sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b4829c528cce46fea15499a8490a25308c79afa30602b00f6d48b25e8f5fde50 | MATLAB | 3,620 | 107 | function [ranovatblb,Mrm1,Mrm2,rm,assumptions] = rm_anova_OPS(data_analysis,group_names,position_analysis,varName)
% [ranovatblb,Mrm1,Mrm2,rm,assumptions] = rm_anova_OPS(data_analysis,group_names,position_analysis,varName)
% rm ANOVA for OPS results
%
% inputs:
% data_analysis - Original dataset
% group_names - N... |
be91d0062e0d02547756a458825968da5c4885527d944fa0cc0b3c0dbe77a030 | MATLAB | 3,622 | 108 | function [allAddr,allTs,ISI,monTime]=loadaerdat(file, path)
%function [allAddr,allTs]=loadaerdat(file);
% loads events from a .dat file.
% allAddr are uint32 (or uint16 for legacy recordings) raw addresses.
% allTs are uint32 timestamps (1 us tick).
% noarg invocations open file browser dialog (in the case of no i... |
0b44fef91cd3b7932757988c49d5d9b91038657171f2ce3a313942b00e7e7695 | MATLAB | 3,625 | 91 | nodeSpacing = 10; % microns
% load mask data
% [maskFileName, maskPathName] = uigetfile('*.mat', 'Pick the .mat file with your skeleton object');
% load(strcat(maskPathName, filesep, maskFileName),'mask','bkgndmask','fileName','pathName');
%
% %% read file
%
% % Use this line if your 2 channels are in one file
[stac... |
5dfb15c4b4996eb53f92a77d66cd715e1a5ad1a280d7db1cdcfe7116afe27197 | MATLAB | 3,627 | 122 | % This script provides a tutorial application of the Gaussian-Copula Mutual
% Information (GCMI) estimator with a 2 category discrete stimulus (face
% vs noise images) event-related EEG data set.
% This script uses cell mode - cells are delimited by %% lines and can
% be run with:
% ctrl-enter (windows, linux) or cm... |
d7ce3eae2bf22522976589a8a249b2914fca49370492955555acb4ffbbca8348 | MATLAB | 3,627 | 94 | 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 (optiona... |
6cb9e31a655feafd7f79fcad2b08ba7e42927400e923a95c75de5cf423795d6c | MATLAB | 3,631 | 111 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
a4aa390fb792e5b55771f1502f38a5a7a6da2c2c52077b30fecb9e114aa55538 | MATLAB | 3,644 | 104 | function BWout = interpmask( varargin )
%INTERPMASK Mask interpolation (tweening) via distance maps
%
% BWq = INTERPMASK(X,BW,Xq) interpolates masks in the logical matrix BW
% at query points Xq. The elements of X corresponds to the successive
% masks along the last dimension of BW. The output BWq is a logical
% ... |
aaadc75a9ff6511967a12676098672fb665be0ec84fb862d5ce0c0d2ce26197a | MATLAB | 3,644 | 95 | classdef NullModelAnalysisUnit
% Holds and executes a single null model analysis, leveraging ConnectomeAnalysisRunner
properties
AnalysisRunner ConnectomeAnalysisRunner
WiringPISimilarity
end
methods
function obj = NullModelAnalysisUnit(randConnMat,randDomDef,randHoldoutOptions... |
42c3aa75b6a502799579e8f055e9271e4b220a919a90d362ecdf7f6fb9c3469c | MATLAB | 3,648 | 113 | function p = userpath(inArg)
%USERPATH User environment path.
% USERPATH returns a string specifying the first folder on the search path.
% MATLAB adds the userpath to the search path upon startup.
%
% The default userpath is platform-specific:
% Windows: user's "Documents" folder appended with "MATLAB"
% ... |
0e95ae2d262a74b1bb19091676c18cfc8d9e38c1654c43ab2d683d9deaf05478 | MATLAB | 3,657 | 108 | function [s_pe, s_ep, prior_pd, post_pd] = spm_cpm_get_ppd(PRF, coords, idx, nsamp, use_parfor)
% Sample from the prior (or posterior) of a pRF model and run samples
% through the likelihood, to give the prior (or posterior) predictive
% density (PPD).
%
% PRF - estimated PRF
% xy - coordin... |
8c56e2da62dc6539dad43ed745527d31900d3b1c5ec9950f1da2395abbcffbda | MATLAB | 3,667 | 82 | function [markerdat_micro, markerdat_macro] = readstimdata(cfg,micromed_markers)
fname_output = fullfile(cfg.datasavedir,['stimdat_',cfg.postfix,'.mat']);
if exist(fname_output,'file') && cfg.force == false
fprintf('Loading precomputed data: %s\n',fname_output);
load(fname_output,'markerdat_micro','markerdat_m... |
1e9d59aa5f7f72fb3a25e7521072f7faf7fd7caed4b44e8b7b779a77195d90cc | MATLAB | 3,671 | 61 | function experiments = get_experiment_redux(klusta)
% function creates the selected experiment plus correlated parameters from
% the specified excel file
% input variable optional (vector), if not defined: all experiments are selected,
% if defined: selected experiments will be used
if nargin < 1
klusta = 0;
end... |
b63aec0173cb17b549802e00ca186e1a9978b09a49e59c58e3e95e3dfe61db2d | MATLAB | 3,679 | 140 | function map = perlin3(s,depth,f0,fn)
% PERLIN3(OUTSIZE,POWER,F0,FN)
% general function to generate 3-D perlin noise maps
% this lazy pointwise method is much slower than PERLIN()
% but the results are repeatable and can support OUTSIZE(3)>3
% output is double, scaled [0 1]
%
% OUTSIZE is a... |
d38fb03ddd6b6204aace9124504907c7e45139248d998a7c5176c5d03445dfe7 | MATLAB | 3,684 | 146 | %
% [basis, r, rho] = getSampleCorrelationBasis(T, fileName)
%
% Description:
% obtain sample correlation basis
%
% Input:
% T - number of time samples
% fileName - file name for caching
% numCPU - number of cpu used for parallel processing
% isVerbose - verbosity
%
% Output:
% basis - sample... |
b67c496a6492b56ca5903fe412a4b147ab93dad4f2f18c2c17b0b24e3e169a52 | MATLAB | 3,686 | 68 | function [MuseStruct_new] = PET_cut_long_epochs(cfg, MuseStruct_orig, markername, max_epoch_length, new_epoch_length)
% Cut epochs into sub-epochs if they are too long.
MuseStruct_new = MuseStruct_orig;
markerstart = cfg.muse.startmarker.(markername);
markerend = cfg.muse.endmarker.(markername);
for ipart = ... |
8cf1cae4c91d0122973144f32073c0d6453fe3f3e250cd27f0f4eef859e35a9b | MATLAB | 3,694 | 89 | function [auroc ciLoUp] = mroc(x,y,varargin)
% function [auroc ciLoUp] = mroc(x,y,varargin)
%
% computes the area under the receiver operating characteristic (ROC) curve
% optionally, provides bootstrapped confidence intervals and plots the curve
%
% note that x and y must exclusively consist of integers!
%
% results v... |
859d26a0de6ad93e21b6ac2ea91c6394ecb21baa6dd8178dad6e8d233e829968 | MATLAB | 3,702 | 100 | % RANDSUBSPACE Generate k random vectors x that are orthogonal to z but have the same projected
% coordinates along the columns of A, i.e. A^T x = A^T z for all x, as well as the
% vector norms of x being the same as that of z.
%
% Inputs
% ========
% A : m-by-n matrix for which... |
1c51f20903284ba0bffd6070b36ed273b4532b8bcf5ed610ca10c9d90aa25a3c | MATLAB | 3,706 | 152 | 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... |
83ebbedb02de8b661b56ef53b0df59e08b3dfd364b39199656716e622a042d41 | MATLAB | 3,707 | 76 | function plotstats(cfg)
nrows = 18;
ncols = 3;
% SpikeTrials_timelocked = readSpikeTrials_MuseMarkers(cfg);
SpikeDensity_timelocked = spikeTrialDensity(cfg);
for ipart = 1 : size(SpikeDensity_timelocked, 2)
fig = figure;
orient(fig, 'portrait');
col = 1;
for markername = string(fields(Spike... |
77950a9985a8ad144960d424f1b2422d595aada1cca2c78fcb65fa12ae9e92c4 | MATLAB | 3,709 | 103 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2019 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
40516820c0c2f66f1acc64d8c8d9fc1b084268e8ab228e801e5820566f746c09 | MATLAB | 3,720 | 111 | classdef BrainRegionInformation < handle
% BrainRegionInformation
% Handles brain region metadata and keeps AnnotationIndex for linkage to BrainSpace3D
properties
RegionTable table
end
methods
function obj = BrainRegionInformation(tbl)
arguments
tbl tabl... |
92569c2575ed200641ec6c4a67e2d59149f01b0408e103611947f2b44a776f2d | MATLAB | 3,721 | 115 | function bwMask = multiROI(figHandle, axHandle)
% multiROI: Interactively specify 2D freehand ROI
%
% Overlays an imfreehand ROI on an image.
% Gives the ability to tweak the ROI by adding and
% subtracting regions as needed, while updating
% the ROI boundaries as an overlay on the image.
% Returns a logical matri... |
e5189a45e5ff9e3c3d178316d2ec56b81d5cd0ac7f8c6476797f89071579ae83 | MATLAB | 3,725 | 80 | function [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params)
% Helper function to convert structure params to variables used by the
% various routines - also performs checks to ensure that parameters are
% defined; returns default values if they are not defined.
%
% Usage: [tapers,pad,Fs,fpass,err,trialave,para... |
4ef6117edab5bec89f13a62ee6e868259413889556ed44b6bba461708d5bc3b5 | MATLAB | 3,733 | 100 | function dtx_plot_patients_seizure
% Set parameters
if ispc
addpath \\lexport\iss01.charpier\analyses\lgi1\Git-Paul\fieldtrip;
addpath (genpath('\\lexport\iss01.charpier\analyses\lgi1\Git-Paul\EpiCode\projects\dtx'));
addpath (genpath('\\lexport\iss01.charpier\analyses\lgi1\Git-Paul\EpiCode\external'));
... |
b77fc3e701846a50306c73f96b8117fc50ab37d9701c74ae4d770091a2d5ee8a | MATLAB | 3,734 | 105 |
% Correlate varA with varB accounting for confounds (SPM setup)
clear, clc, close all
%% Paths / data
path_batches = 'D:\Projects\2023_multib\MK_multi_b\Scripts';
cd(path_batches)
load('Table_297_subjs_demographics_biomarkers_2024_05_03.mat')
n_subjects = size(T_subjects,1);
path_stats_grp = 'D:\Proj... |
6ebb5ac88537b73aff8587288dc6a0c9110ab700a3058e19e1aabca7a65d4025 | MATLAB | 3,737 | 89 | function BatchResults = Batch_InterictalDetection(filename,threshold,channel,toDenoise)
% USAGE
%
% BatchResults = Batch_InterictalDetection(filename,threshold,channel,toDenoise)
%
% Main function for the interictal-like spike detection. Filter the signal, receive
% the interictal-like spikes, group t... |
ee1be52b813b00774f2e9ea922e415ed1208798e1b80fe5db83641ef083fc2c4 | MATLAB | 3,737 | 90 | %**************************************************************************
%
% morse_unfold unfolds aliased images given pinv of sensitivities.
% input "data" contains:
% a global header in .reference
% acquired, aliased k-space in .data as [N_coils, RO, PE1, PE2, echoes, sets]
% ... |
457a7149a8ac635f2311be81488b38ed059debd782d34c4b9b07e282ec3a4ec3 | MATLAB | 3,738 | 106 | function h=subaxis(varargin)
%SUBAXIS Create axes in tiled positions. (just like subplot)
% Usage:
% h=subaxis(rows,cols,cellno[,settings])
% h=subaxis(rows,cols,cellx,celly[,settings])
% h=subaxis(rows,cols,cellx,celly,spanx,spany[,settings])
%
% SETTINGS: Spacing,SpacingHoriz,SpacingVert
% ... |
eb854323c51a00b8803f5dc24579d3bf3e4845aab4dd6ac5a13abe37364cd28f | MATLAB | 3,740 | 109 | function [DG_point,DG_accepted,DG_line_image,outer_points,inner_points,hilus_points]=trace_Hilus_outline(settings,images_all,composite_img,roi_names,roi_idx,roi_fname,magnification,roi_subfolder,DG_line,DG_out_line)
%%% Trace DG outline - Version 4 %%%
DG_accepted=0;
nuclear_image_roi = images_all.nuclear_img;
dc... |
1677a7e08f7e0bb0a737f28600077f79f1e7c33adecd4d0274cc02b88badaacb | MATLAB | 3,742 | 89 | function CBIG_AuthorTopic_EstimateComponentSmoothness(allKs, maskPath, ...
bestSolutionDir, outputDir)
% CBIG_AuthorTopic_EstimateComponentSmoothness(allKs, maskPath, ..
% bestSolutionDir, outputDir)
%
% Estimate the smoothness of the estimates for the probability of a
% component activating a voxel (Pr(voxel | co... |
9c7cc730f214b57c767ed9da17f4fb55c352e073f0cf5d2eb0e62c2e5fb33923 | MATLAB | 3,747 | 88 | function [StimPowerRamps] = getStimulationPowerSingleRamps(experiment,...
CSC, save_data, repeatCalc, folder4stim_props, folder2save)
% by Mattia, 01/21
% this script computes the power for individual stimulations of our
% "classic" ramp optogenetic stimulations. It assumes a ramp length of 3s
% and a total stim t... |
10f71f57e022113a28b6d6ecb1e3696ce49f1232677258bd43546b625568b318 | MATLAB | 3,748 | 137 | function outpict = impatmap(inpict,G,ugl,varargin)
% OUTPICT = IMPATMAP(INPICT,PATGROUPS,LEVELS,{OPTIONS})
% Using a sorted collection of grayscale (ostensibly tileable) patterns,
% approximate a multilevel grayscale representation of another image.
% This is the tool used to apply the output from impatsort(... |
dab85aed2456aaaa1b6ecfc2dcc00796aa0fae768eeddb9104776e776fbc7289 | MATLAB | 3,756 | 93 | function slurm_preictal_project(ielec)
restoredefaultpath
if ispc
addpath (genpath('\\lexport\iss01.charpier\analyses\vn_preictal\scripts\EpiCode\shared'))
addpath (genpath('\\lexport\iss01.charpier\analyses\vn_preictal\scripts\EpiCode\external'))
addpath (genpath('\\lexport\iss01.charpier\analyses\vn_prei... |
54082239b6ecd0ee05e0a02525ea26b5e1e03d379ecbacdfadfb4e99f4ae5341 | MATLAB | 3,760 | 70 | function mov = denoiseCIinTime(mov, varargin)
% denoiseTracesWavelet(fuObj, varargin)
%
% Function to denoise calcium imaging data in time using wavelet
% denoising. To avoid the missing data problem, error frames from burst
% errors are filled in using cubic spline interpolation.
%
% 2020 - Adam Charles
%%%%%%%%%%... |
b06252b5da83e0258e4679fa5b31c8b6d9adacfd95ad3c879e6bf122adb9b197 | MATLAB | 3,767 | 98 | function borders = moveBorders(data,options)
% move parameter-boundaries to save computing power
%function borders=moveBorders(data, options)
% this function evaluates the likelihood on a much sparser, equally spaced
% grid definded by mbStepN and moves the borders in so that that
% marginals below tol are taken away... |
6811f10a786ac031d309f8f3ea2a43ce298fddc0a1267a79d9d8883e2ffd8ccb | MATLAB | 3,768 | 94 | function [result, SI] = readScanImageTiffLinLab(fileName)
% readScanImageTiffLinLab:
% Uses ScanImageTiffReader to read in a ScanImage file with the name
% fileName
% We use this because scanimage.util.opentif is unbearably slow
%
% Usage:
% [result, SI] = readScanImageTiffLinLab(fileName);
% - result is a a 5D matrix... |
6c30fc158d861e72adc44fecb70c8a146fb92afbd078fddadeab17684db07cf0 | MATLAB | 3,776 | 95 | function make_movie_fmri(bfpdir,fmridatfile,outgiffile,TR, sc)
if ischar(TR)
TR=str2double(TR);
end
%sc is upper and lower limit on the colorscale
cmap=bipolarcmapW(100,[-sc,sc],'linear','br');
dfs_refL = readdfs(fullfile(bfpdir,'supp_data/bci32kleft.dfs'));
dfs_refL=smooth_cortex_fast(dfs_refL,0.1,1000);
nV=leng... |
2e453242a7fc3a80b5af6eb78ff8c3f0cdeadf915cae1f02329dcfd2a5e33026 | MATLAB | 3,779 | 101 | function MBmodel = optimiseMBparams_APLgain_Ctheta(MBmodel, PNactivity)
% sigmoid_factor = -0.9;
% Sigmoid_derivative = @(x) exp(-sigmoid_factor.*x)./((1.+exp(-sigmoid_factor.*x)).^2) ;
% Sigmoid = @(x) 1./(1.+exp(-sigmoid_factor.*x)) ;
sigmoid_factor = -1.11;
Sigmoid_derivative = @(x) exp(-x./sigmoid_factor)./((1.+ex... |
5d5e30708e48942ac758f2cb9dc9c80ce605a10632fa8ccf5d946997aa35c7ec | MATLAB | 3,780 | 128 | %Script to create the design matrix A in A*beta = b, where the columns of A are features extracted from layer x of the DQN.
function S05_design_matrix_layer_x(subject, game, DQN)
root_path = 'YOUR_DATA_PATH';
main_dir = strcat(subject, '/', game) ;
sess_no = 5;
GLM_name = 'GLMs_Layer_x';
TR = 0.987;
load('hrf_15hz... |
77ffbea6ad8541ebe7369e5da1bab66c512d70777244eb6fd012b88b14950261 | MATLAB | 3,791 | 114 | function [] = displayMultiActivityMaps(allMaps, fileprefix, registerF0)
% displayMultiActivityMaps:
% Usage:
% displayMultiActivityMaps(allMaps, fileprefix, registerF0)
% allMaps is an array of activityMap objects
% Will display 2 figures:
% 1. All the maps in allMaps, one per row.
% Each row will be an 1 X N montag... |
a8017d5ff4d0f525c515b7b74e20c2e875eb9874cd2c88c4678773ea5fa1a682 | MATLAB | 3,792 | 130 | function outpict = imannrotate(inpict,angle,varargin)
% IMANNROTATE(INPICT, ANGLE, {OPTIONS})
% Rotate an image using simple annular shifting to crudely maintain boundary geometry.
% This is not intended for any technical purpose requiring accuracy or reversibility.
%
% INPICT is an I/IA/RGB/RGBA image ... |
e8f6deab2121cdc71242066931f7247f8041da6be8d113dfdfd5360761384cfa | MATLAB | 3,793 | 115 | function [W] = mc_undist_loop(V)
nx=V.nx;
ny=V.ny;
tim1=V.im1;
tim2=V.im2;
b00_best=0;
b01_best=0;
b02_best=0;
b10_best=0;
b11_best=0;
b20_best=0;
[X,Y] = meshgrid(1:nx,1:ny);
cost_best = 9e99;
adjustX_lin = ones(ny,1) * (([1:nx]-(nx+1)/2)/((nx+1)/2));
adjustX_sqr = adjustX_lin .^2;
adjustY_lin = (([1:ny]'-(n... |
532f08401425942bca43a0d85b93a9ef74c6a44646d20cb94435eb322aacc38b | MATLAB | 3,801 | 73 | function wf = getWaveForms(gwfparams)
% function wf = getWaveForms(gwfparams)
%
% Extracts individual spike waveforms from the raw datafile, for multiple
% clusters. Returns the waveforms and their means within clusters.
%
% Contributed by C. Schoonover and A. Fink
%
% % EXAMPLE INPUT
% gwfparams.dataDir = '/path/to/da... |
b921cc696dd003a8afae7c1613b4c8a1d0e523fcaff9b141aa38ac8b07bea969 | MATLAB | 3,802 | 136 | function out = zfdither(img)
% ZFDITHER(INPICT)
% Apply Zhou-Fang VC dither to an I/RGB image
%
% The ZF algorithm is a modern variable-coefficient
% error-diffusion dither based on the Ostromoukhov algo.
% https://www.cs.unc.edu/~xffang/paper/siggraph03.pdf
% Zhou-Fang dither implementa... |
f4b4dc1c1f21f10d2a7817e5abca9d75c9a3b56de2e439d4b444486bc7b6a914 | MATLAB | 3,808 | 110 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
36fd74297c3f6df6f832b908cb4a8d8c48cba89833bd3ece2accbbf7a1b530c0 | MATLAB | 3,813 | 107 | % =========================================================================
% Title: Spectral Feature Extraction from chemogenetics manipulation
% experiments
%
% Author: Gabriele Mancini
% Date: 2025-12-10
%
% Description:
% This script processes experimental LFP and MUA neural data to extract periodic and
% aperiodic... |
b69a7a7b790d7d6b35b1f836612cd054b6e22cdafd2922c361de4e182cce382d | MATLAB | 3,816 | 95 | function plotTimeCourses_new(cfg, LFP, TFR)
for ipart = 1 : size(LFP, 2)
for markername = string(fieldnames(LFP{ipart}))'
cfgtemp = [];
cfgtemp.hpfilter = 'yes';
cfgtemp.hpfreq = 1;
LFP{ipart}.(markername) = ft_preprocessing(cfgtemp, LFP{ipart}.(markername));
end
end
f... |
29bdd825b6cd3c4b9f73102d7eb8d0d64adb06af3c3bc4da94d6efcc5c4e606a | MATLAB | 3,819 | 115 | function outpict = perlin(outsize,varargin)
% PERLIN(SIZE, {OPTIONS})
% Generates pseudo-perlin noise fields or volumes. Compared to PERLIN3,
% behavior is nonrepeatable, but the execution is much faster. Instead
% of generating a perlin noise volume to create a multichannel image,
% PERLI... |
9bd779f6bba15c6e373a1074da36acae185fab4bad5917c2ca2bae13db79d863 | MATLAB | 3,819 | 73 | classdef Acquisition
properties (Access = public, Hidden, Constant)
% Acquisition flags
ACQ_FIRST_IN_ENCODE_STEP1 = bitshift(uint64(1), 0)
ACQ_LAST_IN_ENCODE_STEP1 = bitshift(uint64(1), 1)
ACQ_FIRST_IN_ENCODE_STEP2 = bitshift(uint64(1),... |
9d99eac0455ea02537e5880a8284a2f9d36279c5ab45d05e2d3e0f67524918ff | MATLAB | 3,821 | 145 | %% Fig.2
% Fig.2
% plot using GraphPad Prism 9.
%% Fig.3
% Fig.3a, b, and c
% inflated brain surface were ploted using SUMA (https://afni.nimh.nih.gov/Suma).
% axial maps (CanlabCore)
clear;clc;close all
imgname = 'glm_NA-NV_fdr05.nii';
mask = which('gray_matter_mask.img');
img= fmri_data(imgname,mask)... |
be0e22adfb78b1853f1a175717b15ec231150377d18ab816aa86dbd9ea3b5785 | MATLAB | 3,832 | 68 | function hspike_cluster_template(ipatient)
%% Analysis script for SLURM cluster
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
%% preamble
feature('DefaultCharacterSet', 'CP1252')
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
hspike_setpaths;
labels = ["BAD__STAR... |
9427c4e7de68c0211afce1d7520dbaf896882d8e8f9150e727e4ca8c26f373f6 | MATLAB | 3,844 | 106 | function h=subaxis(varargin)
%SUBAXIS Create axes in tiled positions. (just like subplot)
% Usage:
% h=subaxis(rows,cols,cellno[,settings])
% h=subaxis(rows,cols,cellx,celly[,settings])
% h=subaxis(rows,cols,cellx,celly,spanx,spany[,settings])
%
% SETTINGS: Spacing,SpacingHoriz,SpacingVert
% ... |
49505022df2c7f5294e1e6f554c8893d038668637cfa015b43ea113022a6ba4d | MATLAB | 3,849 | 125 | function transform_data_affine(data_file, data_coord, output_file, ...
reg_moving_file, reg_static_file, reg_mat_file, method)
% General function to transform nii/dfs using affine matrix estimated using
% register_files_affine.m. No sophisticated checks are performed for
% file-coordinate checks.
%
% data_file - f... |
6d7182df103d030805211abd2e8ff6dddcfd7e82ba682127f0853816c28038e1 | MATLAB | 3,864 | 78 | classdef MajorRegionBlockRandomizer
% Applies randomization method to each MajorRegion pair block, or to the whole matrix
properties
RandomizationMethod function_handle
UseBlockwiseLogical (1,1) logical
end
methods
function obj = MajorRegionBlockRandomizer(randomizationMethod,... |
4305a473505c4056881cd99c0d64eec85cc8db2e2dac44d7c47baae00d5e5065 | MATLAB | 3,876 | 161 | function inpict = maketileable(inpict,tiling,varargin)
% OUTPICT=MAKETILEABLE(INPICT,TILING,{METHOD},{INTERPOLATION},{REVERTSIZE})
% Adjust the geometry of an image so that its height and width
% are integer-divisible by given numbers. If dimensions are already
% integer-divisible, no adjustments are made.
% ... |
c5055f47f390ae725a247d00174b50ead9f4d639252b146e4b2a95b89ef59879 | MATLAB | 3,879 | 128 | % preprocessing for TMS-iEEG
% including four parts:
% Part 1: Basic preprocessing
% Part 2: Split sessions [optional]
% Part 3: Detrend
% To do:
% use more specific names;
% add plot: plot them together or seperate figures, with example channels;
%% -------------------------------------------------
%% Part 1: Basic... |
5820c8eadaf1db119a19d541e9a2e7e8e6d027335538e57f84af305c5607e3bf | MATLAB | 3,881 | 160 | function outpict = puttext(BG,thistext,varargin)
% OUTPICT = PUTTEXT(INPICT,TEXT,{OPTIONS})
% A simple tool to insert text into an image using image composition.
% All text is monospaced and binarized (no antialiasing).
%
% INPICT is an image of any standard image class. Multiframe images are not supported.
% ... |
102a38ca1af358e374f75061eb2dae905895f8012b9e9269fee38b177fd460d5 | MATLAB | 3,884 | 156 | function I = mi_model_gd_vec(x, y, Ym, biascorrect, demeaned)
% MI_MODEL_GD_VEC Vectorized MI calculation between multiple Gaussian variables
% and a common discrete variable in bits based on ANOVA style model comparison.
% I = mi_model_gd_vec(x,y,Ym) returns the MI between the (possibly multidimensional)
% ... |
6d923a019ec4a773681b64caf2bba566b2c99ae432140601adcd55d9550431d0 | MATLAB | 3,896 | 104 | function [OPS_object_data] = Circular_object_detection_OPS(OPS_object_data,save_path,position_analysis,centers,radii,lengthpix,Files,idx,ind_mouse,phase)
% [OPS_object_data] = Circular_object_detection_OPS(OPS_object_data,save_path,position_analysis,centers,radii,lengthpix,Files,idx,ind_mouse,phase)
% Detect circular... |
cb148ce657d5b3f17f4bd62ab5b68f7b10001ccf4e95ca68bf9232835ebb14f4 | MATLAB | 3,897 | 104 | function [vol_reslice, nii] = myreslice_nii(vol, method, X_grid, Y_grid, Z_grid, fileOut, gz)
% Reslice the nifti image (VOL) to a grid in world-coordinates i.e. applies the sform transformation
% on the image matrix. When [X_grid, Y_grid, Z_grid] is not defined, the image is resliced on a grid
% with same resolution a... |
7ecd3d6e992ef3932983002765b3a4f02a19d1086610a4e05f3f69b3533bde2b | MATLAB | 3,903 | 86 | function MuseStruct = read_nev_Muse(cfg,MuseStruct)
% READ_NEV_MUSE crawls and searches through patient directories to
% extracts event timings created in the .nev file during the data
% acquisition.
% It adds each event in MuseStruct so it can be used the same way as the
% events created in Muse. The name of the ev... |
028d789de1c3001f7ea64fe748fa10221a43dfdf32f2bd05f889b92f8b4d026f | MATLAB | 3,904 | 130 | %% Alamar Blue SAP experiment
%%
clc;
close all;
clear all;
%% Matlab folder
matlab_folder = '/Users/sofiaperessotti/Docs/VM_stim/Analysis';
addpath(genpath(matlab_folder));
%% Folders
base_folder = '/Users/sofiaperessotti/Library/CloudStorage/OneDrive-ImperialCollegeLondon/PhD_project/Cell_Experiments/SAP_stim/';
... |
3635550069538f7b9e8b99d8b569342457254e5d843d08b649eb9370366e7c56 | MATLAB | 3,904 | 113 | function plotTimeCoursesExamples(cfg)
fig = figure('visible', true);
set(fig, 'PaperPositionMode', 'auto');
set(fig, 'position', get(0,'ScreenSize'));
% set(fig, 'PaperOrientation', 'landscape');
% set(fig, 'PaperUnits', 'normalized');
% set(fig, 'PaperPosition', [0.2 0.2 0.8 0.8]);
ncols = cfg.plot.ncols;
icol ... |
f17ccc8143c2d567a24bf6859dee1d2835fa04378ca6bd0d6138b6529dee3a55 | MATLAB | 3,907 | 140 | clc; clearvars; close all
% load and define specific parameters
load("par.mat")
dt=0.001;
par.tspan = 0:dt:100;
par.opts = odeset('RelTol',1e-6,'AbsTol',1e-8);
par.I0=0.20; % KNDy baseline
par.k=10;
par.je=0.5;
antag = 0.5; % interaction strength suppression
stim = 0.5; % amplitude of stim sine wave
stimB = 2.6; % ma... |
cdc4bb57e7c63bd9669b90be128216651bf8f37cf63c6f9ea633edfdf1abc874 | MATLAB | 3,910 | 134 | function Srf = spm_prf_export_samsrf(PRF, hemi, name)
% Exports an estimated PRF to SamSrf format
%
% PRF - PRF structure (estimated)
% hemi - hemisphere ('lh' or 'rh')
% name - name for the file
%
% Outputs:
%
% Srf.Values - field names of estimated parameters {p x 1}
% Srf.Data - vertex-wise estimated parameters... |
aba22dcccc413771b6065fc402db7a4e5b000307bb1854d96f198e02cf50af05 | MATLAB | 3,921 | 90 | % input: structure with a field data arranged as [1 nx ny nz nechoes nsets]
% (output of ESPIRiT_unfold)
function next = BSS_classic_or_GLM_B1map(input,header)
addpath(genpath('/usr/local/romeo_linux_3.2.5/matlab/NIfTI_20140122'))
%%% BSS parameters ( requires the conversion siemens to ismrmrd
%%% with IsmrmrdParame... |
342ba7b3671bd6ff4d2778e89b0e1256a5c8303398803f6a26cdccd107b14a37 | MATLAB | 3,926 | 117 | %Map values to the surface
%load a csv file with the loadings you want to map to surface
wd = '/Users/polona/20241126_region2surf_mapping';
csv = cat_io_csv(fullfile(wd,'Y_loadings_sPLS_multi_canonical.csv'));
neuromorph = csv(44:numel(csv(:,1)),:);
load_cobra = csv(1:43,:);
hemi = {'lh.','rh.'};
for hi = 1:numel(he... |
ae0dd4eea617d0719f582613d2e6903f199440366ff6d9650c809cac437e422e | MATLAB | 3,928 | 105 | function [vol_reslice, nii] = myreslice_nii(vol, method, X_grid, Y_grid, Z_grid, fileOut, gz)
% Reslice the nifti image (VOL) to a grid in world-coordinates i.e. applies the sform transformation
% on the image matrix. When [X_grid, Y_grid, Z_grid] is not defined, the image is resliced on a grid
% with same resolution a... |
9a069ff5134bcb61d45538fbe9e90b248138145bea81834627f8a28bdf139d7c | MATLAB | 3,930 | 103 | function [quality] = checkspikequality(cfg,force)
warning('off','all')
ft_warning off
ldir = dir2(fullfile(cfg.eegdir,cfg.directory_searchstring));
ldir = ldir([ldir.isdir] == 1);
fname = fullfile(cfg.outputdir,[cfg.prefix,'_qualitycheck.mat']);
if exist(fname,'file') && force == false
load(fname,'quality');
el... |
078b10525cca0344fae4b32d9efb29c67addc419c17a131accb483782cef4c07 | MATLAB | 3,931 | 110 | function CBIG_compute_singleKRR_PFM(feature_file, singleKRR_dir, sub_fold_file, score_ind, outstem, outdir)
% CBIG_compute_singleKRR_PFM(feature_file, singleKRR_dir, sub_fold_file, score_ind, outstem, outdir)
%
% This function computes the predictive network features of single-kernel
% ridge regression (under <CBIG_CO... |
1e490d6199820cc609cb8dcdefee439420722033a903c8b42f1809ba0f65884d | MATLAB | 3,933 | 101 | % Coupling of the KNDy network model with MePD outputs
function dx = KNDyXMePDU(t,x,par)
dx=zeros(6,1);
%% KNDy model parameters
d1 = par.d1; % Dyn degradation rate
d2 = par.d2; % NKB degradation rate
d3 = par.d3; % Firing rate reset rate
k1 = par.k1; % Maximum Dyn secretion rate
k2 = par.k2; % Maximum NKB secre... |
7bf677745eb0dd979106e09a7f71f6c22f6c32564563e2ea6fb2f18c23952666 | MATLAB | 3,933 | 97 | function [ets,ech]=LLspikedetector(d,sfx,llw,prc,badch)
%jon.kleen@ucsf.edu 2016-2023
% Transforms data into linelength then detects events (spikes) surpassing
% the designated percentile threshold. Note that this function assumes any
% detections in any channel occurring simultaneously are involved in the
% same spi... |
6672ea8b4b337ce291bd39dec7e4f010637cdbba2e318f351cf70384b9063571 | MATLAB | 3,934 | 128 | function alltrials=RunTrials(alltrials, data, iti, trans, fc, mmultiply, nd, dotsize, leng, test);
%
% PARAMETERS
prompt = ' <- | -> '; %Text prompt after each trial
rand('state',sum(100*clock)); %Initialise the random generator
%Set input variable defaults if necessary
if fc==... |
92455f992c396ee60ebd2fee0ef44d805924bdd8c24e5347c24ebe830ba123ff | MATLAB | 3,934 | 84 | function SUAdata_pulses = getPulseSpikeMatrix(experiment, save_data, repeatCalc, ...
folder2save, folderSM, folder4stim_props)
% by Mattia 10/20
% create a spike matrix (actually a tensor) for pulses stimulations
% this script arbitrarily creates a matrix of 100ms centered around the
% pulse, and consideres an 8ms... |
02f5fb0268caebdd0abe59f4c2bfd1e7e0f7581e443e334f617b5ac46710e6b4 | MATLAB | 3,946 | 91 | % -------------------------------------------------------------------------------------------------
% (c) 2025 Leon F. Heffer, David J. Sly, James B. Fallon, Rick Minter, Rebecca C. Felsheim,
% Mathias Dietz and Stephen J. O’Leary.
%
% This file is part of a repository that contains the data originally recorded by He... |
84af3c7dab5611e6938eb7c63c5b20830c7e0693612823462c793ad7ff20c6e3 | MATLAB | 3,949 | 127 | function hline = plotMarginal(result,dim,plotOptions)
% plots the marginal for a single dimension
%function hline = plotMarginal(result,dim,plotOptions)
% result should be a result struct from the main psignifit routine
% dim is the parameter to plot
% 1=threshold,2=width,3=lambda,4=g... |
bb9bbc9b13b6ad742593db96e274577d838ef1560b4c2bf5588ef636e304c40a | MATLAB | 3,949 | 135 | %% Compare the second dominant mode of SVD on the whole windows and the mode_wake - mode_sleep
clc,clear all;close all;
sub_folder = ['../data/EEG/'];
ls = dir([sub_folder,'ds*mat']);
% Focus on the first half hours
fs = 100;
t_start = 1*fs;
t_end = 1800*fs;
t = linspace(t_start,t_end,(t_end - t_start + 1)) / fs;
% ... |
e805913e305a896e217155c889fa2712ec661f7569e79cce196b837eeaac5be2 | MATLAB | 3,950 | 90 | function [mat opt] = mwa(tspx,tevents,trefevents,winsize,winpos,varargin)
% function [mat] = mwa(tspx,tevents,winext,winshift)
%
% code to compute the area under the ROC curve for two spike count distributions at different time points
% and different time intervals
%
% note that function requires mroc and mnspx in Mat... |
7c7214cc120de2202c9c52b67dced222ac4e5b2c38dd4b961c3f6217daf441ee | MATLAB | 3,957 | 94 |
% Extract mean DWI parameters and GM volume within significant clusters
clear, clc, close all
%% Load subjects and prune
load('Table_297_subjs_demographics_biomarkers_2024_05_03.mat')
list_subjs_to_remove = [47,69,135];
T_subjects(list_subjs_to_remove,:) = [];
n_subjects = size(T_subjects,1);
%% Paths an... |
f3115b24c0c22062b22cfc38d3fab291a8da50c547425a248f7f4c3babd1f6f5 | MATLAB | 3,957 | 85 | function [EEG_integrals, EEG_deltas,indices_integrals,EEG_epoched_AT] = pred_events(EEG, event_name_d, event_name_i, epoch_window)
%% Get EEG in right format; epoched with all GLM parameters
%
% **Usage:** [EEG_integrals, EEG_deltas,indices_integrals] = pred_events(EEG, event_name_d, event_name_i,epoch_window)
%
% Inpu... |
e7907c2c9bf8dd163fc02d196a4bfa6a6cc59aed589a9de4feb8a04efa7bea42 | MATLAB | 3,963 | 113 | function status = CBIG_check_job_status(job, varargin)
% status = CBIG_check_job_status(job, varargin)
%
% This function checks whether your job is successful. It will first check
% whether your jobs are running or not. After they are all finished, it
% will check your log file or output file. You can check either, bo... |
fd2f79accc54920ddd07a000c761d178ebc70dd7356155a65fe0f56b00034140 | MATLAB | 3,964 | 115 | function bucket = read_bucket(socket)
meta = read_bucket_meta(socket);
data = read_bundle(socket, meta.data, meta.data_stats);
ref = read_bundle(socket, meta.ref, meta.ref_stats);
waveforms = read_waveform(socket, meta.waveform);
bucket = gadgetron.types.Bucket(data, ref, waveforms)... |
a74c07c2ff50de1dbb822c445517183641bd77422be19587159900546d69017f | MATLAB | 3,966 | 113 | %WAVETEST Example Matlab script for WAVELET, using NINO3 SST dataset
%
% See "http://paos.colorado.edu/research/wavelets/"
% Written January 1998 by C. Torrence
%
% Modified Oct 1999, changed Global Wavelet Spectrum (GWS) to be sideways,
% changed all "log" to "log2", changed logarithmic axis on GWS to
% a normal a... |
49ae03e9af083ea4f9d81b7130aed3c91bc28f155bf7f6ea7dd81ef237aff022 | MATLAB | 3,971 | 104 | function cohLFP(suffix)
% LFP COHERENCE - Compute LFP-LFP coherence for given time and
% frequency values.
%
% Read parameters
Params = read_params(suffix);
freq = Params.freq_start_1 : Params.freq_step_1 : Params.freq_end_1;
time_window = Params.time_1;
time_step = time_window / 4;... |
624cd9e4ccb3dd4ecb27aceadf6b0bdb57edb7c2f49e5e9ca269b1349cf453f9 | MATLAB | 3,976 | 122 | function [y,stepList]=nt_destep(x,thresh,guard,depth,minstep);
%[y,stepList]=nt_destep(x,thresh,guard,depth,minstep) - remove step glitch from MEG data
%
% y: step-removed data
% stepList: indices of steps
%
% x: data to clean (time * channels)
% thresh: threshold for variance reduction [default: 0.1]
% guard: min... |
51b10597fd6b50ab2e82503d13e5ff30ae2249e28258b0067e9f46059b2617a9 | MATLAB | 3,980 | 144 | function out = arborddither(img,kfactor,cmode,indexarray)
% ARBORDDITHER(INPICT, {KFACTOR}, {COLORMODE}, {INDEX})
% Multilevel ordered dither with support for arbitrary index arrays
% Available presets offer a range of simple dither patterns
% As the purpose of this function is image degradation, pr... |
ba0418ac34d4beb9de94e6d1e1b300ca7bee0dfddfdf91b71c8310c6b755a291 | MATLAB | 4,008 | 105 | function [PSD, PSD_slow, PSD_fast, freqs, freqs_slow, freqs_fast, time_slow, time_fast] = ...
getPSD_across_timescales(LFP, fs, freq2analyze, slow_freqs, fast_freqs, folder2save, animal_name, save_data)
% from Mattia 06.20
% compute power spectra:
% 1. down to very low frequencies using multitapers of different len... |
fe5b08d94d93d270585ba9f804b734694e2a8c5520b4fbf96c8a2b3233b2e33b | MATLAB | 4,009 | 114 | function [newPhi, newVarBound] = ...
CBIG_AuthorTopic_ComputeVariationalTerm__N_c(params, newPhi, ...
newVarBound, varBoundFlag)
% [newPhi, newVarBound] = CBIG_AuthorTopic_ComputeVariationalTerm__N_c(
% params, newPhi, newVarBound, varBoundFlag)
%
% Compute the expectation and variance of the count N_{..c.}^... |
c7391a57a987d7de69c6ff0a129b253a277bc17be72a574ac0cef31c9e5fd32d | MATLAB | 4,016 | 118 |
% Correlate varA with varB accounting for confounds (SPM)
clear, clc, close all
%% Paths / data
path_batches = 'D:\Projects\2023_multib\MK_multi_b\Scripts';
cd(path_batches)
% load('Table_demographics_biomarkers_2024_04_09.mat')
load('..\Biomarkers\XCPD_analysis\Table_demographics_biomarkers_2024_10_29.ma... |
9752d8b3c6e4fa844c0657c34ecd8610dc1971f508b9a7a290b612b4654834c3 | MATLAB | 4,020 | 121 | %% Load dataset
% Decoding data
datPath = '/Users/woojaejeong/Desktop/Data/USC/DARPA-NEAT/Code/Decoding/svm/Result/svmDecoding_sentiment_sen_3pc_lepoch_congruency_linear_commonPCA.mat';
wPath = '/Users/woojaejeong/Desktop/Data/USC/DARPA-NEAT/Code/Decoding/svm/Result/senPCAweight.mat';
% Subject index
indexPath = '/Us... |
afd30536dc37cd8e7545f24409c328c4feeeb6fc997115774bd6162efeb9c166 | MATLAB | 4,022 | 109 | function [LFP] = rerefLFP(cfg, MuseStruct, force)
% READLFP rereferences epoched data according to details in the config.
% Use as
% [LFP] = rerefLFP(cfg, LFP, force)
%
% cfg.LFP.demean = 'yes';
% cfg.LFP.baselinewindow = [-0.5 0];
%
% This file is part of EpiCode, see
% http://www.github.com/step... |
bb8dab53dc07da42935d58e7aa1666e7ca53aee77cf4941bd5af289b3d78509d | MATLAB | 4,023 | 110 | function outpict = driftds(inpict,numframes,direction,bluramount,blurmode,disableagrad,coloroffset)
% DRIFTDS(IMG,NUMFRAMES,DIRECTION,BLURAMOUNT,BLURMODE,DISABLEGRAD,COLOROFFSET)
% returns an image sequence consisting of spatially downsampled
% copies of the original image. When animated, changing superp... |
82a543fb605acd995263c201335ab4295cbc10a6d7844cdef8ad88284d6be8ee | MATLAB | 4,026 | 138 | function [Delta490] = DeltaFevent(Ch490,Ch405,Ts,Event,name,varargin)
% Smooth and process 490 channel and control channel data for fiber
% photometry.
%Inputs:
% 1--Ch490-GCamp Channel
% 2--Ch405-isosbestic control channel
% 3--Ts-Series of timestamps related to te Ch405 and 490 channels
% 4--Event-Two colum... |
de3124dcfd9da428e5dfc88c0f0792bd4c7337e2d85fdfd3fea913486edce275 | MATLAB | 4,030 | 70 | function [sdf] = sdfStats(cfg, SpikeTrials, force)
fname = fullfile(cfg.datasavedir, [cfg.prefix, 'sdfStats.mat']);
if exist(fname, 'file') && force == false
load(fname, 'sdf');
return
end
for ipart = 1 : size(SpikeTrials, 2)
if ipart > size(SpikeTrials,2)
continue
end
... |
4218bea89fc9299b4d815bf53a2157e4826fb6f54f92a375db9cf795ffe73de3 | MATLAB | 4,034 | 100 | classdef ConnectomeRandomizationMethods
% Collection of randomization strategies for connectome matrices
methods (Static)
function [randomizedMat,randDomDefMat] = randomGeneration(conMat, domDefMat, ~)
arguments
conMat (:,:) logical
domDefMat (:,:) logical;
... |
519552bee50bdd622aa1777ae07d53804ae28d84cc2ccb322633bf708f4d39c2 | MATLAB | 4,035 | 111 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
3a3a46604439fe3989052673f7b77675704aa06a5da3d13b393d6e1fa5fb3d34 | MATLAB | 4,036 | 97 | function [cfg] = writeSpykingCircusFileList(cfg, force)
% WRITESPYKINGCIRCUS writes a concatinated data file for SpykingCircus and
% sampleinfo is returned for later (cutting results back up)
%
% use as
% writeSpykingCircus(cfg, MuseStruct, force, varargin)
%
% third argument "force" is to force recalculation of sam... |
3e96c1ced9d6eaff9ff83200e0cebc12e03dd48ef59af0e76c393fb084fd4ac0 | MATLAB | 4,039 | 108 | function [sens, noise_cov] = vrc_phase_correction(sens, ref_mag, PPIparams, N_coils, gadNoiseDir, scaleNoiseCov, vrc_mask_thr, noise_cov_power)
%**************************************************************************
%
% vrc_phase_correction
%
% input sens: image space sensitivities [RO, PE1, PE2, N_order,... |
a75537fa871aa7c45f46f958de0985b485c5f09ee50f823542c9a0c76354231a | MATLAB | 4,051 | 98 | clc; clear;
load('jrr_tyr_ccc_peri.mat');
ccc_peri_together = mean(peri_all_stack4(:,8:13)');
ccc_peri_apart = mean(peri_all_stack5(:,8:13)');
ccc_peri_diff = ccc_peri_together-ccc_peri_apart;
load('/Users/jglab/Desktop/lfp_coh_raw/jrr_tyr_cc_SaveData/jrr_tyr_cc_peri.mat');
cc_peri_together = mean(peri_all_stack4(:,... |
f0b5e8ae567a882545ae61af99046da8dab497a947b9e915d4a92217363fb4fb | MATLAB | 4,057 | 119 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2019 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% mo... |
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