sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
17367bb237bdc0330c5250465da3ace968dc02ba706013350e76db6dc30276f5 | MATLAB | 5,381 | 198 | function plot_fig_2ab_PeakMetrics_HFA(path)
% grand average structure
ga_0 = struct();
ga_25 = struct();
ga_75 = struct();
% colors
cb = {'#008450', '#EFB700', '#B81D13'};
%% Plot peak latency frontal
% load data
tbl = readtable(fullfile(path.data, 'SourceData.xlsx'), 'sheet', 'Fig_2a upper left');
ga_0.pfc.late... |
7d1b5793c8c7534683cdc21b102c1a7c6144e7214bb060308c35e1b754c3a5d5 | MATLAB | 5,389 | 149 | clear all
close all
clc
repo_home = '';
addpath(genpath(repo_home))
winning_model = '4P_SM_WSecdf_LEX_meanLevenshtein___SEM_mean.mat'; numP = 4; % 4P, wins on AIC
mdl = load(winning_model)
clear conId patId
%-------------------------------------------------------------------------
% subject inclusion
iSja = [101,... |
10e06b2d28ce5b3d969ae151edebef0625e7a97f53b5dc0d6537ce5a39de484d | MATLAB | 5,394 | 144 | % SENSE_homodyne_recon_demo.m
% demos use of SENSE_homodyne_recon.m, which combines
% SENSE and partial Fourier reconstruction. Input image can be rectangular,
% but both dimensions should be even
%
% resulting figure shows the improvement from demodulating with the
% reference image and compares MSE to reconstru... |
a5126e9b284edcb37209b05572af53fafe89253b057689fd2d9d09d950c6de47 | MATLAB | 5,397 | 149 | function rename_dicm(files, fmt)
% rename_dicm(files, outputNameFormat)
%
% Rename dicom files so the names will be human readable.
%
% The first input is the dicom file(s) or a folder containing dicom files.
% The second input is the format for the result file names. Support format
% include:
%
% 1: Protoc... |
61e9f203a72fd621328684aeb7ae5736ddf865169e348fc4d5408998e3a8c3ab | MATLAB | 5,405 | 132 | function SBJ10a_conn_lag0(SBJ, method, proc_id, an_id, roi_id, atlas_id, Nbins, chansel)
%% Set up paths
if exist('/home/knight/hoycw/','dir');root_dir='/home/knight/hoycw/';ft_dir=[root_dir 'Apps/fieldtrip/'];
else; root_dir='/Volumes/hoycw_clust/';ft_dir='/Users/colinhoy/Code/Apps/fieldtrip/';end
addpath([root_dir 'P... |
8fc2ae3c6a7257e533dce64a0a740176bb8e7434f82cadd750fb76d5ded93e15 | MATLAB | 5,405 | 151 | %% Thomas_Yang_et al, 2023 @Nuo Li lab
%% Fig. 3a ALM selectivity map
clear all
close all
addpath('../func/');
load Figure_3_a_data
im_CCF = imread(['..\CCF_alignment\ARA_template\AllenRefVolCoronal_100275.tif']);
im_CCF_anatomy = imread(['.\ALM2x_mergedRGB_slice300_cltr1247_P55_NL09.tif']);
im_CCF_an... |
1525ebbfa54c5960fef49e239be3bbb56f63cbf4d4dc7b6ba0ef1b683839c808 | MATLAB | 5,413 | 103 | %% Set Directories
wpms.plugins = 'Insert EEGLAB and FieldTrip Directory'
wpms.chanlocs = 'Insert channel locations directory'
wpms.data = 'Insert data directory with each subject ID identifier starting with 0'
%% Add all plugins
addpath([wpms.plugins filesep 'EEGLAB_FieldTrip\eeglab_current\eeglab2019_1'])
add... |
943135b5eacf8724fdc4ffd1a89808b2c48c94d66e0a8afe1235975d8e0f5a8e | MATLAB | 5,417 | 148 | function plot_timeWarpedCorrelationScoreCurves(cells)
% Load Params
if ~exist('paramsPath','var')
params = readtable('./UniversalParams.xlsx');
else
params = readtable(paramsPath);
end
samplingRate = params.TimeBin;
ds_factor = params.ds_factor;
secsInMin = 60;
conversionFactor = secsInMin/(ds_factor*samplin... |
e45f19550a2450e904ee5d10393a5ca4a5b35a3493bc58632da3ec1c42931b75 | MATLAB | 5,417 | 150 | function BHV02b_RL_model_plot(SBJ,proc_id,model_id,varargin)
%% Plot single SBJ behavior with RL model fit
% Scatter of single trial tolerance and outcomes
% Scatter of block accuracy and average tolerance
% Sigmoid from logistic regression fit on top
% INPUTS:
% SBJ [str] - ID of subject to run
% proc_id [st... |
ae3e9e2985179b68a8ea6ff535d1e750ec08871eac58f4e5a980a88d5d63571f | MATLAB | 5,420 | 144 | %% Run scripts for RL GLM analyses
if exist('/home/knight/hoycw/','dir');root_dir='/home/knight/hoycw/';ft_dir=[root_dir 'Apps/fieldtrip/'];
else root_dir='/Volumes/hoycw_clust/'; ft_dir='/Users/colinhoy/Code/Apps/fieldtrip/';end
%%
addpath([root_dir 'PRJ_Error/scripts/']);
addpath(genpath([root_dir 'PRJ_Error/scripts... |
ee7c7a47dd81d3edad0e6c03a5fe3219e1a6fc0fed459b021bee102f997ed393 | MATLAB | 5,422 | 227 | function mas = xray_read_mac(mtype, varargin)
%function mas = xray_read_mac(mtype, [options])
%|
%| Read mass attenuation coefficients for a given material type.
%| Returns a strum that can interpolate onto desired energies.
%|
%| in
%| mtype 'aluminum', 'copper', 2, '2', '02-helium', ...
%| See xray_material_file... |
bec04449c8b4bcde6d332f9512435df2230bcfcf307be9983891cfcbcda5ddc5 | MATLAB | 5,428 | 160 | function plot_autocorrelation_before_and_after_dchPeriod(cells)
% function constants
plotWidth = 500;
plotHeight = 1000;
spatialBinNum = 200;
MPP = 0.125; %Minimum Peak Prominence
numCells = size(cells.metadata,1);
drawFig = true;
% declare global vaariables
all_pcntrl = NaN(numCells,1);
all_pdch = NaN(numCells,1)... |
51bf2a0bdee14451bc137874f8b0516c1cef76f750eb8731c0bd3a666484985a | MATLAB | 5,430 | 136 | function SBJ10a_corrRT_regressRT_ANOVA(SBJ,an_id,stat_id)
%% Run ANOVA with potential RT regression before
% Set up paths
addpath('/home/knight/hoycw/PRJ_Error/scripts/');
addpath('/home/knight/hoycw/PRJ_Error/scripts/utils/');
addpath('/home/knight/hoycw/Apps/fieldtrip/');
ft_defaults
rng('shuffle'); % seed randi wit... |
b33c01ff23fdb18c01d02d5d98be43e0ec371818eeba3060988757804a471e69 | MATLAB | 5,433 | 194 | function fig = nyu_plot(surf_brain,sph,elec,elecname,color,label,aparc_annot,radius,alpha,add_figure,pointalpha,braincolors)
if ~exist('color','var')
color = 'w';
end
if ~exist('label','var')
label = 0;
end
if ~exist('alpha','var')
alpha = 1;
end
if ~exist('radius','var')
radius = 1;
end
if ~exist('apa... |
d060d356f3928c3c4c2c445b25863e107a631a43001faa5eb81c8ac7fec13dad | MATLAB | 5,433 | 89 | % fitting scattering and birefringence of brain tissue
% run this after OCT_recon.m is finished
folder = '/projectnb2/npbssmic/ns/Ann_Mckee_samples_10T/CTE_8572/'; % OCT file path ADJUST FOR EACH SAMPLE!!!
P2path = '/projectnb2/npbssmic/ns/Ann_Mckee_samples_10T/CTE_8572_2P/'; % 2P file... |
a9966d99427049f8849e42e32961fa9a33a56189ea5dd394e182d83a25de762b | MATLAB | 5,439 | 136 | function [estimationSuccess] = getParams(f_orco, s, keyNdx, xGrid, yGrid, zGrid, ratio, ...
state, kin, Thresh, K, border, figN,sbpltN)
% getParams does a grid search to determine model params. Note that this
% does not automaticaly look for the elbow point. The user should look at
% the cost function to m... |
969a92e6ef0764bf1fe6510d44ee447b8b1df038088293328d0cffdcc7346500 | MATLAB | 5,442 | 142 | function [outBestPeriodIndices,outSampleFreq] = IPEMMECFindBestPeriods(varargin)
% Usage:
% [outBestPeriodIndices,outSampleFreq] = ...
% IPEMMECAnalysis(inValues,inValuesFreq,inPeriods,inPlotFlag,...
% inMergeType,inDecisionType)
%
% Description:
% Finds the best matching periods corr... |
96588f70ebd5760681db4ecde7bd0717a14c7da982a12fafd6d75d8587eecb7d | MATLAB | 5,446 | 124 | % Dumps all the paramters to a figure
function fig = plotParameters(obj,fontsize)
if(obj.plotFigures == 0)
disp('plotParameters: plotFigures = 0, hiding figures!')
visFlag = 'off';
else
visFlag = 'on';
end
fig = figure('visible',visFlag);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
bb568811926144f56f49b8c0bcc18c2f7f972cde7077d5583c6c0fccc2d461fc | MATLAB | 5,448 | 191 | function [] = Faber_Extract2(savedata,savefigs,blockname1,tankdir,filename1,filename2,trimstart,trimend)
clearvars -except blockname1 filename1 filename2 savedata savefigs tankdir trimstart trimend;
close all;
warning('off','all')
warning
blockname = blockname1;
tankname = tankdir;
sd=savedata;
sf=s... |
705667c133e7df79bbd9efff818ce45b2b7e657a6a2fbedf37632daabe4a8bac | MATLAB | 5,452 | 114 | folder= '/projectnb2/npbssmic/ns/BA4445_4/';
datapath=strcat(folder,'dist_corrected/');
P2path = '/projectnb2/npbssmic/ns/BA4445_4_2P/'; % 2P file path
% add subfunctions for the script. Change directory if not running on BU SCC
addpath('/projectnb/npbssmic/s/Matlab_code/fitting_code');
addpath('/projectnb/npbssmic/... |
50ff1739d72baad1cb4ef9977c161239fdefc91a59a53fd956cb8f74d2836a4b | MATLAB | 5,464 | 153 |
%% State Space Model
for i = 1:2
tic
dataToFit = useData(1e4+1:2e4,i);
[omega, ampEst, allQ, R, stateVec, stateCov] = fit_MKModel_multSines(zscore(dataToFit),[.5,2.4,20], Fs,[.99,.99,.99],...
[.1,.1,.1],.01);
rhythmLoc = find(omega > .1 & ome... |
970274c759d114598cfe1454e63906323d022f660b210e412e0f2dd84ad94233 | MATLAB | 5,466 | 185 | %% Calculate and plot PSD
%
% For information about NatMEG-PD please refer to the data descriptor:
%
% Vinding, M. C., Eriksson, A., Comarovschii, I., Waldthaler, J., Manting, C. L.,
% Oostenveld, R., Ingvar, M., Svenningsson, P., & Lundqvist, D. (2024). The
% Swedish National Facility for Magnetoencephalography ... |
59eaf16f78c5e8ed09aee0da9dedc6435273457c92938473f5e57996d9dd36ec | MATLAB | 5,470 | 147 | function save2ExcelFile(filename, mat, varargin)
% This is a wrapper function that allows OTBR Toolbox users to create
% Excel files either in MATLAB or in Octave on a Raspberry Pi!
% To create Excel files on the Raspberry Pi the package IO has to be
% installed.
%
% Usage: save2ExcelFile(fullFilename, dataAsCell, vara... |
d32ab63107b6f18db32ea1764aea746c4938f15e41555c1e2c2882b5493d7694 | MATLAB | 5,471 | 142 | function fix_lines(fname, fname2)
%FIX_LINES Improves the line style of eps files generated by print
%
% Examples:
% fix_lines fname
% fix_lines fname fname2
%
% This function improves the style of lines in eps files generated by
% MATLAB's print function, making them more similar to those seen on
% screen. Grid l... |
fa65d97ac551ac2ae2e02d7b36f12b0d32a7ad2b3c733cbfc784233ddea5482c | MATLAB | 5,472 | 186 | function [dyn_obj dce] = ir_mri_dce_obj1(varargin)
%function [dyn_obj dce] = ir_mri_dce_obj1(varargin)
%|
%| Generate dynamic object for DCE MRI simulations of GRE sequence.
%|
%| option
%| 'TR' [s] repetition time (default: 5e-3)
%| 'TE' [s] echo time (default: 0)
%| 'flip' [rad] flip angle (default: pi/6)
%| '... |
06cacfb95a996ed85723a8a838dff695bec0e61a4d344b3eb11a5a771de855d6 | MATLAB | 5,474 | 100 | load('region_value_f0_percept.mat'); region_value_f0_percept=region_value;
load('regions4barplot_f0_percept.mat'); regions4barplot_f0_percept=regions4barplot;
load('region_value_fdiff_percept.mat'); region_value_fdiff_percept=region_value;
load('regions4barplot_fdiff_percept.mat'); regions4barplot_fdiff_percept=regions... |
1c4b1645ac5f7d4633cbe51408fae1120bf18b0b51e61c2062cc588912cb8684 | MATLAB | 5,475 | 139 | %% Produce a figure of Stimulator Output required per individual to fix intensity at cortical target
% (c) Carys Evans, UCL
% carys.evans@ucl.ac.uk
% October 2019
%This script produces one figure showing the distribution of Stimulator
%Output across the sample when dose-controlling to fix E-field intensity in
%the cor... |
552c88b574fb292ed4c032ffde43ff0fea7296e9f6e0328cc2364b39825d59e9 | MATLAB | 5,475 | 181 | % clear all;
Xsize=40;
Ysize=40;
Xoverlap=0.5;
Yoverlap=0.5;
%% get FIJI stitching info
filename = strcat('E:\Jiarui\Data\200714TDE60\fitting\');
f=strcat(filename,'TileConfiguration.registered.txt');
coord = read_Fiji_coord(f,'us');
%% coordinates correction
% use median corrdinates for all slices
% coord=squeeze... |
093e4a35c9ba18ca2fba72d58d32f38de7e85dd6e8a0a4cca1ceb0365d791a85 | MATLAB | 5,479 | 144 | % Make allTrialsAllCellsMatrix
% sessions = dir('/Volumes/groups/giocomo/export/data/Projects/JohnKei_NPH3/fkm_analysis/fr_corr_matrices/*.mat');
sessions = dir('/Users/KeiMasuda/Desktop/fkm_analysis/fr_corr_matrices_noSpeedFilter/*.mat');
filter = 'mec';
sessions = filterSessions(sessions, filter);
% load(sprin... |
8b3165cf9ad0392cd1b8a97274c1ad64f959998f8d0b16771455d6b8e0908e87 | MATLAB | 5,480 | 155 | function [] = fun_calcROIsegs(handles, mode, filename, filepath)
%FUN_CALCROISEGS Summary of this function goes here
% Detailed explanation goes here
I_stack = handles.imageI;
G_stack = handles.imageG;
S_stack = handles.imageS;
[~, ~, n_z] = size(I_stack);
if get(handles.Check_AutoI, 'Value')
Im... |
9d8f54057c84c58e98d1c88c4ced4358ee72a1fde09992ce94f2443b2a56b6fc | MATLAB | 5,481 | 108 | % LEARN_STRUCTURES_BY_DENSITY
%
% Input
% samples: logical matrix where each row is a sample and each column a node
% relative_lambda: relative regularization factor (relative to the lambda
% that drives all coefficients to zero.
% densities: vector of densities to be tried.
% option variable_groups: arra... |
58b3ac6419b7c972ce46f7c75961cd2989d343e37114b1a0017d785cd4dce4f7 | MATLAB | 5,483 | 296 |
% Code responsible for generated the heatmap and mean trace plot of
% heterozygous and homozygous valopa knock-out fish found in Fig S7D in "Ciliary
% localization of a light activated neuronal GPCR shapes behavior", PNAS,
% 2023
% Written by Amy Winans
close all
clear all
load valopaKOworkspace
%% Calculate... |
5639e6d909fa946e597bf7ba07321204a8c5f01a0e4628a0da9d0b095be26d07 | MATLAB | 5,486 | 170 | % Estimate the Fisher information of stimulus in the neuronal responses of a single
% recurrent network
% Some simplifications is used in this Hawkess process:
% 1). No temporal kernel
% Wen-Hao Zhang
% July 22, 2021
% University of Chicago
if ~exist('Path_RootDir', 'var')
setWorkPath;
end
addpath(fullfile(Path_... |
988779cb57b9defaba9019bec86d0e29442d6952bd5d322e79d5fd6ac89ca0c7 | MATLAB | 5,486 | 156 | function startVideo(vid, varargin)
% Start the playback engine of a video that was loaded with loadVideo.
%
% After calling this function the video is not presented on the screen! Use
% showVideo in a loop to get each frame and to present it!
%
% Usage: startVideo(vid)
% startVideo(vid, varargin)
%
% INPUTS
% ... |
6d16046cbece7449175df395ea8606691dfb84f658e073ebf26e8873f63c66b1 | MATLAB | 5,492 | 142 | function out = wait4NetworkResponse(time2wait)
% Waits until one of the connected experimental computers sends its
% network ID, or until time2wait has passed. An experimental computer
% sends its ID when keyBuffer, started there with the option 'sendNetID',
% ends after a response. With several experimental computers ... |
2f5d82a73616155c9c3e6f923dbd7e686d4d986e52ddbb62dbd95037bf411316 | MATLAB | 5,493 | 176 | % description:
% 1) plot ERP for both conditions in a desired region,
% 2) plot region specific spectrograms w/ or w/o ERP removal
% 3) plot ERP for a given chan, and mean(trials-ERP) in the same chan
% 4) plot idividual trials and trials-erp
% 5) individual channel PSD
close all;
reg = 'CA3'
cue_responsive = 'yes'
s... |
e9447770a4d9fa69fdf1fdf34fa187bab436f7527404de6cd917debed32387c2 | MATLAB | 5,493 | 128 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MAIN - PWelch analysis - 20 subjects - MEG - Desikan-Killiany
% Authors: MCC
% Date: 25/10/2022
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
close all; clear; clc;
%% to be updated
root_path='/Use... |
17a2c5c55c64f0a55fe332bcc2dc515a0000209703682f414720f5da227449a4 | MATLAB | 5,496 | 111 | function [bestDprimeSVM,bestRR,score] = diliCCAnested(stim,eeg,nCompStimAll,nCompEEGAll,shifts,prefixTmpFile)
if ~exist('prefixTmpFile')
prefixTmpFile = '';
end
% Tuning
% Outer cross-validation loop
if length(nCompEEGAll) == 1 && length(nCompStimAll) == 1
autoTuning = 0... |
26b25372e2565e812041a538e6af47b6b64e516733e31e6286ea3af073df061b | MATLAB | 5,497 | 146 | % Method: 1 for WeightedCorr or 2 for QuadrantRatio
function plot_individual_lap_thetaseq_scores(method)
load('X:\BendorLab\Drobo\Lab Members\Marta\Analysis\HIPP\Chapter 3\Theta sequence scores\thetaseq_scores_individual_laps.mat')
if method == 1
data = lap_WeightedCorr;
quant = 'Weighted Correlation';
else
... |
507079d0087292d2d53b4d0819d403ce68ccc71a1b6829933fac6d9e543a6f94 | MATLAB | 5,497 | 138 | function Optical_fitting_MGH(I, s_seg, z_seg, datapath, zf)
% Fitting code for the data shared by Hui.
% I: volume data for 1 tile
% s_seg: slice number,for initial test, just use arbitrary number like 1
% Z_seg: tile numberfor initial test, just use arbitrary number like 1
% datapath: datapath for original data
% zf:... |
199dc2b2723ee934f45fe378a5db7fd94f796f904372d348ad58b76c54530b92 | MATLAB | 5,504 | 109 | %% IR57 Processing Variables
[root_dir, app_dir] = fn_get_root_dir(); ft_dir = [app_dir 'fieldtrip/'];
if ~contains(path,'fieldtrip'); addpath(ft_dir); ft_defaults; end
%--------------------------------------
% Basics
%--------------------------------------
SBJ_vars.SBJ = 'IR57';
SBJ_vars.raw_file = {'2017032... |
8c1990d92ddea7e2b7268b357e11b5b23eee1a434384fc68c93ddb1f39fdf611 | MATLAB | 5,519 | 171 | function [new_trigger_list] = relabel_EEG_button_press_triggers(recorded_trigger_list, new_response_matrix)
% make a copy of the old trigger list
new_trigger_list = recorded_trigger_list;
% trigger labels
fa_left = 206;
fa_right = 202;
trial_left = 205;
trial_right = 201;
% select false alarm and trial frames
be... |
90f59dcc9c5156f87b026d97e47958a9a81bd5e2ce2d781f910c806a05b42d34 | MATLAB | 5,520 | 218 | %%
master_startup;
datapath = fullfile(path.data_save,'pbupsRT/');
filenames = get_reaction_time_filenames(datapath);
saving = 1;
example_rat = 'X018';
%%
load(path.mat_save + "RT_bootstrap_cond_pych_params.mat");
[ci_bias, ci_lapse, ci_fitbias, ci_fitlapse] = deal(nan(length(filenames),2));
[mean_bias, mean_lapse... |
b0c80e8edaaca5b13e375be28be912476a84100e0a92ed9e7d80cf3b0a37e2c8 | MATLAB | 5,521 | 143 | classdef StackView < handle
properties
stack % stack containing image data
ax % handle of axes object to display image
im % handle of image object
overlay % handle of overlay plot
sliderFrame % slider selecting frame to dis... |
a73cbac7c6cdff61d33f9dbb874f4d44aa90040193015ff6bb7201e12e7ffad5 | MATLAB | 5,522 | 175 | %% Example Script to Plot Data
%% Cut in time
t_f = 40; % Change this to plot till t_f
[~, i_f] = min(abs(time-t_f));
[~, i_f_i] = min(abs(time_i-t_f));
[~, i_f_b] = min(abs(time_battery-t_f));
%% 1) Robot Position and Orientation
figure
hold on
plot(time(1:i_f),pos_base(1:i_f,1),...
... |
974b0105ed1ea3ec0ecb1d03c09c508ecadd7ab03c9a16c81fc7c7ad22359e67 | MATLAB | 5,525 | 164 | function y = convolve2(x, m, shape, tol)
%CONVOLVE2 Two dimensional convolution.
% Y = CONVOLVE2(X, M) performs the 2-D convolution of matrices X and
% M. If [mx,nx] = size(X) and [mm,nm] = size(M), then size(Y) =
% [mx+mm-1,nx+nm-1]. Values near the boundaries of the output array are
% calculated as if X was s... |
12b7d142b7a259316d94880d5b3b17e43d391b1138122bca517626d9a0ef3ab9 | MATLAB | 5,541 | 137 | %% Produce a figure of E-field in target ROI containing four histograms with fitted normal probability density functions
% (c) Carys Evans, UCL
% carys.evans@ucl.ac.uk
% October 2019
%This script produces one figure showing the distribution of E-field
%intensity across the sample in the target ROI. Using each
%[simtag... |
c8a04764fe9fd9fc8dcda6c75c111c6e14e0e1320aed8e9f4eeecdccc4a70293 | MATLAB | 5,542 | 195 | function [vol, M, dcminfo, mr_parms] = load_dicom_fl(flist)
% [vol, M, dcminfo, mr_parms] = load_dicom_fl(flist)
%
% Loads a volume from the dicom files in flist.
%
% The volume dimensions are arranged such that the
% readout dimension is first, followed by the phase-encode,
% followed by the slices (this is not implem... |
1bda884f7e95399da3c21e135afde42837c2f78f1f0bd60aae2e0d8838328bda | MATLAB | 5,549 | 175 | function[]=ret_diff_vol_stitch(id,datapath)
% mosaic parameters
% mkdir(strcat(datapath,'dist_corrected/volume_tmp'));
Xsize=1000;
Ysize=1000;
Xoverlap=0.15;
Yoverlap=0.15;
% add path of functions
addpath('/projectnb/npbssmic/s/Matlab_code/PSOCT_code');
addpath('/projectnb/npbssmic/s/Matlab_code/ThorOCT_code');
addpat... |
36df2e2f065589147286e8e351a6197b01025c45494eb1716fd642e376a9dfb6 | MATLAB | 5,549 | 175 | % This function calculates the effective available gradients,
% assuming there is simple masking due to cis interaction.
%
% [R] + [L] <-> [RL], here we assume k = 1 for the reaction
%
% TODO: See DS concern raised March 29, 2012. However, the cis
% interaction takes place over a larger area than the trans
% interactio... |
64a904876e8fb8b9778062efd55ab01b5530b959acde264f91de18a6536ff3f4 | MATLAB | 5,549 | 183 | clear all
close all
rng(6)
%% initialization of parameters/matrices
run('param_init2.m')
%% creation of presynaptic inputs
run('input_init.m')
%% trial loop
for l = 1:num_trials
%choose a cue
cue_given = cues{l};
u_k = PF_map;
[~,ind_t] = max(u_k,[],2,'linear');
[row,col] = ind... |
4f0c8779c52799efe60e301c8972af314354a4989dddb3969eb8ca91a2addd00 | MATLAB | 5,552 | 168 | %% --- Generate functional connectivity profiles and estimate clusters
% Adapted by M.-Y. Wang, 16-Jul-2023
%% 1.initial parameters
clear all
clc
project_dir ='/Users/wang/Desktop/Research_projects/BBSC/Functional/Parcellation/1_generate_profiles_and_ini_params';
cd (project_dir)
addpath(genpath('/Users/wang/CBI... |
790277e6ba1913d723c93d56c1f4c4e2002c61f3486d6af867aad7d36fa7c56c | MATLAB | 5,563 | 151 | clc; clear;
addpath('/data/hu_esraal/Documents/eeglab2019_0/')
addpath('/data/hu_esraal/Documents/TMSEEG-4.0')
eeglab
%
EEGpath= '/data/p_02186/TMS_ECG2/analyses/EEGsham/';
eegfolder = [EEGpath 'merge/']; cd(eegfolder);
subj_names = {'VP01', 'VP02', 'VP03', 'VP04', 'VP05','VP06', 'VP07', 'VP08', 'VP09', 'VP10', 'VP11'... |
359873d198bff5913f10c6b9ed00d6188ea50dfa8916f10077b66a72a58bcffb | MATLAB | 5,567 | 148 | function SBJ10b_conn_Xcorr(SBJ, proc_id, an_id, roi_id, atlas_id, maxlag, stepsize, chansel)
%% Set up paths
if exist('/home/knight/hoycw/','dir');root_dir='/home/knight/hoycw/';ft_dir=[root_dir 'Apps/fieldtrip/'];
else; root_dir='/Volumes/hoycw_clust/';ft_dir='/Users/colinhoy/Code/Apps/fieldtrip/';end
addpath([root_di... |
d53d77956f6f62aa4b25e51e174aa514740cbf7b80c625370d88f9a7cfc57ef3 | MATLAB | 5,568 | 183 | % Demo of a linear Hawkes process where the E neurons are organized on a
% ring
% Wen-Hao Zhang, July 2, 2019
% University of Pittsburgh
%% Parameters of the model
parsCoupledHawkesNet;
parsMdl.dt = 0.1;
parsMdl.tBin = 20; % length of a trial. Unit: ms
parsMdl.bSample_ufwd = 0;
parsMdl.jxe = 1e-2;
parsMdl.ratiojie ... |
ec68380fa2ee9a32d8ed98a7453c70a1273b23e2d7a92d055cb0cccd05b6a5a5 | MATLAB | 5,569 | 161 | %% --- Generate brain networks for long days or nights
% 1. compute the average profiles
% 2. clustering the networks using the yeo2011 method
% Adapted by M.-Y. Wang, 16-Jul-2023
%% 0.initial parameters
clear all
clc
project_dir ='/Users/wang/Desktop/Research_projects/BBSC/Functional/Parcellation/1_generate_prof... |
d179641de5edd378364c7f675773be9069b807c78969d610c7ea7c1451c8b692 | MATLAB | 5,572 | 131 | function [] = network_params_RMonly(binsize, maxlag)
addpath(genpath('D:\kate_dropbox\Dropbox\Rutgers\Matlab - Rutgers\Firestein Lab\BCT\'));
%parameters
totaltime = 300;
%options
raster = 0;
plotme = 0;
extracalcs = 1;
% ************************************************
totalNumExp = 3;
count.cond0B... |
dff253745ceb806f2573b5c42fc2bbdfb3f8298d9c9b68f8fb0a4f74430905e7 | MATLAB | 5,575 | 141 | function tSC_ratio_oscstate(mainPath, animal, session, ch, isstim, exp)
%TSC_RATIO_OSCSTATE calculates the ratio of different theta cycles during
%different oscillation states.
% TSC_RATIO_OSCSTATE(MAINPATH, ANIMAL, SESSION, CH, ISSTIM, EXP) detects
% oscillation states in the hippocampal LFP (long and short th... |
50df36defe31d61d57572f3e78d52850b6433f8214197c59ee99c469e47390a7 | MATLAB | 5,581 | 178 | function[]=ret_vol_stitch_from_AB(id,datapath)
% mosaic parameters
Xsize=1000;
Ysize=1000;
Xoverlap=0.15;
Yoverlap=0.15;
% add path of functions
addpath('/projectnb/npbssmic/s/Matlab_code/PSOCT_code');
addpath('/projectnb/npbssmic/s/Matlab_code/ThorOCT_code');
addpath('/projectnb/npbssmic/s/Matlab_code/NIfTI_20140122... |
77cb564ff093c9fcb002d15d879a9ae86ef6e7c63a4a02b611e39020ac7f9246 | MATLAB | 5,592 | 186 | function [fNum] = plotROISpatialProb(f_orcoAll,dxy,lab,border,fNum)
if isempty(lab)
lab = '';
end
T_df = [-20,20];
T_f = 15;
ROI_func{6} = @(f,df,baseline) (f-baseline)<0.1 & (df)<0.1;% baseline
ROI_func{1} = @(f,df,baseline) df<T_df(1) & ~ROI_func{6}(f,df,baseline);% negative df
ROI_func{2} = @(f,df,ba... |
1b1ff9e154fe477c3453470a3580d7384eb68c57cd06c00e8261739ef52c73b2 | MATLAB | 5,593 | 164 | function P = spm_eeg_inv_vbecd(P)
% Model inversion routine for ECDs using variational Bayesian approach
%
% FORMAT P = spm_eeg_inv_vbecd(P)
%
% Input:
% structure P with fields:
% forward - structure containing the forward model, i.e. the "vol"
% and "sens" structure in a FT compatible format
% ... |
78e271ca47a225a55e52fff0bc2d6ac9681775119f4f338efa4e514c0a10a84c | MATLAB | 5,594 | 224 | function [xs, info] = ir_diag_majorize_admm1(H, varargin)
%function [xs, info] = ir_diag_majorize_admm1(H, varargin)
%|
%| Use ADMM to find a diagonal matrix D = diag(x) of minimum Frobenious norm
%| that majorizes a given square matrix H, i.e., min_D || D || s.t. H <= D.
%| Assumes that H is positive semidefinite (so... |
8066bda0400a1815df65c30c82886f5350ef534923c96aa4ad6a0b528d1d291c | MATLAB | 5,599 | 173 | function [lm, r, pval] = two_group_scatter(xx, yy, conId, patId, xl, yl, input_options)
% Plots both groups on the same axis, adds trend line, performs a multiple regression
% [lm, r, pval] = two_group_scatter(xx, yy, conId, patId, xl, yl, input_options)
%
% xx x variable, vector
% yy y variable, vector
%... |
2ce7ca36874de3e11aae3381d8ba0a9e5c2698d530e91314e450f1fbfefd36ea | MATLAB | 5,604 | 185 | %% Dipole source analysis
%
% Vinding, M. C., & Oostenveld, R. (2022). Sharing individualised template MRI data for MEG source reconstruction: A solution for open data while keeping subject confidentiality. NeuroImage, 119165. https://doi.org/10.1016/j.neuroimage.2022.119165
%
% Do dipole fits to evoked componet. Sing... |
3fb5c383bffa25f349f1fd237f13e95874c15e4b8f546ed279d8f6a9e62e47b1 | MATLAB | 5,604 | 90 | %% Example script using Fieldtrip function data2bids()
% https://www.fieldtriptoolbox.org/workshop/madrid2019/bids_sedation/
sourcedata = '/Volumes/Samsung T3/data/eeg-sedation/sourcedata';
bidsroot = '/Volumes/Samsung T3/data/eeg-sedation/bids';
cd(sourcedata)
load datainfo
% For each dataset, there is an entry ... |
d0ef465d06bcdc261975f4a932671b8054418440fde101c79133592fc808a37b | MATLAB | 5,607 | 118 | function outResult = IPEMProcessAuditoryModel (varargin)
%
% NOTE:
% This is a modified version of IPEMProcessAuditoryModel.m
% Normally, this is compiled into the Mex interface for the ANI algorithm
% However, due to difficulties with generating mex wrapper code in
% Matlab 7(MCC 4.0), this was bypassed. Inste... |
e055ff3fae80d82adfde204aa9ca0df961ac0103179533c7a67ec27b97a5833a | MATLAB | 5,607 | 157 | close all
clear variables
clc
%Varun Mannam
%date: taken from 29th Sep 2019
%date: 27th July 2020
%DnCNN model with diff lr in keras
%calculate the PSNR on test-mix data raw nbn
format long
font = 14;
%data
addpath('/Users/varunmannam/Desktop/Summer20/Research_SU20/May20/2505/dncnn_keras/dataset/');
%lr files
%addpat... |
f811a916f02a2ff4cc7f97390ce79675a7920aa879665bfa563ec03b980a07b8 | MATLAB | 5,610 | 109 | % PlotPlotBinFirRateBatchResult.m
% This is for Fig5D and E.
% Change the line ste_ave_both(T, pct(1), pct(2), n_baseline, n_poi_stat, p_color) in PlotBinFirRate.m to plot D vs E.
close all;
f_data_type = 2; %1: 1s POI, 2:25sec POI
f_plot_type = 5; %1:bar, 2:violin, 3: box plot , 4:connected lines with ave ... |
6d73db866c8177b74631c550e218dba551a69366ab99c7159a2962bee6b413d1 | MATLAB | 5,612 | 180 | clear all;
Xsize=40;
Ysize=40;
Xoverlap=0.5;
Yoverlap=0.5;
%% get FIJI stitching info
filename = strcat('/projectnb2/npbssmic/ns/190619_Thorlabs/aip/vol10/');
f=strcat(filename,'TileConfiguration.registered.txt');
coord = read_Fiji_coord(f,'aip');
%% coordinates correction
% use median corrdinates ... |
b5c79b362a33b91525335f4ffae21df5ff5b234fe01aa82aa113da1e71edd5f5 | MATLAB | 5,623 | 115 | figX.fig = figure('Name', 'Figure X: Anti vs Ortho');
set(figX.fig, 'Units', 'pixels', 'Position', OSScreenSize([15 8]), 'NumberTitle', 'off');
figX.unsorted(1) = axes('Position', [.05 .55 .275 .4]);
figX.sorted(1) = axes('Position', [.05 .075 .275 .4]);
figX.unsorted(2) = axes('Position', [.375 .55 .275 .4]);
figX.so... |
74d1b86f94051d6db6b3a714d0dac6f4e3b7fc65ade23f4b2dd63d7cbc2f7870 | MATLAB | 5,626 | 179 | function [TargetSound, NoTargetSound,TSquintOnset] = CreateStimuli(currCon, JND,TS)
% include variable length of sequence
fs = 44100;
rhythm = 2;
ISI= 1000/rhythm; %in ms
ISIsamp = zeros(1,ceil((ISI/1000)*fs));
f = 1100;
TSinS = JND;
stimLength = 6; %length in s
TS = TS*rhythm;
% quick and dirty ... |
9be7b08823aea6791f3bed0298f4fa76ac9212bfb8919042be7ed017a0f5886f | MATLAB | 5,627 | 156 | clc; clear;
addpath('/data/hu_esraal/Documents/eeglab2019_0/')
addpath('/data/pt_02333/esra_codes/')
eeglab
%%
ts=[-1000 4000];
eegpath= '/data/p_02186/TMS_ECG2/analyses/EEGmotor/';
motorpath='/data/p_02186/TMS_ECG2/analyses/EEGmotor/FDIdata/events/';
save2folder= '/data/p_02186/TMS_ECG2/analyses/EEGmotor/merge/motor_o... |
f93ed99a00247235de91f859d9c8a234067d5354003ea339699cc6e74ff8830c | MATLAB | 5,627 | 156 | classdef SuhLeafRaker < handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanford Junior University; Herzenberg Lab
% License: BSD 3 clause
properties(SetAccess=private)
epp;
topKey;
leafKeys;
... |
9eab65bc6cc982392076a393550dd795fe90702b403f824d39bee87e84fb83bf | MATLAB | 5,630 | 161 | function AssembliesDynamicsVisualization();
[filename,pathname] = uigetfile({'*_CLUSTERS.mat';'*_CLUSTERS.MAT'},'Open file with assemblies data', 'MultiSelect', 'off');
filenameCLUSTER=fullfile(pathname,filename);
temp=load(filenameCLUSTER);
assembliesCells=temp.assembliesCells;
matchIndexTimeSeriesSignificant=temp.ma... |
4358faace2c004d603311b93c52b39a34fe3c94dc3fb7ff6ae11bcfc95ed5638 | MATLAB | 5,633 | 136 | function Figure_7D_plot
%
% Written by Ayaka Matsumoto, October 2023
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Output: Figures 7D
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
equi_t... |
83e41cb2bd8cdd264e68ce4405094c7ac0c72dfe676283dc8beeb8ad69e5ed9a | MATLAB | 5,640 | 145 | function listSound
% List all sound systems of this computer with their device indices.
%
% The listing is grouped by sound system and sorted from low to high
% latency, so the first entries are the ones worth using. Sound systems
% without a usable output device are reported as not available. A closing
% section lists... |
af7fe973afbfc86f1b1dd5f1d3b62d08e78f1db17277052b2363998065cf27f3 | MATLAB | 5,640 | 157 | %% --- Generate functional connectivity profiles and estimate initialization parameters
% Adapted by M.-Y. Wang, 16-Nov.-2022
%% 1.initial parameters
clear all
clc
project_dir ='/Users/wang/Desktop/Research_projects/BBSC/Functional/Parcellation/1_generate_profiles_and_ini_params';
cd (project_dir)
addpath(genpat... |
fcea596444f92183b797c9830181d25da73ec229384c5abd90ade9116e876325 | MATLAB | 5,643 | 147 | function varargout = spm_shoot3d(v0,prm,args, F)
% Geodesic shooting
% FORMAT [phi,Jphi,v1,theta,Jtheta] = spm_shoot3d(v0,prm,args, F)
% v0 - Initial velocity field n1*n2*n3*3 (single prec. float)
% prm - Differential operator parameters
% prm - 8 settings
% - [1][2][3] Voxel sizes
% - [4][5][6][7][8]... |
ddcbc2a079156ceb138141604348e6eaa3be6be5caaa37c256482d8733c3a9e7 | MATLAB | 5,645 | 189 | %% PANEL FIGURE 3
%Figure description: IC medial prefrontl maps and ERPs from SS v US and
%TFUS (none) 1st row and TFUS (STOP) 2nd row.
%ERP PLOT: Columns are groups (rIFG, S1, and control); Rows are TFUS
%conditions; Color: blue is SS and orange is US
%% Gather IC MAPS and plot central IC
addpath '/Users/user/Library... |
2cbd9e3eee29a6940612256bde5214d21a8c1df2f221b8f048cb9fc555f548df | MATLAB | 5,646 | 138 | %% add path and load file
clear all
addpath('E:\Jiarui\Data\code\');
addpath('E:\Jiarui\Data\code\cortical_thickness');
subject_ID = 'NC_21499';
filepath = ['E:\Jiarui\Data\220401_Ann_15_samples\', subject_ID, '\'];
cd(filepath);
infra = TIFF2MAT('thickness_skel_infra.tif');
supra = TIFF2MAT('thickness_skel_supra.tif')... |
0b10c1796835e2dbecade24aea07b9b71dc50de36c6ee9d9b5590d0bd810b8e6 | MATLAB | 5,654 | 166 | %%%%%%%%%%% BATCH_simulation %%%%%%%%%%%
% - run it section by section
% - results are NOT saved automatically
% - numeric (BM) solution is calculated in NUMERIC_SIM
% it supports 1 water (A), 1 MT (C) and up to 5 CEST/NOE pools (B,D,E,F,G)
% - analytic solution is calculated in ANALYTIC_SIM
% it supports 1 water (... |
61bd27139117b8443108ceae4852c4ea547c20b1b2093ae12e35481337b37c4a | MATLAB | 5,654 | 190 | function err = save_nifti(hdr,niftifile)
% err = save_nifti(hdr,niftifile)
%
% Pixel data should be in hdr.vol
%
% Handles data structures with more than 32k cols by setting
% hdr.dim(2) = -1 and hdr.glmin = ncols. This is FreeSurfer specific,
% for handling surfaces. The exception to this is when the total
% number of... |
3138ee7004742e48a99c0a62fef7ffc02e13c57676f2eb5b42d5dd46f993d1b4 | MATLAB | 5,656 | 152 | function [roiData, EEG, ROISrc] = c_EEG_calculateROIData(varargin)
p = inputParser();
p.addRequired('EEG',@isstruct);
p.addParameter('srcKernel', [], @ismatrix); % if empty, try to pull from EEG.src.kernel
p.addParameter('srcSurf', [], @c_mesh_isValid); % if empty, try to pull from EEG.src.meshCortex
p.addParamete... |
a8b22beafeaf50f345c556f28e32f647d8b24ed88ee569005d30300aedcb038f | MATLAB | 5,660 | 224 | function [C, B, spectrum, R] = ir_reg_diff_zeroed(idim, varargin)
%function [C, B, spectrum, R] = ir_reg_diff_zeroed(idim, varargin)
%|
%| Regularizing finite-differences R = diag(B)*C where C'C is circulant
%| and B is a binary "mask" array that eliminates undesired boundary diffs.
%| (Useful in variable splitting me... |
3939e0fd9dc2d9f46a69fd46a28cda6ef36bf948eec6d5c4054a3c36390b8da0 | MATLAB | 5,662 | 125 | function [CD_correct, dphi_correct, phi_fit, cc_fit, mask_static_refined] = CDPhaCor_Iter_2D_V2(mag1, mag2, dphi, Z1Z2product, mask_static, mask_brain, deg, Niter, bBatch)
% this function correct the phase errors in complex difference iteratively,
% based on user input initial static tissue mask, and do the correctio... |
da271a4dab05e73353267df4277d66b6fb3687f3698cda5788bedae7d48c6409 | MATLAB | 5,663 | 139 | function [cond1,cond2,cond3,cond4] = get_power_subj(subj_list,exp_type,reg, ref, lock)
% Function output: mean spectrogram power for a given region, using a
% single matrix per subj for all conds
cd(['/mnt/yassamri/iEEG/sandra/group_data/groupdata_spectrograms/' ref '_reref/' exp_type '_' lock ])
for iSubj = 1:length(... |
e7fbc9626b4326a48584c6337e087e96d61d05c099831623e6034116d399de80 | MATLAB | 5,663 | 177 | function [psctc, pscf] = psctrans(tc, dim, tp)
%PSCTRANS Perform percent signal change (PSC) transformation.
% P = PSCTRANS(S) transforms the signal S to percentage change (with a
% mean value of 100) along the first non-singleton dimension. This is a
% typical application in functional magnetic resonance imagin... |
57ea0782e5acbe1b3783b361abbb5b98da15e4f32dfbc91b0e7a91607b7e4a4d | MATLAB | 5,664 | 149 | function [outValues,outValuesFreq,outPeriods] = IPEMMECAnalysis(varargin)
% Usage:
% [outValues,outValuesFreq,outPeriods] = ...
% IPEMMECAnalysis(inSignal,inSampleFreq,inMinPeriod,inMaxPeriod,...
% inStepSize,inHalfDecayTime,inPlotFlag)
%
% Description:
% Performs a periodicity analys... |
4f5a5cac1351a6db329284127bbd884022f4244b4c582fa4f6796619477b9842 | MATLAB | 5,666 | 180 | function V4 = spm_file_merge(V,fname,dt,RT)
% Concatenate 3D volumes into a single 4D volume
% FUNCTION V4 = spm_file_merge(V,fname,dt)
% V - images to concatenate (char array or spm_vol struct)
% fname - filename for output 4D volume [defaults: '4D.nii']
% Unless explicit, output folder is the one conta... |
ab3a62d2a6b0a7525efa55d30289d4c62cd2d773e919d852ad2e7536c07c19aa | MATLAB | 5,671 | 125 | % This script can be used to reproduce the figure 3 of the manuscript
% Barbieri, Toepfer et al., 2023. The plot displays GPR-based tuning
% response profiles of 16 voxels of subject 318. The following script is
% divided in 3 parts. The first shows the procedure for selecting the
% searchlight to from which to extra... |
12b16700db5b83b51f5fbd714fd82e05a2c3daccbb3844f3a13a15273e3cc803 | MATLAB | 5,675 | 174 | % mosaic parameters
% mkdir(strcat(datapath,'dist_corrected/volume_tmp'));
id=1;
datapath='/projectnb2/npbssmic/ns/210310_4x4x2cm_milestone/';
Xsize=1000;
Ysize=1000;
Xoverlap=0.15;
Yoverlap=0.15;
% add path of functions
addpath('/projectnb/npbssmic/s/Matlab_code/PSOCT_code');
addpath('/projectnb/npbssmic/s/Matlab_cod... |
bcc52c377176557c6ada5d273dc6643184c3764ac3bbbac9a62857f895b37870 | MATLAB | 5,679 | 145 | function tSC_thetaprop(mainPath, animal, session, ch, isstim, isrun)
%TSC_THETAPROP Calculates theta properties during tSC presence
% TSC_THETAPROP(MAINPATH, ANIMAL, SESSION, CH, ISSTIM, ISRUN) is detecting
% theta cycles expressing different tSCs and calcultes the properties of
% these cycles including the n... |
1a23a0c945ce4b265f9203d4da0505d6293f3dfb47601b7f0c3a11c6ded33b5d | MATLAB | 5,686 | 214 | %% Figure 2c & d
%%
clear
ft_defaults
%%
rng('default');
addpath /Users/'Janweber 1'/Documents/MATLAB/general_functions/ % add functions
%% - LOAD EXAMPLE DATA - %%
path_data = '/Volumes/IMPECOG/iEEG_Data_JW/SingleSubjects/OSL24/Data/HFA/PCA/PCA_ROI_Data/';
load(fullfile(path_data, 'OSL24_activedata_ROI_pc... |
a51c7503b37e117921bafd8ca347613a38430d6edd07f3f487032e7c0823b3c1 | MATLAB | 5,686 | 113 | function sleep_replay_sum_histogram(epoch)
% Plots distribution of replay events over post sleep 2 & 3 for each track and protocol.
% Histogram is calculated as the sum of replay events for each track & for each experiment (always within a protcol),
% and averaged (divided) by number of active sessions at each time b... |
c88ca887362aebecc2ff61329278fca2dfce38a7dbd8f022f4d9a6cae34be4c4 | MATLAB | 5,690 | 166 | %%%%%%%%%%% BATCH_simulation %%%%%%%%%%%
% - run it section by section
% - results are NOT saved automatically
% - numeric (BM) solution is calculated in NUMERIC_SIM
% it supports 1 water (A), 1 MT (C) and up to 5 CEST/NOE pools (B,D,E,F,G)
% - analytic solution is calculated in ANALYTIC_SIM
% it supports 1 water (... |
f35fe59b7e8c562643cbe9465399650376c6fbc9fee5e2065e515337dd664f58 | MATLAB | 5,690 | 94 | % THETA SEQUENCES QUANTIFICATION : QUADRANT RATIO
% MH 2020
% From Feng et al (2015,J Neuro).Decoded probabilities +-50 cm around the animal’s location, and 1/4 theta cycle around the mid-time
% point of the theta sequence, were divided equally into four quadrants:
% Quadrant I & III: summed decoded probabilities oppo... |
029859bcc7de80df33a34ebdb9e9aa9b77e0b4dd0beee6724cbef3bb5586c693 | MATLAB | 5,692 | 112 | function [Im_MIP, Im_SWI4MIP_resliced, ind_SWI4MIP_surround_aTRUPC, Im_minIP] = calc_SWI_MIP(varargin)
% Input:
% dicom_path_aTRUPC: dicom folder of aTRUPC flow-comp images (the first series)
% dicom_path_SWI: dicom folder of SWI
% bCoreg: boolean flag, if bCoreg=1, do inplane coregistration between SWI and aTRUPC
... |
a5557d775114b1ea3b6b299d3133424099a3dc66b56140e62d59260f119e470f | MATLAB | 5,693 | 161 | %% Frequency of single cell oscillations - All sessions
clear all
close all
dbeh_path='C:\Users\xscogno\MATLAB\Flavio2\Waves\Tracking data\';
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\... |
1beb17ce26e8a7299318b82508f88d13a1c46aa3cc25ca805dea201876447b73 | MATLAB | 5,695 | 113 | function [csc_ts, csc, sFreq] = ReadCSC_ag(fname, Trange, output_sFreq)
%
% function [csc_ts, csc] = ReadCSC_ag(fname, Trange, out_sFreq)
%
% note: the main difference from 'ReadCR.m' is that the time is in micros.
% This function allows for downsampling. This is based on
% ReadCR_tsd, but is not stru... |
14b148842846bc6df3ce3fbfa28af9223426ae89d3a0fee6fa46672f640410ee | MATLAB | 5,697 | 176 | function [meta] = Initialize_Params() % clc
% clear all;
% close all;
% Dataset = 'Dataset'
% if ~exist(Dataset, 'dir')
% mkdir(Dataset);
% end
%fin = fopen('Test.xlsx');
%disp(data)
%A = csvread('Test.csv') %, 'columns', {'X, 'Y', 'Z'});
%disp(A)
A = readcell(['... |
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