
cfce67259cde0dab36ca824b665320f134865cc59027290d654489f61c0adab5 | MATLAB | 5,031 | 129 | function [X, A] = PCA_stochastic(A, k)
% Example of stochastic gradient algorithm in Manopt on a PCA problem.
%
% PCA (principal component analysis) on a dataset A of size nxd consists
% in solving
%
% minimize_X f(X) = -.5*norm(A*X, 'fro')^2 / n,
%
% where X is a matrix of dimension dxk with orthonormal columns.... |
b298b7103e31935c54696806fcff34f682f6e2a418ad0001b428bae5af54a68d | MATLAB | 5,032 | 126 | % Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.10.12.335901v1
% Rubén Herzog October 2020
clear;clc;close all;
%% Parameters for raster
N = 100; %Number of neurons
fr = 0.15; %Fi... |
2f90716424771c6bb919ca0006296745a923c869ca983628535826dfe386eb68 | MATLAB | 5,034 | 138 | % STD_READSPECGRAM - returns the stored mean power spectrogram for an ICA component
% or a data channel in a specified dataset. The spectrogram is
% assumed to have been saved in a Matlab file,
% "[dataset_name].datspecgram", in the same
% director... |
54c6be461f8780bf76c62f3902b7e84dc357319aea43ad7b9b618b3c1f9a9bca | MATLAB | 5,036 | 120 | % Analyse behvioural responses
%
% For all those subjects where they have been recorded, calculate responses
% to the task.
clear;
clc;
warning('off');
% % add spm to the path
% initiate bidspm
% Initialize report
% Start a new report
report = {'subject','run','trial_type','keyPress','response_type'};
reportExtr... |
110ef35426bb0b02a892791445be666dec09101948b24aa1aeda18bc904a2c04 | MATLAB | 5,039 | 139 | function ConnFuncHomo
CUTNUMBER=100
% path = '/home/NCPL09/Desktop/MRIDATA/ReseachPlan/Autism/analysis_fun/FunImgARWCSF'
% outdir = '/home/NCPL09/Desktop/MRIDATA/ReseachPlan/Autism/analysis_fun/tongji/FHC'
path=uigetdir;
outdir=uigetdir;
sublist = dir (path)
[TMSPath, fileN, extn] = fileparts(which('TMStarget.m')) ;
... |
95ea998568370a11ac878fee9dd5d5cd0c91cabdf9d6986198044043bf5796de | MATLAB | 5,040 | 135 | function [delta_rats, E2_rats, ratlist_elisa] =...
Estradiol_vs_DeltaInit_bystage(ratlist,...
SerumTable, SerumBehData, detrend_arg)
%relate change in estradiol expression to change in delta initiation times, ie "behavioral sensitivity" (pro -
%di) only for sessions with blood samples
%calculates mean concentra... |
78f55c427f119f245469a8fbd51962b86402a41adfb342d74219f099ae03957b | MATLAB | 5,041 | 162 | %% sepia_addpath(method)
%
% Description: remove all SEPIA related directories from PATH and add
% only the directory(ies) related to the input 'method'
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 10 April 2018
% Date modified: 24 August 2018
% Date modified: 5 June 2019
% Date modified: 9 June 20... |
a2340402c9e58301571120157185d102ac666561ec43ac7b32283d95b99355d5 | MATLAB | 5,042 | 105 | % STD_RENAMECLUST - Commandline function, to rename clusters using specified (mnemonic) names.
% Usage:
% >> [STUDY] = std_renameclust(STUDY, ALLEEG, cluster, new_name);
% Inputs:
% STUDY - EEGLAB STUDY set comprising some or all of the EEG datasets in ALLEEG.
% ALLEEG - global EE... |
d27efbef9323d416db63a827ea37062761dbbcb42ed506170d41471c65206560 | MATLAB | 5,042 | 154 | clc;
clear;
addpath('/cbica/home/lihon/code/Download/cifti-matlab-master');
num_r = 400;
mat_dir = '/cbica/home/lihon/comp_space_recover/ABCD_comp/dl_prediction/data_cog_hcpd_cv_combined';
res_dir = ['/cbica/home/lihon/comp_space_recover/ABCD_comp/dl_prediction/pred_res_cog_abcc_bl_cv/non_dl_hcpd_res_r', num2str(nu... |
df6572ca11e78dc649f10cbfb6e3c36470144634b0c1e3ad4f1910e270121ec2 | MATLAB | 5,042 | 139 | function [coherence,phase,f,sc,sp] = MTCoherence(lfp1,lfp2,varargin)
%MTCoherence - Compute LFP coherence by multi-taper estimation.
%
% The coherence is computed as the average coherogram, using the <a href="http://www.chronux.org">chronux</a> toolbox.
%
% USAGE
%
% [coherence,phase,f,sc,sp] = MTCoherence(lfp1,l... |
eccecd0776a3ff62324e4ff961002c69c71d0f9453efb0c1b47030623c28b5d2 | MATLAB | 5,043 | 136 | function data = DVV_dvv(x, m, Nsub, nd, Ntv)
% Delay Vector Variance method for real and complex signals
%
%
% USAGE: C = dvv (X, m, Nsub, nd, Ntv)
% X original real-valued or complex time series
% m delay embedding dimension
% Ntv number of points on horizontal axes
% Nsub number of reference DVs to co... |
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