sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0cafb9c2547772c591c9014d8c56d52f8a770fc207762f6f3571a79965f8da65 | MATLAB | 4,061 | 101 | classdef NullModelAnalysisUnit_GeneSurrogate
% Holds and executes a single null model analysis, leveraging ConnectomeAnalysisRunner
properties
AnalysisRunner ConnectomeAnalysisRunner
WiringPISimilarity
end
methods
function obj = NullModelAnalysisUnit_GeneSurrogate(surrogateGene... |
8ef2ec08fd66cd4c51a69566615ba76b94ac17788704543d7201f84527dd60ba | MATLAB | 4,070 | 125 | function outpict = imfilterFB(inpict,fk,varargin)
% OUTPICT=IMFILTERFB(INPICT,FK,{OPTIONS})
% Filter an image using a specified filter kernel.
%
% This is mostly a passthrough to the IPT function imfilter(), with an internal
% fallback implementation to help remove the dependency of MIMT tools on the
% Imag... |
292fcc9df4b938f139aa40127410bd37c220c66182b1e0e28191c3209f7789b4 | MATLAB | 4,078 | 160 | %
% 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... |
29e5b3a98e98c01212db4a2e56754aebf2d52c4ebc5947167a8fbe5f1202f86f | MATLAB | 4,084 | 68 | function [SFC, medSFC, freq] = getSpikeFieldCoherence(LFP, MUA, fs, fsMUA, threshold, windowLength, nfft, maxFreq)
% by Mattia: computes Spike Filed Coherence (SFC) and median SFC.
% based on this paper from Pascal Friese https://goo.gl/quC115
%
%% input:
% LFP : entire signal
% ... |
8377dfe331abbc740e9639303160eacf3f6a0bd981f02f11165d22b987ae1a3c | MATLAB | 4,084 | 104 | function [intervals] = inter_trial_intervals(cfg, MuseStruct, force)
%% Make overview of data as segmented by markers aligned to (first) peak
binwidths = [1, 1, 0.25, 1, 1, 0.25, 1, 0.25];
binlimits = [60, 60, 15, 60, 60, 15, 60, 15];
fname = fullfile(cfg.datasavedir, [cfg.prefix,'timings_intervals.mat']);
if nargin... |
c64df16aaa4489969e79f7e4a561038b2ce630d53e828873565734bdab9d5cf1 | MATLAB | 4,087 | 106 |
function [spike_LFP] = spikeLFP(cfg, MuseStruct, SpikeRaw, force)
fname = fullfile(cfg.datasavedir,[cfg.prefix,'spike_LFP.mat']);
if exist(fname,'file') && force == false
fprintf('************************************\n');
fprintf('*** Loading precomputed spike-LFP data ***\n');
fprintf('*****************... |
1033909786f43e74adceb5353dba01a28306b252f43d5de53b6dad53200f2ddf | MATLAB | 4,092 | 89 | function SUAdata = getRipplesSUAspiketimes(experiment, RespArea, save_data, repeatCalc)
% by Mattia
% get SUA spike times with respect to ripples
% usual inputs
if strcmp(RespArea, 'HP')
folder2save = 'Q:\Personal\Mattia\SharpProject\results\ripples SUA\';
folderSUAspiketimes = 'Q:\Personal\Mattia\SharpProject... |
fc6775c073267583c9af8ee1387fc2129072f6df9ba44bebf02b50cf6e9244b3 | MATLAB | 4,097 | 124 | function outpict = imresizeFB(inpict,scale0,varargin)
% OUTPICT=IMRESIZEFB(INPICT,SCALE,{METHOD},{OPTIONS})
% Resize an image array.
%
% This is a passthrough to the IPT function imresize(), with an internal
% fallback implementation to help remove the dependency of MIMT tools on the
% Image Processing Tool... |
dfbfb9314228b7b248f6ca9298b360cd9ada0dc626c1cbf917831df14c6ef42a | MATLAB | 4,117 | 187 | function [c, colors] = bipolarcmapB(m, cRange, method, colors, method_param)
% Returns an approx. bipolar colormap centered at zero (in cRange). Zero
% maps to black.
%
% method is type of interpolation to be used. It can be
% ['sigmoid'], 'linear', 'quadratic', or 'cubic'
%
% method_param defines the parameter for... |
1bf32f4398f80236e787ff4995f98e8f2776971e39481c6222842667db1ebb58 | MATLAB | 4,130 | 107 | function out = Pyramid_astro
out{1} = @init;
out{2} = @fun_eval;
out{3} = [];
out{4} = [];
out{5} = [];
out{6} = [];
out{7} = [];
out{8} = [];
out{9} = [];
out{10}= @Ia;
% --------------------------------------------------------------------------
function dydt = fun_eval(t,kmrgd,par_Is,par_Id,par_gsd,par_gCa,par_p,par... |
219eda63a2b5082db5f25cded8c728f36bf11533ccda20fa3d855a2c170b5d95 | MATLAB | 4,130 | 109 | function coef_vals = multi_infer(dictionary_n, x_im, infer_type, opts)
% coef_vals = multi_l1ls(dictionary_n, x_im, infer_type, opts)
%
% Function to perform inference on a multitude of test vectors. The
% inference algorithm given by infer_type is run on each column of x_im
% with repect to dictionary_n.
%
% Inputs:... |
adc0e09c223b9bb5ced3e5c564db0b0631faae7257ea429a5d7e1d992ec43d7e | MATLAB | 4,137 | 110 | %% main script for mismatch analysis - use only correct trials
framerate = 30;
filterSize = 1.5;
MaxRZRadius = 5;
main_path = "C:\Users\ewell\Desktop\TestCodeGitHub\"; % change this only
rootdir = strings(2,1);
rootdir(1) = strcat(main_path, "\Discrimination 2025 data\CA1 miniscope data\");
rootdir(2) = ... |
510a02ab5e2b44535b92356bff378e28ea4dd9cb46f51dc6c29bc0af48470627 | MATLAB | 4,147 | 120 | function outpict = gbcam(inpict,cmode,upscale)
% OUTPICT = GBCAM(INPICT,{CMODE},{SCALE})
% Emulate the appearance of a photo taken with a Nintendo GameBoy camera.
%
% Images are centered, scaled, and cropped to fit the output frame. If you want
% your image located differently, prepare it accordingly.
%
% You m... |
adb4839ea5d4d66d4828ff7f697aed201a4e58944d084d90b120c3c7f2810503 | MATLAB | 4,148 | 113 | %% Resamples f(t) by computing the average in bins of width deltaT aligned to t0 (t0 is constrained to be a bin center).
%
% Syntax:
% [binnedF, tCenters, t0Index] = binnedResample(t, f, t0, deltaT, [fLo = f(1)], [fHi = f(end)])
% t is assumed to be monotonic.
%
% The average f(t) is computed in each bin by li... |
bd7077e0ee3086ff88ef97caf2ce90a74b399392a979e891c672bbbd91af701c | MATLAB | 4,148 | 127 | function auxiliary_td()
% Creates auxiliary plots for TD learning
% ---------------------------------------------------------------------
% Copyright (C) 2024 Simon R. Steinkamp
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public Lice... |
bbb7a75e7503d6ad1dc4736df2648a4fe920b2ddd3490ec8f083ed7f8a74605d | MATLAB | 4,150 | 96 | % main_script.m
%% Startup
clear; clc;
startup_SPERRFY; % path setting
%% Load data
main_import_processed_data; % import data (.mat)
main_data_preparation;
main_parameter_setting;
%% Run main data analysis
rng(1)
mouseConnectomeDataAnalysis = ConnectomeAnalysisRunner(connectomeMatrix, geneExprLevels,crossInfo, ..... |
3bda33be60815ae9c9f04211bd8263addef8799679ea7a8316c6ab8228bd519b | MATLAB | 4,159 | 120 | %% PCA for weighted datasets, as adapted from Delchambre 2015.
%
% Delchambre, L. "Weighted Principal Component Analysis: A Weighted Covariance Eigendecomposition
% Approach." Monthly Notices of the Royal Astronomical Society 446, no. 4 (February 1, 2015):
% 3545–55. doi:10.1093/mnras/stu2219
%
% Function d... |
c1df03de4e4928e170ce66009e21777269c3ea989635e9dd7eb7b3d45122b9b8 | MATLAB | 4,160 | 78 | function [all_predictions_read] = read_predictions(participant, path_saved_predictions)
%% Prepare data for training.
% Reads the predictions, of the bs_to_tap models, saved as h5 file,
% for all files from one participant
%
% **Usage:** [all_predictions_read] = read_predictions(participant, path_saved_predictions)
%
%... |
bc4139504059b04e18eeb89254bbf48a1da2d0da6c35cb4f0697b4f7c5e4c3e5 | MATLAB | 4,163 | 123 | function [y,yy]=nt_zapline(x,fline,nremove,p,plotflag)
%[y,yy]=nt_zapline(x,fline,nremove,p,plotflag) - remove power line artifact
%
% y: denoised data
% yy: artifact
%
% x: data
% fline: line frequency (normalized to sr)
% nremove: number of components to remove [default: 1]
% p: additional parameters:
% p.nf... |
67998878054d8911d128f0081889d4c10cf11bc3ba8a9c7e91438cb3e30d3953 | MATLAB | 4,168 | 93 | %% demonstration.m
%% Startup
clear; clc;
startup_SPERRFY; % path setting
%% Data Preparation
main_import_processed_data; % import processed data (.mat)
main_data_preparation; % make basic objects for analysis
%%
% Figure 3a
f3a = FigMaker.imageConnectionMatrix_MRColorLabels(connectomeMatrix,crossInfo);
%% Paramet... |
d9b27374b5f3f44c9cdbb98a0840789d787f78bdfba3dce41484768124136e18 | MATLAB | 4,170 | 134 | %clear all;
load([pwd '/init_data/var_combos.mat'],'var_combos','var_names');
load([pwd '/init_data/var_vectors.mat'],'var_vectors');
namesOfNeurons = {'TRN_PV','TRN_SOM',...
'TC_MGB','TC_HO'};
num_rows=4; num_col=1;
numPerBlock = 1000;
[lpp, ~] = size(var_combos);
maxNumBlocks = ceil(lpp/numPer... |
c4e41dca6828378f234dd71fc3d60996108400840c514e52e09e6ea4a633831b | MATLAB | 4,171 | 134 | %clear all;
load([pwd '/init_data/var_combos.mat'],'var_combos','var_names');
load([pwd '/init_data/var_vectors.mat'],'var_vectors');
namesOfNeurons = {'TRN_PV','TRN_SOM',...
'TC_MGB','TC_HO'};
num_rows=4; num_col=1;
numPerBlock = 1000;
[lpp, ~] = size(var_combos);
maxNumBlocks = ceil(lpp/numPer... |
1fe9f7d6bd862ece4b3881e37057c19853d9b17d2db21581c8b001f9e4a86e21 | MATLAB | 4,177 | 124 | function tileCoef = getSTTC(N1v, N2v, dtv, Time, spike_times_1, spike_times_2)
%sttc calculates the spike timing tiling coefficient
% Originally written in C by Cutts and Eglen
% https://github.com/CCutts/Detecting_pairwise_correlations_in_spike_trains/blob/master/spike_time_tiling_coefficient.c
% See their 2014 ... |
882e5404306643b54d85e3737ef1047a8eef00efbdf6406faac0024e32c926fa | MATLAB | 4,181 | 87 | function [cfg, MuseStruct_new] = PET_add_interIED_epochs(cfg, MuseStruct_orig, markername, toi, include_startend_of_file)
% Define periods between two successive markers
MuseStruct_new = MuseStruct_orig;
cfg.interIEDtrials_maxlength = ft_getopt(cfg, 'interIEDtrials_maxlength', Inf);
for ipart = 1 : size(MuseStruct_or... |
bd72c0012f8da3ec98fe984e94b0d326ef74782d5e07135cd3a77c83fb217da7 | MATLAB | 4,185 | 97 | function [lh_rot, rh_rot] = CBIG_spin_test_rotation_surf(mesh, num_rotations, seed, sym_flag)
% [lh_rot, rh_rot] = CBIG_spin_test_rotation_surf(mesh, num_rotations, seed)
%
% This function is used to compute the new vertex points of the left and right
% hemisphere after rotation, relative to the original vertex points ... |
0303d2a43b8203287444d6b7a8bd31fcb0f68fb9b9d2cac45c8be93afdc842c0 | MATLAB | 4,213 | 108 | function [data] = CBIG_read_1header_from_Ncsv( csv_files, subject_header, subjects, data_header, data_type, delimiter )
% [data] = CBIG_read_1header_from_Ncsv( csv_files, subject_header, subjects, data_header, data_type, delimiter )
%
% Given a header name and multiple CSV files, this function find which CSV
% file t... |
a3b02aa4db8a15cf2ca5e30970cdea60fa930b3be878a54fc7d90dc838c81c56 | MATLAB | 4,214 | 123 | function Result = ini2struct(FileName)
%==========================================================================
% Author: Andriy Nych ( nych.andriy@gmail.com )
% Version: 733341.4155741782200
%==========================================================================
%
% INI = ini2struct(FileName)
%
% This... |
694870b477f5e1ee4d83c26d19722eadd4208a6b303ef70851799515ce0f3881 | MATLAB | 4,217 | 145 | function [B S stat] = GraphSC(X, W, num_bases, alpha, beta, num_iters, Binit, pars)
% Graph regularized sparse coding algorithms
%
% minimize_B,S 0.5*||X - B*S||^2 + alpha*Tr(SLS') + beta*sum(abs(S(:)))
% subject to ||B(:,j)||_2 <= l2norm, forall j=1...size(S,1)
%
% Notation:
% X: data matrix, each column is... |
e0a43ba01b56ed1aa2feb2165b1009ff6194e30deb0d9e11004a2a5f713c1e53 | MATLAB | 4,219 | 89 | %% main script to detect onsets and split them based on rest/run and ctxt. Gergely Tarcsay, 2025. To run this properly, make sure that the main_path is set.
%% input data: output of minian (.nc file containing spatial and temporal information for each unit); dlc processed position that contains miniscope frame timesta... |
1c80a48389dd44f3a6946cb678dd10da3ee6a6d703ddbdfd41cb7de9712554e9 | MATLAB | 4,235 | 128 | function outpict = imtile(inpict,tiling,varargin)
% OUTPICT=IMTILE(INPICT,TILING,{OPTIONS})
% Take a 4D image stack and rearrange the individual frames
% into a single-frame image using a rectangular tiling.
%
% MIMT imtile() creates a name conflict with IPT imtile(). I created MIMT imtile()
% ... |
daa492cc1f20ede623e3854973b79fc82ba66f520e91e230acddd54070379e32 | MATLAB | 4,237 | 111 | function [Sc,Cmat,Ctot,Cvec,Cent,f]=CrossSpecMatc(data,win,params)
% Multi-taper cross-spectral matrix - another routine, allows for multiple trials and channels
% Does not do confidence intervals. Also this routine always averages over trials - continuous process
%
% Usage:
%
% [Sc,Cmat,Ctot,Cvec,Cent,f]=CrossSpecMat... |
7be1cd794fd2b9fc34364879daa5816ae87eab96b126e6428a66c28ed2cd8014 | MATLAB | 4,242 | 115 | function [DG_point,DG_accepted,DG_line_image,outer_points,inner_points,hilus_points]=trace_DG_outline(settings,images_all,composite_img,roi_names,roi_idx,roi_fname,magnification,roi_subfolder)
%%% Trace DG outline - Version 4 %%%
DG_accepted=0;
% set(0, 'DefaultFigurePosition', settings.screen_pos);
nuclear_image... |
90f2634498b863620fd2c71aaf2766ee1b8b6886e65ad3c7687604418e011a4b | MATLAB | 4,244 | 127 | 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... |
768b5fd59fbdb5882d929b6a6941c13acf096fb38c3dd3672112bf39055d9366 | MATLAB | 4,246 | 80 | function [isSignificant,adjusted_pvals,alpha]= bonferroni_holm(pvals,optional_alpha)
%% bonferroni_holm, bonferroni_holm(pvals), bonferroni_holm(pvals, alpha);
% Corrects for testing multiple hypotheses.
% This method is more powerful, but less conservative than the Bonferroni method.
% Fixed so that ad... |
96e7bb7a044ad02d4692b59d71dfe5e0f67d8117b5760a83008b91422a8a9c33 | MATLAB | 4,267 | 156 | function [outmask,varargout] = pickblob(inmask,points,varargin)
% OUTMASK = PICKBLOB(INMASK,POINTS,{OPTIONS})
% [OUTMASK LIDX FIDX] = PICKBLOB(...)
% Given a binarized image and one or more sets of points in the image,
% return a mask describing the blobs which contain the points.
%
% INMASK is typically ... |
3ac4eeb8c8e73769233cd1527dd2990b1e620c0dc70b77656f6d49518412dc39 | MATLAB | 4,273 | 131 | % Written by Andrew Lin
% This script processes multiple movies all with the same odor timing,
% saves the activity maps, and calls the map-display function
% 1. Read info on which files, bkgnd signal etc. from user-created text
% file.
% 2. Call activityMap to get map
% 3. Save all the maps in an array
% save to .mat... |
6d9530e8759eeffa7a41ed258935015e6dfe054849d047f4165c7261b0ce78fa | MATLAB | 4,276 | 140 | function outpict = randspots(s,numspots,spotbounds,spotopacity,shape,fill)
% RANDSPOTS(SIZE, NUMSPOTS, SPOTBOUNDS, SPOTOPACITY, SHAPE, {FILL})
% returns an image littered with spots of randomly selected
% location, size, and opacity
%
% SIZE is a vector specifying the output image size
% may be 2-... |
df4acd61460a2f9494905c3091c2279c193bf3535217fac4e0d2cb142a8cf223 | MATLAB | 4,291 | 117 | function [roi,roi_accepted,images_all,composite_img,roi_fname,settings]=rotate_roi(settings,angle_accepted,roi_names,images_all,composite_img,rectangle_roi_subfolder,roi_idx,idx,mouse_name)
%%% Rotate ROI - Version 2 (MGG) %%%
roi_accepted = 1;
% set(0, 'DefaultFigurePosition', settings.screen_pos);
if angle_ac... |
5fbd7a0cbc259b87eaf20fcff17d8c93745aa7847810604a5b4326b12024e02f | MATLAB | 4,295 | 125 | function Result = ini2struct(FileName)
%==========================================================================
% Author: Andriy Nych ( nych.andriy@gmail.com )
% Version: 733341.4155741782200
%==========================================================================
%
% INI = ini2struct(FileName)
%
% This... |
4edd1fdbf4135ef5cafc2ad17136541e0c056bdaa13456d5c986779dfbdb2a36 | MATLAB | 4,303 | 144 | function [data_all] = ft_read_neuralynx_interp(fname)
% FT_READ_NEURALYNX_INTERP reads a cell-array of NCS files and performs interpolation
% and gap-filling of the timestamp axis to correct for potentially different offsets
% across channels, and potential gaps within the recordings. All samples are being
% read out.... |
693fb97d700b4dfdf79136285732e005a41f283124534d4916b995afa4a956b3 | MATLAB | 4,311 | 105 | function [TFR] = doTFRcontinuous(cfg,MuseStruct,force)
% This file is part of EpiCode, see
% http://www.github.com/stephenwhitmarsh/EpiCode for documentation and details.
%
% EpiCode is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% ... |
9dfa880a0fdfdbe156290f31b7f1ac1f37f0457a0993f76148d7b4f62528952f | MATLAB | 4,327 | 118 | function fMRI_epicorr_t1based_bfp(epi_filename, ref_filename, fmri,t1,config)
% epi_filename: input epi file
% ref_filename: reference epi volume that will be used for correction
% fmri: fmri basename (BFP BIDS format)
% t1: t1 basename (BrainSuite BIDS format)
% config: see preprocessing config file from BFP... |
93a5e361e3c051e72173bdb0d55305a3058395c1ace4efbfb0ace64f882d3573 | MATLAB | 4,328 | 162 | function varargout = ft_pimpplot(hfig,cmap,pimp,set_printing_properties)
%--------------------------------------------------------------------------
% FT_PIMPPLOT can pimp single channel time frequency representations and
% topographical representations created by FieldTrip. Basically, it
% replots the plots created by... |
009c1694ec1af6f188c134569517cbbfa49a97a0fa96d7e0b8aa7f912d675d69 | MATLAB | 4,331 | 186 | function outpict = jellyroll(inpict,varargin)
% JELLYROLL(INPICT, {OPTIONS})
% Remap the columns of an image into a spiral with the same geometry as the source image.
%
% INPICT is an I/IA/RGB/RGBA image of any standard image class
% OPTIONS include the following keys and key-value pairs
% 'direction' spe... |
423c28046778d0d56a14000707883498802c4dde4310ae314eebfed412c54d46 | MATLAB | 4,335 | 162 | function varargout=shadedErrorBar(x,y,errBar,lineProps,transparent)
% function H=shadedErrorBar(x,y,errBar,lineProps,transparent)
%
% Purpose
% Makes a 2-d line plot with a pretty shaded error bar made
% using patch. Error bar color is chosen automatically.
%
% Inputs
% x - vector of x values [optional, can be left em... |
da20e1005d87bb5bc9f42dfd429147874e782cfbdefd3f8448dad158f88392bf | MATLAB | 4,338 | 125 | function [coeff, cluster_data_avg, SN_data] = Reachr_transformation_AMR(data, varargin)
%'Reachr_transformation' writen by Ergi Spiro; edited by AMR. Now takes in
%typical data structure with added flash_type and trigtimes (see ....).
%Only takes in one data structure compared to 'Reachr_transformation'.
% argum... |
ff43bc4840693a62ba737873364d879be2100996aaeb8ae738c25e20dfa6a25b | MATLAB | 4,340 | 135 | function [senseMaps, eigenValues] = PISCO_bart_loop(input, output, FFT_interpolation, Threads)
%% Loading data
addpath(fullfile(getenv('BART_TOOLBOX_PATH'), 'matlab'));
kData_raw = double(readcfl(input));
kData = squeeze(kData_raw); % Remove singleton dimensions
size(kData_raw)
[N1, N2, Nc, Nz] = size(kData);
% ... |
3ca38b220774c2e5e555d90b9078da9a2575d0f9e9246b993f88874863c89aba | MATLAB | 4,345 | 114 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 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 ... |
7fc6b37fa35b2ef7b0e00fe2c6f5f5b01bda94cc988938fbb07dd9d5fa1f921c | MATLAB | 4,378 | 155 |
warning('off','all')
addpath /network/lustre/iss01/charpier/stephen.whitmarsh/WhitmarshEpilepsy
datapath = '/network/lustre/iss01/epimicro/patients/raw';
outputdir = '/network/lustre/iss01/charpier/stephen.whitmarsh/data/qualitycheck';
% loop through patients
clear patlist patdatlist prefix
i = 1;
dlist = dir2(fullfi... |
4960f6916ff346f8e69c32fb4226e48d213e640f20a5cf3014e9aece9f134270 | MATLAB | 4,386 | 134 | % ===============================
% Fig 3D : Monthly variations in average water level and flow rate
% + Table 2 statistics output (based on ALL monthly water levels)
% ===============================
clear; clc; close all;
% ===============================
% Load data
% ===============================
data... |
f8137c7b16aaa0665ed7432c913d7122eb9bdc7a71692b01a556626f54dfc3e0 | MATLAB | 4,387 | 129 | function FigureS1
config = pnh_setparams;
macro{1} = {'_1pNs_1', '_1pNs_2', '_1pNs_3', '_1pNs_4', '_1pNs_5', '_1pNs_6', '_1pNs_7', '_1pNs_8'};
macro{2} = {'_Casd_1', '_Casd_2', '_Casd_3', '_Casd_4', '_Casd_5', '_Casd_6', '_Casd_7', '_Casd_8'};
macro{3} = {'_TNmi_1', '_TNmi_2', '_TNmi_3', '_TNmi_4', '_TNmi_5', '_TNmi... |
5670854df818e262f89c86041759b6dce4f11543a6026dc2d0ef3b8e0c6f6a42 | MATLAB | 4,394 | 148 | function outpict = imdetile(inpict,tiling,varargin)
% OUTPICT=IMDETILE(INPICT,TILING,{OPTIONS})
% Take a single-frame image, subdivide it into tiles, and rearrange
% into a 4D image stack. Conceptually, this is the reverse of an
% image tiling process as would be performed with IMTILE.
%
% INPICT is a s... |
71535949a4fbabb19622f7a1ff2794fb89aad4386e88758ab0233bde545d1032 | MATLAB | 4,394 | 120 | function [md2D, markers, xcenterw, ycenterw] = mdprepare_single(w1data, azimuth, invert, trans, offx, offy, plotsize, walkersize, xcenter, ycenter,scramblespat, scrambletemp,fr)
%DC hacked to allow scrambling (spatial and temporal) of the md walker data
%[md2D, markers, xcenterw, ycenterw] = mdprepare_sin... |
4a45614df65c61ac411df6880174bf2098e704e3f468fcc58852c656384cb632 | MATLAB | 4,395 | 182 | function generate_eig_file(L1, L2, L3, V1, V2, V3, outputFileName)
%GENERATE_EIG Generate .eig file. Eigenvalues (L1, L2, L3) &
% Eigenvectors(V1, V2, V3) can be nii structures or .nii.gz or .nii files.
%
% outputFileName - file name with/without extension (with full path)
%
workdir = tempname();
mkdir(workd... |
89b11d7f1333b9859876ba34f7ce7065847fea8380c5a8188bf63c8087704e7a | MATLAB | 4,399 | 164 | function I = mi_mixture_gd_vec(x, y, Ym)
% MI_MIXTURE_GD_VEC Vectorized MI calculation between multiple Gaussian variables
% and a common discrete variable in bits from Gaussian mixture.
% I = mi_mixture_gd_vec(x,y,Ym) returns the MI between the (possibly multidimensional)
% Gaussian variables x and the d... |
6eb857e7ec7983ce4c97c5bb622bec76baa47c5aed02b42649d26a1dc636c15e | MATLAB | 4,401 | 103 | function slope = getSlopePC(result, pCorrect, unscaled)
% function slope = getSlopePC(result, pCorrect, unscaled)
% This function finds the slope of the psychometric function at a given
% performance level in percent correct.
%
% result is a result struct from psignifit.
%
% pCorrect is the proportion correct where to ... |
a6bab0e4d55949e2ce951b0542def92d2ac9562a310601e5450fb6dec002c114 | MATLAB | 4,414 | 144 | function [I,rc] = line_plane_intersection(u, N, n, M, verbose)
%% line_plane_intersection : function to compute the intersection point
% between the (N,u) line and the (M,n) plane of the 3D space.
%
% Author & support : nicolas.douillet (at) free.fr, 2019-2020.
%
%
% Syntax
%
% [I,rc] = line_plane_intersection(u, N, n,... |
70fd72f223313a520b8ac3be6e2714c0444b3d0c4b130898af5d129b88d05bce | MATLAB | 4,425 | 156 | function plotWindowedData(cfg, MuseStruct, dat)
ncols = 1;
nrows = size(dat, 2);
cm = cool(5);
ipart = ft_getopt(cfg, 'ipart', 1);
i = 1;
clear bad_t1 bad_t2
for idir = 1 : size(MuseStruct, 2)
for ibad = 1 : size(MuseStruct{idir}.markers.BAD__START__.clock, 2)
bad_t1(i) = MuseStruct{idir}.mark... |
928a2681518cf6994fb5202c164cda0e28c76764704bee75a60bca768c7395bd | MATLAB | 4,429 | 106 | %% wrapping function for vector remap analysis
function [All, Cohort]= WrapVectorRemap(workdir, discrimination)
All.CellComposition = zeros(length(workdir),4); %
All.OrthogonalHDC = zeros(length(workdir),2);
All.VectorRemap = [];
All.SpatialRemap =[];
All.Curves = [];
All.Length = [];
All.Angle = [];
All.Con... |
ed9ace131f9001f09251593fd4b97dd820328ae4618d806b9d9f12d56434e7eb | MATLAB | 4,430 | 112 | function MuseStruct_concat = concatenateMuseMarkers(cfg, MuseStruct,force)
% Concatenate markers over all the dirs
fname_out = fullfile(cfg.datasavedir, sprintf('%sMuseStruct_concatenated.mat', cfg.prefix));
if exist(fname_out,'file') && force == false
fprintf('Reading %s\n',fname_out);
load(fname_out,'MuseSt... |
6e72df4c2a94a53aaddaf2f4e5583504cfe43ff8dc289771e5c30ad06eca0a37 | MATLAB | 4,432 | 129 | function Figure4
% settings
cfg = pnh_setparams;
nodulenr = [1, 4];
seizurenr = [1, nan, nan, 2];
% seizurenr = [1, nan, nan, 1];
channelnr = [1, nan, nan, 1];
ipart = 1;
xlimits = [-1, 5];
% load data
x = load("\\lexport\iss01.charpier\analyses\vn_pnh\data\pnh\2230-SpikeTrials_Timelocked... |
14720016e5fe7cbfde332ecd48816b62be4d7ec5e295e65d320ff374a7827bde | MATLAB | 4,438 | 99 | %% this code investigates the effect of varrying network parameters
% one at a time, PN-KC weights, KCs spiking thresholds and number of inputs
% on the memory performance of model fruit-flies Drosophila
% this simulation uses realistic odor responses recordings from
% (Hallem-Carlson 2006) and transformed from ORN to ... |
bcf3420a863ad19e8ab9f515d7d1fe9c21420a28fc5f99dd8ce1dc74e9d97e3d | MATLAB | 4,442 | 105 | function skeletons = normalizeSkeletonsFlpTagCalyxDivide(filenames, spacing)
% Let's start with filenames as an cell array of strings specifying the .mat
% files
% calling function must supply the value of 'spacing' which is the node
% spacing on the 'standardized' skeleton
% The purpose of this function is normaliz... |
27988fa05b67ea64ecabb230408ddb8b0f8e9d61d2cc6f55e696927ebe341b2b | MATLAB | 4,452 | 109 | function [csc_trials, stimulus_ids] = cpm_trials_to_csc(trials, n_timesteps, ...
csc_idx, ...
relevant_stimuli, ...
reward_timestep, ...
... |
31c9baace1bc26019facb32fc003e1c1e27e070d191ae928c00aaeb799ce5ffb | MATLAB | 4,452 | 118 | function dtx_eegrodents_cluster(ipatient, config_script)
%% 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\... |
9efde431b754cb8dbd02a11ca018947e63e0b7d49fe0e5679c34b0919b8ebc43 | MATLAB | 4,458 | 136 | function G = G_matrices_2D(kCal, N1, N2, tau, U, varargin)
% Function that calculates the G(x) matrices directly without calculating
% H(x) first.
%
% Input parameters:
% --kCal: N1_cal x N2_cal x Nc block of calibration data,
% where N1_cal and N2_cal are the dimensions of a
% ... |
bc04dbc086bedea60108285535ae7adb3443f14795f3ddf079f222518c198669 | MATLAB | 4,460 | 132 | function RGBnew = uwredcomp(RGB,varargin)
% OUTPICT = UWREDCOMP(INPICT,{OPTIONS})
% Adjust underwater photographs to compensate for wavelength-dependent light
% attenuation and contrast loss due to diffusion effects.
%
% Roughly based on:
% Underwater image enhancement based on red channel weighted compen... |
c3be5c12af8a18fed3090101cf156b4ed3ae8fbaff3a4d92efc078858c742503 | MATLAB | 4,460 | 94 | function [stPR, pop_coupling, pop_coupling_1sthalf, pop_coupling_2ndhalf] ...
= get_stPR(spike_matrix, max_lag, animal_name, repeat_calc, save_data, output_folder)
%% by Mattia 09.19
% compute stPR (spike-triggered population rate) and population coupling
% as described in Okun et al., 2015 Nature.
% inputs:
% - ... |
80e7e2671fc9790efecef5157e801c0b3aba920d122ea5f3ca879d27f204013a | MATLAB | 4,465 | 106 | % -------------------------------------------------------------------------------------------------
% (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... |
547a7f38dfab5136da8525b53e41556df0f923264435a260ce2e69461ed7f18e | MATLAB | 4,467 | 119 | function [md2D, markers, xcenterw, ycenterw] = mdprepare_single(w1data, azimuth, invert, trans, offx, offy, plotsize, walkersize, xcenter, ycenter,scramblespat, scrambletemp,fr)
%DC hacked to allow scrambling (spatial and temporal) of the md walker data
%[md2D, markers, xcenterw, ycenterw] = mdprepare_sin... |
67cc11176c04e7793b7fdf80bfb75649b872aefe26c59af68469cc77c812a9da | MATLAB | 4,471 | 135 | function outpict = imappmat(inpict,mat,varargin)
% OUTPICT=IMAPPMAT(INPICT,MAT,{OUTOFFSET},{INOFFSET},{OUTCLASS})
% Apply a color transformation matrix to an image, similar to IPT imapplymatrix().
%
% INPICT is an image array of any standard image class; 4D images are not supported.
% MAT is a matrix of size C0... |
b86a34c5d71ee07551ddc09be21a26ee24ea6de40f40c6e805a8b74ddc492d72 | MATLAB | 4,471 | 109 | function BatchResults = Batch_InterictalDetection(filename,threshold,channel,toDenoise)
% USAGE
%
% BatchResults = Batch_InterictalDetection(filename,threshold,channel,toDenoise)
%
% Main function for the interictal detection. Filter the signal, receive
% the interictal peaks, group the peaks to detect an ev... |
fa29214b218eb863b1751ec24de96bfd2cc3ef7fa06b42a185f7491ffd659b6d | MATLAB | 4,491 | 168 | function inpict = imlnclite(inpict,varargin)
% IMLNCLITE(INPICT, {OPTIONS})
% Levels & Curves tool for images. This is a simplified version of IMLNC
% for reduced memory requirements when operating on very large images.
% Required parameters can be determined using STRETCHLIMFB or IMMODIFY,
% ... |
3a42e739845f43bf22d91b468a762e1dc66888c3d375d816e51debc8fff74098 | MATLAB | 4,506 | 113 | function pnh_cluster(ipatient)
%% Analysis script for Valerio Frazzini's study on electrophysiology of pathoanatomy
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
% requires bandpassFilter.m from Mario
% requires releaseDec2015 from Neuralynx website
%% Add path
restoredefaultpath
%% Stephen's paths
if i... |
9af02f347c4382ce9dc8f93b6bc4d75b4daf6e252886c7b166273651f8dc8849 | MATLAB | 4,511 | 121 | function wideTable = tableLong2wide(longTable, factorColumns, valueColumn, idColumn, newVarPrefix)
%% Convert a long-format table to wide format with multiple factors.
% If 1st argument is a file path, the table is imported from there.
%
% INPUTS:
% longTable - Input table in long format, or file path to such t... |
80421ac29e83406151c65891802ebd3cade437cdc89368febb11bcb573326579 | MATLAB | 4,521 | 116 | function [Sc,Cmat,Ctot,Cvec,Cent,f]=CrossSpecMatpb(data,win,params)
%
%
% Multi-taper cross-spectral matrix - another routine, this one allows for multiple trials and channels
% Does not do confidence intervals.
% Also this routine always averages over trials - binned point process
%
% Usage:
%
% [Sc,Cmat,Ctot,Cvec,C... |
4645fc7ee99c4f08b86c1d480d72e978c44b919fb014eff0c18af9f0d18c805a | MATLAB | 4,529 | 98 | function wod_concatenateLFP(slurm_task_id)
% code copied from writespykingcircus.m
% Must used a modified version of ft_writedata to give the good channel
% name to Muse. On added line, which is commented with %Paul.
if ispc
addpath (genpath('\\lexport\iss01.charpier\analyses\wod\EpiCode\shared'))
addpath (gen... |
2d92e1df0c2e97c3fa0e4c11b0a25a10a9c3da373e86a07ea0bba4d4b66c022a | MATLAB | 4,531 | 107 |
% This is a sample main file that reads two grayordinate fmri files generated by bfp and outputs the synced files.
clc;clear all;close all;
addpath(genpath('/home/ajoshi/coding_ground/svreg'));
addpath(genpath('../'));
load LBO_right
LBOr=LBO;
load LBO_left
%ids={'sn8133','sn4055','tr4277','sn7915','sn5895','sn7602',... |
334bedf3d05f23d67040fd9fe9bd0705e4e049e7d8d2eaa78a0ee52553279350 | MATLAB | 4,531 | 101 | function plotOverviewPreictal(config, MuseStruct, SpikeTrials_windowed, SpikeStats_windowed)
% threshold artefacted based on total time artefacted per window
for ipart = 1 : size(config.directorylist, 2)
for iunit = 1 : size(SpikeStats_windowed{ipart}.window, 2)
SpikeStats_windowed{ipart}.window{iunit... |
0a9362c5c78b4d0de671b04ac7389387bb19d94eaf972339801ac269b5ee3d29 | MATLAB | 4,544 | 117 | %% DEMO_001 basic useage
% The Psignifit 101
%% save data in right format
% First we need the data in the format (x | nCorrect | total)
% As an example we use the following dataset from a 2AFC experiment with 90
% trials at each stimulus level. This dataset comes from a simple signal
% detection experiment.
data = ... |
2571333fe8669ec4c1f8f36762c9f3e5baa45f025a7e74288629348a849be458 | MATLAB | 4,547 | 159 | function outpict = padarrayFB(inpict,padsize,varargin)
% OUTPICT=PADARRAYFB(INPICT,PADSIZE,{OPTIONS})
% Pad the edges of an array (ostensibly an image) with zeros or other content as
% specified by the available options.
%
% This is a passthrough to the IPT function padarray(), with an internal
% fallback i... |
78277c0d59b2db9d269043ad6b20f2f40d324f4cf2ac66847db0fb64880b4235 | MATLAB | 4,562 | 114 | function next = morse_unfold_unaccelerated(input, PPIparams)
%% %**************************************************************************
%
% morse_unfold_unaccelerated computes sensitivities using MORSE and compute SENSE-1
% recon via S^H * data
% input "data" contains:
% a global header in ... |
e03d961fb176b34bee1187120f917f3329421a391a863cc5a235018d4cf8b53e | MATLAB | 4,568 | 118 | function [newPhi, newVarBound] = ...
CBIG_AuthorTopic_ComputeVariationalTerm__N_t(params, newPhi, ...
newVarBound, varBoundFlag)
% [newPhi, newVarBound] = ...
% CBIG_AuthorTopic_ComputeVariationalTerm__N_t(params, newPhi, ...
% newVarBound, varBoundFlag)
%
% Compute the expectation and variance of the count N_{.t..... |
e3e9a117ef7c4638d95163a7bd0a5f6fcef7c904da000722a7f465370972050d | MATLAB | 4,572 | 107 | function metadata = createMinimalOMEXMLMetadata(I, varargin)
% CREATEMINIMALOMEXMLMETADATA Create an OME-XML metadata object from an input matrix
%
% createMinimalOMEXMLMetadata(I) creates an OME-XML metadata object from
% an input 5-D array. Minimal metadata information is stored such as the
% pixels dimensio... |
9412d57dc2664fc97e1bd522759bcfa3145978d622f239a435ac61b81488cedc | MATLAB | 4,574 | 127 | function outpict = tonecmyk(inpict,Tc,Tm,Ty,Tk,Tsat,enforcement,presetmode)
% OUTPICT = TONECMYK(INPICT,TC,TM,TY,TK,TSAT,RANGETYPE,{PRESETMODE})
% Adjust image tone by adjusting CMYK components relative to the
% CMYK and saturation distribution in an image.
%
% This is based on Iain Fergusson's GMIC tools.
% https... |
84d80f34e2bd99c94e52370a93dda1d79041369329cc2e96d739f56e11c6edff | MATLAB | 4,580 | 104 | function [EEG, simple,ep_blind_bs,ep_blind_model] = decision_tree_alignment(EEG, BS,create_diagnostic_plot, participant_selection)
%% Decides when to choose the model based alignment, BS based alignment, or old alignment
%
% **Usage:** [EEG simple] = decision_tree_alignment(EEG, BS, create_diagnostic_plot)
%
%
% Input(... |
a81ab6bd2651f70c78ffdb6cf2140c0a20f27de8bda9d3db7e5f03676e4b1339 | MATLAB | 4,588 | 120 | % 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 it... |
6735d6f0b78fd0fbc7a254138be8e6e14b2121ffc90ef17338315fd82b59864c | MATLAB | 4,595 | 111 | function out = Pyramid_astro_exp_decay
out{1} = @init;
out{2} = @fun_eval;
out{3} = [];
out{4} = [];
out{5} = [];
out{6} = [];
out{7} = [];
out{8} = [];
out{9} = [];
out{10}= @Ia;
out{11}= @Ie;
% --------------------------------------------------------------------------
function dydt = fun_eval(t,kmrgd,par_Is,par_Id,p... |
dd2b0d236bf1dd6e4fd94847c57068a05073a2393cb2c40704594193243e0f79 | MATLAB | 4,596 | 181 | function addaxis(varargin)
%ADDAXIS adds an axis to the current plot
% you can add as many axes as you want.
%
% usage:
% use it just like plot, except, you need to specify the abscissa
% and the third input argument should be the axis limits, if at all.
%
% example:
%
% x = 0:.1:4*pi;
% plot(x,sin(x... |
1ffc1cb38cd31d154eb718eebbe346ae3b16476f476fab2fc2971ea8cbb96dcf | MATLAB | 4,604 | 139 | function [A B] = matchchannels(A,B,varargin)
% [A B] = MATCHCHANNELS(A,B,{MODE})
% Force correspondence between the channel arrangements of color tuples or images.
% One use may be when a color needs to be specified for use in an image. MATCHCHANNELS
% performs expansion or reduction as required for both i... |
f1b4b82d6b3550080cdf2930cfb41b2c907bf373c5a506a9cea8d42a7ecf8b7e | MATLAB | 4,605 | 151 | function outpict = imrotateFB(inpict,angle,varargin)
% OUTPICT=IMROTATEFB(INPICT,ANGLE,{METHOD},{BOUNDARY})
% Rotate an image array.
%
% This is a passthrough to the IPT function imrotate(), with an internal
% fallback implementation to help remove the dependency of MIMT tools on the
% Image Processing Tool... |
f679f1fc1201ed9dad0caf4c783b0d1d4d2628ed699293d3004d0332de852e86 | MATLAB | 4,607 | 101 | % With the same functionality as cvpartition, but fully customizable
classdef CustomCVPartition
properties (GetAccess = public, SetAccess = public)
%TYPE Validation partition type.
% The Type property is a string with value 'kfold', 'holdout',
% 'leaveout' or 'resubstitution'. It indicat... |
8988ce9654b72b4d51f596841b53e4c6f4ca6fdb3df5d4858a1e6330edc992cf | MATLAB | 4,620 | 104 | function [config, MuseStruct] = addSlidingWindows(config, MuseStruct)
% [config, MuseStruct] = addSlidingWindows(config, MuseStruct)
% Add a "window" field to the config and MuseStruct, allowing sliding
% time-window analyses for both LFP, TFR, FFT and spike data.
%
% ### Necessary input:
% cfg.prefix = pre... |
2ca441ee6caebda2803c7158fe7c716a68f0dc3cbba1429d9096c360ffcb4bba | MATLAB | 4,633 | 172 | function outpict = roiflip(inpict,mask,dim,varargin)
% ROIFLIP(INPICT, MASK, DIM, {CONTINUITY})
% returns a copy of the input image wherein all pixels
% selected by the mask are flipped along a specified dimension.
%
% INPICT is an I/RGB image of any standard image class
% MASK is an I/RGB logi... |
2efc3544fa03d7c555e93457256554c941436d4b463a0d70e5ddba2a7e6103ef | MATLAB | 4,636 | 151 | function [Amatrix,Binvector,Unit_order,As_order]=assembly_assignment_matrix(As_across_bins,nneu,BinSizes,display)
% Display the Assembly assignment matrix.
% USAGE: [Amatrix,Binvector,Unit_order]=assembly_assignment_matrix(As_across_bins,nneu,BinSizes,display)
%
% ARGUMENTS:
% As_across_bins - structure containing a... |
6e64cac4e5cba7490669784cd1b2097686c18b87176c8ba9bbaa19c7f862dafd | MATLAB | 4,641 | 122 | %% Analysis script for Valerio Frazzini's study on electrophysiology of pathoanatomy
%
% (c) Stephen Whitmarsh, stephen.whitmarsh@gmail.com
%
% requires bandpassFilter.m from Mario
% requires releaseDec2015 from Neuralynx website
%% Initialization
if isunix
addpath /network/lustre/iss01/charpier/analyses/stephen.... |
982a770bcc2f88b52f39a75fdfae8c44cfe57e8aa3ec46f33a21f5e788c9268c | MATLAB | 4,645 | 173 | function [u, u_hat, omega] = VMD(signal, alpha, tau, K, DC, init, tol)
% Variational Mode Decomposition
% Authors: Konstantin Dragomiretskiy and Dominique Zosso
% zosso@math.ucla.edu --- http://www.math.ucla.edu/~zosso
% Initial release 2013-12-12 (c) 2013
%
% Input and Parameters:
% ---------------------
% signal - t... |
3bc2405dc886fdf9f204a6212d969166c44fcd652e70047ec64611e33e459744 | MATLAB | 4,665 | 120 | % MVNRNDSMOOTHRESAMPLE Generate a n-by-d-by-nSamples matrix R of random numbers sampled from a
% data distribution D of size n-by-d, preserving the column mean and
% covariance structure D^T D.
%
% Inputs
% ========
% D : n-by-d matrix to rand... |
d50caa83bae8a1f64ce372630b2ca4fe2300b3c03db8a7e73be58b680970dd2a | MATLAB | 4,667 | 115 | function [cell_numbers, cell_type, cell_type_number] = get_cell_indices(datarun, cell_specification)
% get_cell_indices get cell numbers matching to the cell specification
%
% usage: [cell_numbers, cell_type, cell_type_number ] = get_cell_indices( datarun, cell_specification )
%
% arguments: datarun - datarun... |
d102bc83a7d0b8de68b1fc18cd1584ef4bfceb26b63cf0881d339858c374951d | MATLAB | 4,668 | 143 | function [idx,score_vector,score]=nt_split(x,depth,thresh,guard,minstep)
%[idx,score_vector,score]=nt_split(x,depth,thresh,guard,minstep) - split time series into intervals
%
% idx: index at which to split
% score: proportion variance reduced
% score_vector: score as a function of split position
%
%
% x: data (ti... |
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