sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
50e20a53946918d77487d00d06661dda7200492b701d053fbfcba19e52881973 | MATLAB | 19,347 | 797 | %% Pattern analysis
%compute pattern space
%~60 dimensional, consistent over animals and in total
%highly overlapping over animals and days: siloette score
%an active sleep bout traces out a trajectory in this space
%and overlapping
%distributions in nearest points (all-all vs within octopus). Should look
%within... |
2aca344686dc092d3cdce4335bfeec71d011af3d98920115ac901fa0b1d008ad | MATLAB | 19,405 | 476 | function [dat,info]=loadIntanRHD(filename,timeRanges)
% load intan files
% timeRanges=[start,end] in sec
% modify from read_Intan_RHD2000_file, 2022-07-18
% read_Intan_RHD2000_file
% Reads Intan Technologies RHD data file generated by Intan USB interface
% board or Intan Recording Controller. Data are parsed a... |
326c90017e443908e445f72813adbacbe2529eec8b13bdc4345d8c210353cbdc | MATLAB | 19,736 | 451 | function [] = Training_assolearn_fmri(suj_code,orig_path)
% INPUTS: - suj_code (ex: 'P01')
% - orig_path
% - run_nb (0 to 5)
%
% OUTPUTS: in the folder Results/suj_code, Results_Assolearn_fMRI_suj_code_Run_nb_time_exp.mat', with trial_list:
% c1/ block number - 0 (training) t... |
8b480df358cc6270fa5da4c1acf0ae6e4294dd3fb91356ca885468a076084a14 | MATLAB | 19,860 | 514 | classdef ImageType < handle
% This class is compliant with itk::Image class
% by Alberto Gomez, 2011
%
% Update: add Support for passing several points, for speed (start 18/oct/2011)
properties(GetAccess = 'public', SetAccess = 'public')
data=[];
size=[];
origin=[]; % fi... |
fa87606eefd597d37e11671a4c137615436eebe4e218afade9bf5ea20f64da71 | MATLAB | 20,047 | 547 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MRI Estimation for MEG Sourcespace (MEMES) using Elekta rather than
% Yokogawa data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function MEMES3_elekta(dir_name,fif_file,path_to_MRI_library,me... |
12e3d6e911707b8f6278289584e0d7035a4238288e71efe5e37ccbac067e3bde | MATLAB | 20,124 | 380 | % This script loads saved outputs from TargetRFMap_Figure2_SavedOutputs,
% GratingRFMap_Figure2_SavedOutputs and Expt_Screen_Info
% Using this data it plots the RF centres for both the Grating and Target
% RFMaps for all neurons. Comparisons of Target and Grating RFs screen position are also made.
% Note this analysis... |
18f89664b0b6968c5f2bd2f1696f4c4d45b8f3562196c50bf4bf66e36cfbf183 | MATLAB | 20,155 | 588 | function handles = plotSpread(varargin)
%PLOTSPREAD plots distributions of points by spreading them around the y-axis
%
% SYNOPSIS: handles = plotSpread(data,binWidth,spreadFcn,xNames,showMM,xValues)
% handles = plotSpread(ah,...)
%
% INPUT data: cell array of distributions or nDatapoints-by-mDistributions
% ... |
2d0738bc4906e42ce6065f911571db618030c40948b25a6756095c939db0d736 | MATLAB | 20,197 | 420 | function [Ysrc,Ycls,Yb,Yb0,job,res,T3th,stime2] = cat_main_updateSPM(Ysrc,P,Yy,tpm,job,res,stime,stime2)
% ______________________________________________________________________
% Update SPM preprocessing.
% Subfunction of cat_main.
% ______________________________________________________________________
%
% Rober... |
ba18a0001d5814d7dabefc8202dfd34d78a7bbe86dd251b6fe5a3ef8d486f2b0 | MATLAB | 20,265 | 590 | function handles = plotSpread_modified(varargin)
%PLOTSPREAD plots distributions of points by spreading them around the y-axis
%
% SYNOPSIS: handles = plotSpread(data,binWidth,spreadFcn,xNames,showMM,xValues)
% handles = plotSpread(ah,...)
%
% INPUT data: cell array of distributions or nDatapoints-by-mDistrib... |
8e3c17405e8453d692d8e66f949c3ecd5758f5c6d24dfd1176cabbb8f0470858 | MATLAB | 20,312 | 419 | %%% runafew
clear
close all
clc
%%
%path_temp = 'S:\R-MNHS-SPP\Bellgrove-data\4. Dan Newman\Participant Folders_new\'; %Monash PC
path_temp = 'C:\Users\Dan\Desktop\Big_Dots_Data\';
%%
subject_folder = {'LK_07_04_14','AR_08_04_14','MH_14_04_14','AA_15_04_14','NT_16_04_14', ...
'OF_28_04_14','RO_25_04_14','PR_20_04_... |
786f00f39982a3782956ef943d650335e0a8e05b02de327614d198eaca76aed0 | MATLAB | 20,393 | 438 | % This script loads saved outputs from TargetRFMap_Figure2_SavedOutputs,
% GratingRFMap_Figure2_SavedOutputs and Expt_Screen_Info
% Using this data it plots the RF centres and directionality of both the Grating and Target
% RFMaps for all neurons. Comparisons of Target and Grating RFs directionality and screen position... |
d6b40e345ddd2e260889249b7d70f36fd1d3c25a652ca6e0325a3a9938bab39b | MATLAB | 20,482 | 370 | %Script to plot Extended Data Figure 3: neural responsiveness varies as a function of stimulation parameters
%
%To use this script, first set path to response_calibration_data.mat file
%
%Next, define which calibration type you want to plot (set variable calibration type). The options are as follows:
% - 1: Interpuls... |
64cd94218ff4a13930b2442ad2362d21c86ccb218a3c900ad363e5d2a9da88b5 | MATLAB | 20,605 | 293 | %-----------------------------------------------------------------------
% Job saved on 25-Apr-2020 11:25:08 by cfg_util (rev $Rev: 7345 $)
% cfg_basicio BasicIO - Unknown
% spm SPM - SPM12 (7771)
%-----------------------------------------------------------------------
% ----------------------------------------------... |
274aecc88ed54fdedaf84d695b765058c1f8200cefdf71e96bd873f09294dc59 | MATLAB | 20,745 | 530 |
function [DD_session1, DD_session2, VV_session1, VV_session2,LDV_session1,LDV_session2,RDV_session1,RDV_session2, ...
within_session1, within_session2, between_session1, between_session2, ICCvalue, ICCvalue_CI ] = REL_helper_CalculateConnandRel(method,dataDir,subjects,analysisSpace, sessions, CorrType, roiTS,fileN... |
c025e60f696907d70b3c1a7be0d347a4e3a3975bd71d55f3d4a11aad5f42482b | MATLAB | 20,750 | 503 | function [map,num,typ] = brewermap(N,scheme)
% The complete selection of ColorBrewer colorschemes (RGB colormaps).
%
% (c) 2016 Stephen Cobeldick
%
% Returns any RGB colormap from the ColorBrewer colorschemes, especially
% intended for mapping and plots with attractive, distinguishable colors.
%
% Syntax (basic... |
4a77250579dfbf1b0e2636cff4a8449f1c00dc7ec30ebfc187e8133a7c95b9e3 | MATLAB | 20,772 | 412 | auto_stimulus_period = true; %stimulus_period is found by autocorrelation if this is true
BTA_playback = false;
stimulus_period = 60*14-1;
starting_shift = 0;
relevant_track_fields = {'BehavioralTransition','Frames'};
load('reference_embedding.mat')
%load('C:\Users\mochil\Dropbox\LeiferShaevitz\prelim data\Vibrations... |
b48d629182927b489485a838c238129bb01f15bf5c66eeeb651d29c2b56f5150 | MATLAB | 20,794 | 400 | % Written by Aleh Sudakou (https://www.researchgate.net/profile/Aleh-Sudakou)
% Nałęcz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences
% This is one of the codes shared on https://github.com/asudakou/Analyzing_TD-NIRS
% Last updated: 20 May 2023
%% Description:
% Using LMA ... |
cf1eb7874b89eaa8297c1cb3fe8e9febc645604ced08b34252c9d2edec20d983 | MATLAB | 20,905 | 530 | %This Matlab code is associated with Chowdhury et al PLOS Computational Biology
%It gives an example of the major algorithms used in the paper
%
%It can be run directly from the data file that has been uploaded
%
%It starts by performing a neural network relating the sequences on the
% peptide array to the bin... |
bb6913893a47551a3e156d2dc540397c833f74b8644198a0a0c5096c3a29f5de | MATLAB | 20,951 | 572 | function bh = figure_boxplot(data_input,...
text_label_in,label_xaxis_data_in,text_title_in,label_orientation_choice_in,...
box_color_in,box_lineWidth_in,box_widths_value_in,box_color_transparency_in,...
median_lineWidth_in,median_color_in,...
whisker_value_in,...
outlier_marker_in,outlier_mark... |
c931be519d7186c0975866c9b3aadc3757ddc2f3b10bb5e09bfff5969131ebbb | MATLAB | 20,993 | 519 | %% Spike trigerred power plots
clear all
%close all
%% Load files
cell_id=[];Is_ratio3=[];d_id=[];
pT=[];pT2=[]; nn=0;nn1=0;
CHANNEL=1;
i_motion_threshold=300; % image motion threshold
sw_t=2;
for gh=[ 1 2 ]
if gh==1
%cd('/home/hanlabadmins/eng_handata/eng_research_handata2/Hua-an_Tseng/Data/SomArc... |
4f9e2c1f95ee671ee7ca2e8537931d3fec5b31f666ef133b670df31e1cd056f8 | MATLAB | 21,309 | 440 | function DynamicPredictions_RUN_ERFdynamicRSA_searchlight(cfg,iSub,~)
% You can run this function locally (by looping over subjects), or send to a cluster (which I did using the accompanying "cluser_shell.m" function)
% set some directories depending on running this locally or on a cluster:
if isfield(cfg,'cluster... |
4e1028927971dbdec3265e4ff6ace09de1baed24f002be23948b9e85bdb696ae | MATLAB | 21,368 | 420 | function output = fitCHTC(config, name, user)
% fitCHTC
% This function creates a zip file containing the files necessary to perform a gLASSO/wgLASSO fit on CHTC or other
% HTCondor systems
%
% config: This struct contains all the necessary information for the configuration to be run on CHTC.
% Details ... |
05d312de9f5d24e5064f06116322294e916fa26fc6fa833b58dcb5bcc6ef02d5 | MATLAB | 21,391 | 526 | %% Online performance when changing stanchion
% ReFIT both monkeys - changing stanchion
monkey = { 'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joke... |
54324a978d0d4c71280968352547fc89f9fb3d9343bba33e22d7152615d258e9 | MATLAB | 21,625 | 530 | function [img,img_out]=general_NCZLd(image_name, stim_radius, mida_min, epsilon, kappay, normal_output)
% NCZL main file
% stimuli location
addpath([pwd '\black_and_white_stimuli_Sets_1_to_4\'])
% mirror (toroidal) wrapping
do_toroidal_wrapping = 1;
%-----------------------------------------------------------------... |
6d1d46371fca9e1da324f7e78456529d716a336d19027512618a31c1308f19c2 | MATLAB | 21,692 | 576 | function MEMES3(dir_name,grad_trans,headshape_downsampled,...
path_to_MRI_library,method,scaling,varargin)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MRI Estimation for MEG Sourcespace (MEMES)
%
%%%%%%%%%%%
% Inputs:
%%%%%%%%%%%
%
% - dir_name = directory fo... |
c38c000479aeb85950ffd0b135aa19f9e124666fc5295e21baa4894feba40390 | MATLAB | 21,758 | 720 |
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% global settings
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
highres = false;
%FM = 'BM';
FM = 'MBM';
%highres = true;
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
label2 = load_unto... |
379c11d923051c61e4235433944f82330636ae685c862cb3f667996a1b4773a5 | MATLAB | 22,245 | 461 | function Obj=SOFAconvertConventions(Obj,varargin)
% Obj = SOFAconvertConventions(Obj) converts a SOFA object to SimpleFreeFieldHRIR
%
% Supported conventions:
% SimpleFreeFieldSOS
% SimpleFreeFieldTF
% SimpleFreeFieldHRTF
% FreeFieldHRTF
% some special cases of GeneralTF, GeneralTF-E.
%
% When usin... |
a6662e55535a8c61655ab8424f0359b837b7d5b5101d9c8f43966d780a5cd680 | MATLAB | 22,273 | 593 | % Some parameters
samprate = 50000; % 50k sampling rate
use_textures = 1;
if use_textures
samprate = 20000; %sampling rate was only 20k for McDermott files
%Needt remember this for when port over to check performance
end
fband = 32; % Frequency... |
81f32769d93a34f08c47678d711469328c2cfefcf08e5faf15582be5498c119c | MATLAB | 22,330 | 380 | function [] = analyse_behavior_conf(suj, group, comp)
% ---------------------------------------------------------------------------
% Analyze the associative learning task of the fMRI study
%
% INPUTS:
% - Subject code: suj = 'ML_C01' for instance
% - Group: group = 'NT' or 'ASD'
% - Comp: co... |
88617ffb85516a85d693551807c3937a1ee7ead821427794de934222a54005e2 | MATLAB | 22,379 | 265 | % Marjan Biria; 14/01/2022
% This scripts uses the GM, WM, CSF segmentations for the whole brain (taking C1,
% C2,C3 which are respectively GM, WM,and CSF; It takes one file from the spectroscopy data to
% find the location of our voxels, running it for ACC, SMA, and OCC to get
% tissue-fractions. It has a for loop to ... |
2ac1339226173f474e542c97ccc2e145e37251edc4ca939db783d5432eba4c1f | MATLAB | 22,426 | 449 | load('reference_embedding.mat')
%load('C:\Users\mochil\Dropbox\LeiferShaevitz\Papers\mec-4\AML67\behavior_map_no_subsampling\Embedding_LNPFit\LNPfit_behaviors_reordered_20171030.mat')
% LNPStats = LNPStats_directional_ret;
% meanLEDPower = meanLEDPower_directional_ret;
load('C:\Users\mochil\Dropbox\LeiferShaevitz\Paper... |
c8b49f052a5671558bb84ac5a9fdc07e1a8c759fa883bbd80b4dd9887207d239 | MATLAB | 22,635 | 473 | function DynamicPredictions_RUN_ERFdynamicRSA_ROIsource(cfg,iSub,iROI)
% You can run this function locally (by looping over subjects), or send to a cluster (which I did using the accompanying "cluser_shell.m" function)
% set some directories depending on running this locally or on a cluster:
if isfield(cfg,'cluste... |
56aa7d41b43ef1cb78381b0a3597a4fc5eafdbb068f60ad0e39291a5a4079f09 | MATLAB | 22,776 | 239 | function [varargout] = ...
Vulintus_Collate_Functions(start_script, collated_filename)
%
%Vulintus_Collate_Functions.m - Vulintus, Inc., 2016
%
% Vulintus_Collate_Functions collates all of the *.m file dependencies
% for the Vulintus program specified by "start_script" into a single *.m
% file with a filena... |
f46fad688963ccf83dbd86a66ecd98dbc4396c04e21a631ccab34baf94c8317f | MATLAB | 22,777 | 550 | % This script is used to analyze each neurons response to dual stimuli
% traversing the target RF, stimulated with a small target, and the grating
% RF, which is stimulated using a bar of varying heights and comparing
% these response to the same neurons response to the individual stimuli.
% It then calculates and p... |
a0a94aceac85c019ba0725bbb3a7e36ad67c54b51af8c872fa31b6a9cf60a9d5 | MATLAB | 22,878 | 550 | %% Offline prediction plots for multiple days
clearvars
runFiles = {{'Z:\Data\Monkeys\Joker\2021-08-05\Run-003',
'Z:\Data\Monkeys\Joker\2021-08-05\Run-004',
'Z:\Data\Monkeys\Joker\2021-08-05\Run-005'},
{'Z:\Data\Monkeys\Joker\2021-08-12\Run-003',
'Z:\Data\Monkeys\Joker\2021-08-12\Run-004',
... |
a254757ae31dcade8e068afda38475c6c0196ccd92b723bb0c797e219687fb38 | MATLAB | 23,111 | 522 | function [] = Main_code_assolearn_conf(suj_code,orig_path)
% INPUTS: - suj_code (ex: 'P01')
% - orig_path
% - run_nb (0 to 5)
%
% OUTPUTS: in the folder Results/suj_code, Results_Assolearn_fMRI_suj_code_Run_nb_time_exp.mat', with trial_list:
% c1/ block number - 0 (training) t... |
7ed7bd5062c28cf7a950547bbe02e56b7cea576075dcded88c0933c10059d4dc | MATLAB | 23,141 | 691 | function [gx_final,gy_final] = Rmodelinductiond_v0_3_2(Iitheta,struct)
% from NCZLd_channel_ON_OFF_v1_1.m to all the functions for implementing Li
% 1999
%-------------------------------------------------------
% get the structure and the parameters
% scale=wav.scale;
% orient=wav.orient;
wave=struct.wave;
use_fft=st... |
b22909eba3ac2c8d37be0ba4ea82df182a4642e60ec9883a13a5452da87870cd | MATLAB | 23,240 | 514 | function [] = Main_code_assolearn_fmri(suj_code,orig_path,run_nb)
% INPUTS: - suj_code (ex: 'P01')
% - orig_path
% - run_nb (0 to 5)
%
% OUTPUTS: in the folder Results/suj_code, Results_Assolearn_fMRI_suj_code_Run_nb_time_exp.mat', with trial_list:
% c1/ block number - 0 (tra... |
c17d62b67c3460c9218d972c9bad8053e68bdb12484efed8afb158cf2f983acf | MATLAB | 23,407 | 637 | function HelperData = dspCMap2T(map,ChanPos,varargin)
% dspCMap2 - Display topographic scalp maps
% ----------------------------------------
% Copyright 2009-2011 Thomas Koenig
% distributed under the terms of the GNU AFFERO General Public License
%
% Usage: dspCMap(map,ChanPos,CStep)
%
% map is the 1xN voltage map to ... |
249e264bba5c3f412f046a04c76d46baf134c1cea3dad9106fbc9847947c8dc5 | MATLAB | 23,688 | 593 |
function [DD_session1, DD_session2, VV_session1, VV_session2,LDV_session1,LDV_session2,RDV_session1,RDV_session2, ...
within_session1, within_session2, between_session1, between_session2, ICCvalue, ICCvalue_CI ] = REL_helper_CalculateConnandRel_Segmental(method,dataDir,subjects,analysisSpace, sessions, CorrType, r... |
4eb966bbb65fd14a99f8aa57992961d3df1199fe88196263fafba9be8c0e37f4 | MATLAB | 23,781 | 487 | % Written by Aleh Sudakou (https://www.researchgate.net/profile/Aleh-Sudakou)
% Nałęcz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences
% This is one of the codes shared on https://github.com/asudakou/Analyzing_TD-NIRS
% Last updated: 20 May 2023
%% Description:
% This scrip... |
2b22ebd8a9fc5cd0c9c05151cd1406264f4dd70f287b5887eb73dfc5273c0a89 | MATLAB | 24,004 | 438 | % plot figures that will go in the paper
% please download the following plotting toolbox and add it to the folder "export_fig": https://www.mathworks.com/matlabcentral/fileexchange/23629-export_fig/
% created in matlab R2021a
clear all
close all
export_figPath = what('export_fig');
cleanupFcn = onCleanup(@() rmpath... |
345b16dcd69ea4a205932817111536eedbe0d95728c6c78fbc893af7cd68194a | MATLAB | 24,213 | 882 | close all
clearvars
addpath(genpath('figureDataFunctions'));
%% params
caxis_fixed = [0 30];
drawColors = [0,0,0;...
230, 159, 0;...
86, 180, 233;...
0, 158, 115;...
213, 94, 0]/255;
speed_bins = linspace(0,50,500);
speed_bins = interp_resample(speed_bins',100);... |
5d55d50ab8baeaed77a30f8415b492216f9e8e7434f80ee83b1a84ca79da6304 | MATLAB | 24,282 | 596 | % noise on weights (stimulus and behavior) to compute robustness
% local weights for optimal decoder stimulus and behavior
% global weights for fish decoder (computed with EArmse)
% M Metzen 01/23
% needs the following:
% datafiles: Binaries*; EArunsRMSE* (-> unpack Binaries.zip and EArunsfiles.zip !!)
% for ... |
f2b51c1b40a80b4abea8ab13a36fd7dbdebb4a02ce5673601ae6d15a422befcb | MATLAB | 24,360 | 599 | function [par] = readpar(parfile)
%[par] = readpar(parfile);
%read scan parameters from exported PAR files (Philips research tools)
%
% output :
% - par : scan parameters and image scaling factors -
% float_data = (int_data * RS + RI) / (RS*SS)
%
par.problemreading=0; % will be set to 1 when an error occ... |
38edafd5929a6ebbb5add9220681a34f8b430dd69d8bf89b95aae013110bb812 | MATLAB | 24,838 | 529 | function [status] = ft_hastoolbox(toolbox, autoadd, silent)
% FT_HASTOOLBOX tests whether an external toolbox is installed. Optionally
% it will try to determine the path to the toolbox and install it
% automatically.
%
% Use as
% [status] = ft_hastoolbox(toolbox, autoadd, silent)
%
% autoadd = 0 means that it will ... |
efeb89cf6cb513124847aab2645302120a8a13b01338d4810466eadfc30cdf6f | MATLAB | 24,944 | 714 | %This code is for 1x10 min long movies and
%with movement detection. It is based of Jake Jordan's version and ABC
%version
%subtract offset of position data (new baseline at zero)
clear all
filelistdata2 = dir('filelist') %location of first movie (any file will do)
MaxIterations=1; %set number of iteratio... |
92baffd0755a5ceff187866f5a02505ea65be76a771fac1cb0aea650eebd22ff | MATLAB | 25,007 | 549 | clear all
close all
dataset_list_paths = [ ...
{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\d5HT1b_similar_od_handovers.xls'};...
{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\c305a_similar_od_handovers.xls'};...
{'C:\D... |
327c0bcb0cd20ad9384913ec02ecebfb707481198bfa17945de120fd26b3f52e | MATLAB | 25,430 | 595 | % Written by Aleh Sudakou (https://www.researchgate.net/profile/Aleh-Sudakou)
% Nałęcz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences
% This is one of the codes shared on https://github.com/asudakou/Analyzing_TD-NIRS
% Last updated: 20 May 2023
%% Description:
% This scrip... |
d2ff22bed6d15cdcd1ed593abc033c1ce9e189363c55d058c034c556007959a5 | MATLAB | 25,760 | 678 |
%% Running notes
%2022-09-29 Decide to make this its own separate file instead as toggling
%this in addition to all of the other toggles will be obnoxious. Need to
%figure out exactly what Yale meant...only do this for correlation
%analysis? Make the null distribution from randomly sampling from all
%correlation ma... |
a08e51f08c72241c753492359ec324c4efd240fc3182a6c4f699b47de0976dd9 | MATLAB | 25,791 | 597 | function fMRI_Preprocessing(group, comp, fieldmapcor)
% -------------------------------------------------------------------------
% Original code downloaded on https://github.com/ilcb-crex/CREx_fMRI (http://www.blri.fr/)
% Modified by Laurie-Anne - February 2020 - for the fMRI Assolearn experiment
% INPUTS:
% ... |
b78b43a9c649817f6ffdac89a868df95d3f6fbc6a78398d940c56c969b0a9eea | MATLAB | 26,307 | 510 | function Track = initial_sweep(image_stack, Track, parameters, plot_index)
% given a sequence of worm images, this function finds the centerlines
%% STEP 1: define parameters %%
nPoints = 20; %20 Numbers of points in the contour
gamma = 15; %Iteration time step
ConCrit = .1; %Convergence cr... |
7efce97ac95ca453fbee2fa83c7787a443c2db27640ff80e252f1e52fb7a9853 | MATLAB | 26,476 | 751 | %% get raw spikes at different time bins for decoding
dwindow=[-0.5 2.5];
dbinsize=0.25;
dbinEdges=dwindow(1):dbinsize:dwindow(2);
dbinTimes=dwindow(1)+dbinsize/2:dbinsize:dwindow(2)-dbinsize/2;
preRun = true;
if preRun
load('dactivity.mat');
else
dactivity=cell(totalNeurons,6);
NN=0;
for incses=1:su... |
9aa2c82a4729ebb3d1babfc98196aa93c801a31cd3fb975b465da7d02f31d1e3 | MATLAB | 26,479 | 833 |
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Evaluating the Mutual Information (MI) between Schaefer ROIs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ParRunFiles store the presentation of each block for each par for each
% run
ParRunFiles=addpath('C:\Users\dk00549\OneD... |
822061b32db522008100b3daf7bc42cd7f5f5dc72748fa49c2b75632bd543d91 | MATLAB | 26,633 | 674 | function child_MEMES(dir_name,elpfile,hspfile,confile,mrkfile,path_to_MRI_library,bad_coil,varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MRI Estimation for MEG Sourcespace (MEMES) cutomised for child MEG.
%
% Written by Robert Seymour (Macquarie Univ Dept of Cognitive Sci... |
d6e9acec438a3cfa2b8749d9fd6cd8d8a2fbc627e32e8d3216b435d72c938d76 | MATLAB | 26,798 | 656 | function cat_main_reportfig(Ym,Yp0,Yl1,Psurf,job,qa,res,str)
% ______________________________________________________________________
%
% Display CAT report in the SPM grafics window and save a PDF and JPG
% file in the report directory.
%
% cat_main_reportfig(Ym,Yp0,Psurf,job,res,str);
%
% Ym .. intensity no... |
0a55af50588532328f9f6ea9f3d2cd3255e916e7ca23bd372f0cb042d108e052 | MATLAB | 27,134 | 495 | % plot figures that will go in the paper
% please download the following plotting toolbox and add it to the folder "export_fig": https://www.mathworks.com/matlabcentral/fileexchange/23629-export_fig/
% created in matlab R2021a
clear all
close all
export_figPath = what('export_fig');
cleanupFcn = onCleanup(@() rmpath... |
e5a6700dde278727e21855f860ba8afcb9d2c9f8c71b2773f3cc2a5b555bac6e | MATLAB | 27,414 | 514 | function success = track_image_directory(folder_name, analysis_mode)
% tracks and saves individual worms for all the images in a directory
addpath(genpath(pwd))
parameters = load_parameters(folder_name); %load experiment parameters
%% STEP 1: initialize %%
if nargin < 2
analysis_mode = 'al... |
5ced4053e8d0894bf3f7643a2b7adc321acadbbd2a0849bd673432587000ce73 | MATLAB | 27,565 | 685 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MRI Estimation for MEG Sourcespace (MEMES)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function MEMES(dir_name,elpfile,hspfile,confile,mrkfile,path_to_MRI_library,mesh_library,initial_mri_rea... |
278ee67e430b63f377d42e2461430dc657cb6620b32c10742139a3a7f7109fec | MATLAB | 27,857 | 693 | %% Offline prediction plots for multiple days - kinematics
clearvars
runFiles = {{'Z:\Data\Monkeys\Joker\2021-08-05\Run-003',
'Z:\Data\Monkeys\Joker\2021-08-05\Run-004',
'Z:\Data\Monkeys\Joker\2021-08-05\Run-005'},
{'Z:\Data\Monkeys\Joker\2021-08-12\Run-003',
'Z:\Data\Monkeys\Joker\2021-08-1... |
06089d5344447e5e922fb31bfd705de3bb8bd1bbab1cc936995a1f260cf94495 | MATLAB | 28,085 | 616 | function cat = tbx_cfg_cat
% Configuration file for segment jobs
%_______________________________________________________________________
%
% Christian Gaser
% $Id: tbx_cfg_cat.m 1605 2020-04-14 18:44:36Z gaser $
%
%#ok<*AGROW>
addpath(fileparts(which(mfilename)));
addpath(fullfile(fileparts(which(mfilename)),'cat_ru... |
d9a440a1e5d94c41e983f483eecfd4c10f63bf93bc6641fb0ddcb733e8fee8b4 | MATLAB | 28,170 | 444 | function [] = analyse_behavior_mri(suj, group, part, type, comp)
% ---------------------------------------------------------------------------
% Analyze the associative learning task of the fMRI study
%
% INPUTS:
% - Subject code: suj = 'ML_C01' for instance
% - Group: group = 'NT' or 'ASD'
% ... |
ec24fc07193eac287a869ff3dadc60518e6e94bf4838d5f2572540eea9e3c8c0 | MATLAB | 28,187 | 832 | function [axh,figh] = lassoPlot_YC( B, plotData, varargin )
%LASSOPLOT Plot coefficient values or goodness of fit of lasso or elastic net fits.
% [AXH,FIGH] = LASSOPLOT(B, PLOTDATA) creates a Trace Plot showing the
% sequence of coefficient values B produced by a lasso or elastic net fit.
% B is a P by nLambda matr... |
1b0b3ad86d0f6b769ea7270635861d6a360a74023476b9cc84279eb76ab5dc26 | MATLAB | 28,381 | 703 | %% Online performance when using two models
% KFs changing model - both monkeys
monkey = { 'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Joker',
'Batman',
'Bat... |
c6779476194e0bfc0f90301bd16d91b9928af5c06740961de808a8e3effb51e5 | MATLAB | 28,792 | 472 | % This script is used to map a receptive field (RF) for each neuron based
% on the output files of the TargetScan function, which extracts responses
% to small target traversing the entire height or width of the screen in
% either direction into 20 bins for each height and width.
% For each of these 400 positions, ... |
adbb2ae2a87e60819771d68c239b306c72ab2a1eef21142efc6ed2f0542813d8 | MATLAB | 29,624 | 1,118 | %% Example traces
cd('/home/sam/bucket/octopus/8k/oct_06')
[bb,aa]=butter(3,[.5/(24/2)],'low');
currMI=h5read('OCT14936.MP4.meanInt','/int');
currMI=filtfilt(bb,aa,currMI);
frames=[405, 783, 1181,1522, 1941, 2318,2668]
figure
plot((1:length(currMI))/30,currMI)
hold on
scatter(frames/30,currMI(frames),'k')
xlabel('t... |
a0018eb983559f5987a8387ee50f6e2f2c4dcb20f2ce0639f816dc5ea0dd2d81 | MATLAB | 29,759 | 967 | function [tmp2,name]=get_the_stimulus(M);
if strcmp(M,'mach')
tmp=imread('Mach_OP.ppm');
name='Mach_OP';
elseif strcmp(M,'im_ver_2')
tmp=imread('im_ver_2.png');
name='im_add_ver_2';
elseif strcmp(M,'im_ver_4')
tmp=imread('im_ver_4.png');
name='im_add_ver_4';
elseif strcmp(M,'im_ver_6')
tmp=imread('im_ver... |
7c75a21f120a41a63b08d2a48e915a075c364d136a5e92939b4eaf07d5a4005f | MATLAB | 30,162 | 665 | clear all
close all
%MBONA3 imaging
dataset_list_paths = [...
{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\Berry_handover_WTalpha3_fedshock_PAplus.xls'};...
{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\Berry_handover_WTalpha3_fedshock_BAplus.xls'};... |
13ad82da5639fa30c94e3fd214735c5db268031f32cb2b01ab59aa0cc71973b3 | MATLAB | 30,196 | 540 | %not used in paper
load('reference_embedding.mat')
%load tracks
% relevant_track_fields = {'BehavioralTransition','Path','Frames','LEDPower','LEDVoltages','Embeddings','Velocity', 'LEDVoltage2Power'};
relevant_track_fields = {'BehavioralTransition','Frames', 'Size'};
%select folders
% folders_platetap = getfoldersGUI... |
a82ebef9ddd55deff142059087364c59195ae6edc5b5599e4f8a4dd3128a7a09 | MATLAB | 30,374 | 1,078 | % This code takes in one cleaned excel sheet and produces all desired
% graphs and processed information regarding myelinated and unmyelinated
% lengths of traced processes
% Rev 2 only uses overall average fiber radius for conduction velocity
% estimates
% plot unmyelinated length vs myelinated length
% plot histogr... |
3b127f8575716e63872fa2faaa417608e966d0dc78e39340735ca9d8e8baf751 | MATLAB | 30,611 | 642 | clear all
close all
dataset_list_paths = [ ...
%{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\d5HT1b_similar_od_handovers.xls'};...
%{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\c305a_similar_od_handovers.xls'};...
{'C:... |
0f4545b0686c6ba4f1b898084bc561b1a3a8e6b27fe557b2f3971a884c25b9f3 | MATLAB | 31,370 | 785 | %BlandAltman Draws a Bland-Altman and correlation graph for two datasets.
%
% BlandAltman(Data1, Data2) - Data1 and Data2 have to be of the same size
% and can be grouped for display purposes. 3rd dimension is encoded by
% colors and 2nd dimension by symbols. The 1st dimension contains
% measurements with... |
24228d74a771372bd739712f611b62720f93269a1c38e31cf3c21e07ed9f02ed | MATLAB | 31,658 | 564 | function DiffusionSimulation(data)
%% Show window with diffusion sumulation the real data
%% repsesnted as a set on polygons and calculated cylinders.
% After simullation graphs show up.
global TimePeriod GTimeStep np charge interCoef diffCoef simComplexity plotTimeStep
global figures stopSimulation
... |
fe073753035a3317ec653745e41e86108b009f35db6d15c8258e01214f940649 | MATLAB | 31,669 | 587 | auto_stimulus_period = true; %stimulus_period is found by autocorrelation if this is true
BTA_playback = true;
stimulus_period = 60*14-1;
starting_shift = 0;
relevant_track_fields = {'BehavioralTransition','Frames'};
load('reference_embedding.mat')
load('C:\Users\mochil\Dropbox\LeiferShaevitz\Papers\mec-4\AML67\behav... |
513a5cdad381d4a33dca1a1a1fe2ea440fe1daa0a605a55ed1c2afbdbaff560a | MATLAB | 31,939 | 874 | % This script is used to analyze each neurons response to a leading edge,
% trailing edge and a discreet object of different heights (3°, 84° or 138°)
% traversing the target RF, the grating RF or both.
%% Filenames to be analysed - Bar eSTMD model
clear all
folders = {'211006_N03P01'
'211005_N01P01'
... |
59052f162bb3fa1dff73edfa78d05fba5a248ac055ae9020de463a62a5db9ff3 | MATLAB | 32,017 | 848 | function ft_write_cifti(filename, source, varargin)
% FT_WRITE_CIFTI writes functional data or functional connectivity to a cifti-2
% file. The geometrical description of the brainordinates can consist of
% triangulated surfaces or voxels in a regular 3-D volumetric grid. The functional
% data can consist of a dense o... |
ad6e21cfc00cfd5e6be3a3e554b9e159d5aec2d31652a329861b0f9caa13963f | MATLAB | 32,210 | 384 | function ardy = Connect_MotoTrak(varargin)
%Connect_MotoTrak.m - Vulintus, Inc., 2016
%
% Connect_MotoTrak establishes the serial connection between the computer
% and the MotoTrak controller, and sets the communications functions used
% for streaming data.
%
% UPDATE LOG:
% 05/09/2016 - Drew Sloan - Separat... |
5bb6296255e115cec69df336726a3a1acad6cc1c6fe4d43c91b7fac9867f661f | MATLAB | 32,529 | 1,100 | %initialize ephys recordings
initEphys
%% amplitude over channels during active sleep %taking mean/max starting at wake transition
allLFP=zeros(384,120000);
allOct=[];
allDset=[];
allBout=[];
for currOct=1:9
dsets= find(oct==currOct);
for dset=1:numel(dsets)
currDset=dsets(dset);
... |
0f4e9f25b692f09c617cf965735d912a3b2a8e0a248d75a4a2972a408500684c | MATLAB | 32,744 | 692 | classdef preprocess_ct < matlab.apps.AppBase
%PREPROCESS_CT A GUI for cropping and re-orienting CT scans.
%
% Use this GUI to crop and re-orient your CT scans to comply with the
% coordinate system used in this toolbox (Rigth, Anterior, Superior).
% Follow the steps outlined in the GUI, check that the pink labels ar... |
2b3151bdb42518dc6f0652700f01257cbfbe814b28426cb47d3c85042b2d9911 | MATLAB | 32,955 | 790 | % Written by Aleh Sudakou (https://www.researchgate.net/profile/Aleh-Sudakou)
% Nałęcz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences
% This is one of the codes shared on https://github.com/asudakou/Analyzing_TD-NIRS
% Last updated: 20 May 2023
%% Description:
% This scrip... |
068ad282df77832b00d5dc29a6655fee09346026b1d8fd01d4e4c18ba0206191 | MATLAB | 34,518 | 978 | % Figures for the Gnomes project
%
% Other m-files required:
% figset.m (common stats and figure settings)
% EEGLAB toolbox https://github.com/sccn/eeglab
% brewermap: https://github.com/DrosteEffect/BrewerMap
% subtightplot: https://uk.mathworks.com/matlabcentral/fileexchange/39664-subtightplot
% cspy: https://uk.ma... |
1331690e8cef21fe3881d09c0432bf0c90b37f28c81080fb21a65b08d1fbbf16 | MATLAB | 34,735 | 816 | clear
close all
clc
chanlocs = readlocs('cap64.loc');
% path_temp = 'D:\Participant Folders_new\'; %TCD Laptop
% path_temp = 'S:\R-MNHS-SPP\Bellgrove-data\4. Dan Newman\Participant Folders_new\'; %Monash PC
path_temp = 'C:\Users\Dan\Desktop\Big_Dots_Data\';
%% Create paths for subjects
subject_folder = {'LK_07_04_14... |
f3fcd9df91cbd49e2d7a9940197c8d2c4c8896fedc46499b6ac4ca5f34bca324 | MATLAB | 34,740 | 953 | function [shape] = ft_read_headshape(filename, varargin)
% FT_READ_HEADSHAPE reads the fiducials and/or the measured headshape
% from a variety of files (like CTF and Polhemus). The headshape and
% fiducials can for example be used for coregistration.
% The input can be a filename (a string), or a cell array of filena... |
a01ca9f7ada6814b2776af4b629ca558e73207f22ada9fe3298409d60c38db75 | MATLAB | 35,148 | 620 | auto_stimulus_period = true; %stimulus_period is found by autocorrelation if this is true
BTA_playback = true;
stimulus_period = 60*14-1;
starting_shift = 0;
relevant_track_fields = {'BehavioralTransition','Frames'};
load('reference_embedding.mat')
load('C:\Users\mochil\Dropbox\LeiferShaevitz\Papers\mec-4\AML67\behav... |
c62ae0bf96e6baa07861345caab9a4e732e697890700bda432ba9a569e39dd57 | MATLAB | 35,148 | 578 | % This scipt loads data that has been used to map a receptive field (RF)
% using a local sinuoidal grating moving in different directions at
% different locations on the screen. It assumes that the experiment has been
% designed so that the patch appears in one location ant moves in x different
% directions, before mov... |
aa42af095347f5a8ce428a6dd52ef5429283fafe999b09b5beccd49546772ed8 | MATLAB | 35,322 | 632 | function fMRI_RunSecondLevel_HGF()
%--------------------------------------------------------------------------
% Process the 2nd level analyses
% Model used: Standard whole-brain (event-related) GLM
%
%
% Contrasts:
% - 1: Tilt
% - 2: Tilt_Eps3: PM epsilon 3 on regressor tilt
% - 3: Tilt_Eps2: PM... |
135f475e3275a5f9ab9d600a5667f3eb4fd88595e0bf3fac3552ae48dcefcb89 | MATLAB | 35,575 | 998 | % miro :: Measured Impulse Response Object
%
% miro Class Definition
%
% MIRO V1, Release 1.04 - 07/Feb/2014
% MIRO V1, Release 1.05 - 25/Dez/2016
% MIRO V1, Release 1.06 - 20/Sep/2017
% #Author: Benjamin Bernschütz (2012-2014)
% #Author: Johannes M. Arend (2014-2017)
% #Author: Christoph Pörschmann (TH Köln, Universi... |
9bb4a06c0cba1dbcf1c5a22c1dd46a4675c4083d96d235bbb98861249ba78b5b | MATLAB | 36,362 | 789 | classdef AABB_tree < handle
% This class defines a AABB_tree
% by Alberto Gomez, 2012
%
properties(GetAccess = 'public', SetAccess = 'public')
rootNode = AABB_node();
mesh; % structure with input Meshes
max_tree_depth=Inf; % we want that each ending leaf is a single... |
2bce8819bb2d6ee2095f2f90d3bc295934e23a7c70b89c8e9968cc43030d9d95 | MATLAB | 36,812 | 842 | function [Yml,Ymg,Ycls,Ycls2,T3th] = ...
cat_main_LAS2(Ysrc,Ycls,Ym,Yb0,Yy,T3th,res,vx_vol,extopts,Tth)
% This is an exclusive subfunction of cat_main.
% ______________________________________________________________________
%
% Local Adaptive Segmentation (LAS):
%
% This version of the local adaptive intensity corr... |
fa5ecc9d1531668396be251b077861a0d25ca371de6eeb76a2f92f7b38accc35 | MATLAB | 36,916 | 917 | function source = ft_read_cifti(filename, varargin)
% FT_READ_CIFTI read functional data or functional connectivity from a cifti-1 or
% cifti-2 file. The functional data can consist of a dense or a parcellated
% representation. The geometrical description of the brainordinates can consist of
% triangulated surfaces or... |
df34d5c233860b02eb4c400e9a63aa7f9d1961a6190b0031995a0cc2b5e3bc49 | MATLAB | 38,664 | 805 |
%GLOSSCATS_CALCFEATURES.m
% Image analysis code for Schmid, Barla, & Doerschner (2023) Nat. Hum. Behav.
% Last update: A.C.S., March 2023
%------- References: ------------------------------------------------------
% Please cite:
% Schmid, Barla, & Doerschner (2023) Material category of visual objects compute... |
d2de5c5f8f21bb19342416f72031492b621f728cf0771ffd20d86339caff5d22 | MATLAB | 38,881 | 1,182 | % Script to analyze olfactory conditioning data across day 3 of each odor set
githubDir = 'D:\GitHub';
addpath(genpath(fullfile(githubDir, 'npy-matlab')))
addpath(genpath(fullfile(githubDir, 'steinmetz-et-al-2019')))
direc = 'D:\GitHub\ottenheimer-et-al-2022\Imaging';
addpath(direc);
%% behavior summary
mice={'pl08',... |
b950c107e71769febaf653098e2b2e0433c1b3fda86055af9f22e1605db60cca | MATLAB | 39,116 | 855 | clear all
close all
dataset_list_paths = [...
{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\MBONG2_PaBaEl_simp_pairing_Berry.xls'};...
%{'C:\Data\Code\general_code_old\data_folder_lists\Janelia\MBONG2_PaBaEl_handover_pairing_Berry.xls'};...
... |
d850b563bf480f14736f0c5d3766aa86770e9067b33eefdd467faa31a2d8ed0a | MATLAB | 39,295 | 962 | % In this code, the preprocessing steps are listed for the following
% manuscript: "" and for the following dataset:
% https://openneuro.org/datasets/ds004386
% In order to run this code the Spinal Cord Toolbox (version 4.2.2 or higher -
% note that for the manuscript version 4.2.2 was used)
% and FSL should be added ... |
499f5368856eca9875d2c49cc512499ab785b6f72eea6c0b96bedef8bbf9d2a4 | MATLAB | 40,089 | 925 | function varargout = cat_vol_qa(action,varargin)
% CAT Preprocessing T1 Quality Control
% ______________________________________________________________________
%
% Estimation of image quality measures like noise, inhomogeneity,
% contrast, resolution, etc. and scaling for school marks.
%
% [QAS,QAM] = cat_vol_qa(act... |
5f11e677d776f04e7bfe2f74f963c9ab112ec0b69ba606963f14e268ea6cfa9b | MATLAB | 40,279 | 540 | %% 3DEPI distortion correction piplines at 7T for in-vivo data
% No-correction, B0 field mapping and reversed-PE (fsl_topup) techniques
% V Malekian, FIL Physics
clc;clear;close all;
addpath('/export/home/vmalekian/Matlab_lib/spm12/')
%% Topup LSR and Jacobian
%%3DEPI fsl topup
for sub=1:22
dir1= [... |
e898aedce0146b496e92543f0066ab2b22acb44125ce5bedf92208ba1d381ea5 | MATLAB | 40,936 | 941 | clear all
close all
base_order_paths = [{'C:\Data\Data\Raw_data\Adithya_airgap_expts_v220210610\30s_Test\CS+_First\'};...
{'C:\Data\Data\Raw_data\Adithya_airgap_expts_v220210610\30s_Test\CS-_First\'}];
vid_path = 'C:\Data\Data\Analysed_data\Analysis_results\air_gap_traj_an\vert_al... |
6c01d92557120493d93d87b0adce5132b292b370799b3350f13cef4a74b332c9 | MATLAB | 41,073 | 1,183 | % Script to analyze olfactory conditioning data across day 3 of each odor set
githubDir = 'D:\GitHub';
addpath(genpath(fullfile(githubDir, 'npy-matlab')))
addpath(genpath(fullfile(githubDir, 'steinmetz-et-al-2019')))
direc = 'D:\GitHub\ottenheimer-et-al-2022\Imaging';
addpath(direc);
%% behavior summary
mice={'pl08','... |
d34410938b42b28528cdbba46e8d7f0eef9c2fedccf30eb716ce1ed91fe3eeda | MATLAB | 41,199 | 899 | function cat_run_job(job,tpm,subj)
% run CAT
% ______________________________________________________________________
%
% Initialization functions for the CAT preprocessing
% * creation of the subfolder structure (if active)
% * check of image resolution (avoid scans with very low resolution)
% * interpolation
% ... |
ba4bf923502c7e4237c6d4e79aa73c8e8baacbaab3daea041d668d19fa8b591f | MATLAB | 42,025 | 965 | clear
close all
clc
chanlocs = readlocs('cap64.loc');
% path_temp = 'D:\Participant Folders_new\'; %TCD Laptop
path_temp = 'S:\R-MNHS-SPP\Bellgrove-data\4. Dan Newman\Participant Folders_new\'; %Monash PC
% save_path = 'D:\Participant Folders_new\';
%% Create paths for subjects
subject_folder = {'LK_07_04_14','AR_08... |
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