sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7008c7af9d7bd5100b870469fbe05f25f8d4cece50eef367716c436fd5638a26 | MATLAB | 27,756 | 900 | function aedes_fmri_gui(DATA,mask)
% fMRI tool GUI
% Check input arguments
if nargin == 0
error('Too few input arguments.')
elseif nargin == 1
mask = [];
elseif nargin > 2
error('Too many input arguments.')
end
% Check data
if isstruct(DATA) && isfield(DATA,'FTDATA')
Dat.data = DATA.FTDATA;
elseif isnumeric(DAT... |
b24ade783c41e10308cdc35fb8763ad6f953393858e029a0d31a3f350bef8255 | MATLAB | 28,072 | 839 | function [z,s,exitflag] = smoothn(varargin)
%SMOOTHN Robust spline smoothing for 1-D to N-D data.
% SMOOTHN provides a fast, automatized and robust discretized spline
% smoothing for data of arbitrary dimension.
%
% Z = SMOOTHN(Y) automatically smoothes the uniformly-sampled array Y. Y
% can be any N-D ... |
ce9d7c4c12e3399e8efefc9b2715803aacefa8b3e69cae480c335c947116af57 | MATLAB | 28,143 | 804 | function cancel = multiWaitbar( label, varargin )
%multiWaitbar: add, remove or update an entry on the multi waitbar
%
% multiWaitbar(LABEL,VALUE) adds a waitbar for the specified label, or
% if it already exists updates the value. LABEL must be a string and
% VALUE a number between zero and one or the strin... |
faa6918912b92793bdfe806bf0b83f6b220df002adaaa64123c91d3aae8ba2b1 | MATLAB | 28,598 | 745 | % Bootstrap: Resample with replacement to generate new samples and return the
% statistic(s) calculated by evaluating the specified function on each resample.
%
%
% -- Function File: BOOTSTAT = bootstrp (NBOOT, BOOTFUN, D)
% -- Function File: BOOTSTAT = bootstrp (NBOOT, BOOTFUN, D1, ..., DN)
% -- Function File: BOOTSTA... |
4c3cd6d6a867d39fd87a60e980cb12bdaa95a9d7990063bc8d47b3f41745bf20 | MATLAB | 28,620 | 769 | %% retrain JAABA classifier using FlyTracker tracks
%behavior = 'chase';
behavior = 'FeAgg';
fakectraxnames = false;
missingtrainingdata = true;
switch behavior,
case 'chase',
jaabaloc = '/groups/branson/home/bransonk/behavioranalysis/code/Jdetect/Jdetect/perframe';
rootoutdir = ['/groups/brans... |
de5f98e9e6912b444acc0afd8685094a60a9a5bc40a8c58985a6001ca41a7452 | MATLAB | 28,622 | 682 | clear all
close all
clc
addpath('/data/jux/BBL/projects/pncBaumStructFunc/scripts/rotate_parcellation-master/Matlab')
addpath('/data/jux/BBL/projects/pncBaumStructFunc/spin_test/spin-test-master/scripts')
addpath('/data/jux/BBL/projects/pncBaumStructFunc/scripts/colorbrewer/cbrewer/cbrewer')
addpath('/data/jux/BBL/pro... |
824c7e1b4f9f41fb85c3c078845fd24184d905d4d8928d89399d2ea701444cb3 | MATLAB | 28,735 | 881 | % makeFunctionsScript.m
%
% Script for making all the functions, ordered in numerical order
%
% CREATED: 2/14/21 - HHY
%
% UPDATED:
% 2/15/21 - HHY
% 3/10/21 - HHY
%% Some constants
% load ephysSettings
[~, ~, settings] = ephysSettings();
% how long functions usually are, in frames, set by panels
defaultLength =... |
5b916e96d8f2e1363b2cb3bc36e8066584dd8cda3802bbbe1f8e81b23861757a | MATLAB | 28,846 | 722 | % Performs wild bootstrap and calculates bootstrap-t confidence intervals and
% p-values for the mean, or the regression coefficients from a linear model.
%
% -- Function File: bootwild (y)
% -- Function File: bootwild (y, X)
% -- Function File: bootwild (y, X, CLUSTID)
% -- Function File: bootwild (y, X, BLOCKSZ)
% -... |
e96d72442f466ceae4e0a2a52b67c7c59a6e8413b8bb9956a5fb45405bac86d4 | MATLAB | 28,857 | 789 | classdef norm_cytof
properties
data
header
channelnames
markernames
time_col
cell_length_col
dna_channels
marker_channels
bead_metals
bead_channels
beads
xp
yp
bead_data
smo... |
66fa18010a62ae1cdc3335aed22fdde08f795b6db20fde1425cd655367cdd936 | MATLAB | 28,885 | 643 | function [CNT,h,e]=cntopen(arg1,arg2,arg3,arg4,arg5,arg6)
% CNTOPEN opens neuroscan files (but does not read the data).
% However, it is recommended to use SOPEN instead of CNTOPEN.
% For loading whole Neuroscan data files, use SLOAD.
%
% see also: SLOAD, SOPEN, SREAD, SCLOSE, SEOF, STELL, SSEEK.
% $Id: cntopen.m 87... |
cf8667bf400539c05513af3970615351f41856b67c8d8670e1c5d4ec1979e8c6 | MATLAB | 29,137 | 672 | classdef Edf2Mat < handle
% Edf2Mat is a converter to convert Eyetracker data files to
% Matlab file and perform some tasks on the data
%
% The new procedure uses code from SR-Research that returns all info of
% the edf and not just part of it. The new routine is based on the work
% of C. Kovach... |
423009a227ef9a757e24102fba6e06e3c7a3923602f7bca14e08ac91167397ef | MATLAB | 29,194 | 777 | %% Script for finding relationships between vasculature and hypoxic pockets in the mouse barrel cortex
% Uses the output of OxygenDynamics_Master analysis script and annotated
% png images for arteries and veins
% Run the script on the masterfolder that contains all the recordings.
% In the masterfolder have ... |
7521de8e559c114457576c96b76f15baff6b15c6411a302f196a4c6521a4d134 | MATLAB | 29,199 | 694 | function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine,verbose)
% avw_img_read - read Analyze format data image (*.img)
%
% [ avw, machine ] = avw_img_read(fileprefix,[orient],[machine],[verbose])
%
% fileprefix - a string, the filename without the .img extension
%
% orient - read a specified orienta... |
1dd77a8e2c0e2dd64b16d9064e73002009da6f21e67461490202164e5cf8d6e5 | MATLAB | 29,230 | 603 | %% cal the spike-field coherence among the different brain regions in both spontaneous pain epochs and no spotaneous pain epochs
% final version 2023/7/2
% In fact the file contains all type of events (include 6 type stimuli, and
% 3 type duration) is only 7 file
% the file contains 6 type stimuli and spontaneous pain ... |
fb68aa564c05edcec855987e153ac52d9addbc6b140c6fe93c49dc5ac94fea5f | MATLAB | 29,318 | 591 | function [TFNBS_Result] = gretna_TFNBS_ftest_MS_NMO(data_group, M, Mask_net, Pthr, E, H, Cova)
%==========================================================================
% This function is used to perform the TFNBS algorithm to search
% connections that show significant group effects for one-way experimental
% design... |
08fcaf9b5c176904d8d9a756a9c9926e56fb48dedd52748c7905e6c87dca5f1e | MATLAB | 29,334 | 526 | %function update_unitsTable(Sesname, elec,unit,field, val)
clear all; close all;
globals; initglobals;
DATA_TYPE = 'OF';
DATA_TYPE = 'EM';
PLOT_VARHISTS = 0; % if to plot individual hists for each Var
PLOT_VARSUMMARY = 0; % if to plot summary bar graphs for all Vars
PLOT_CROSS = 0; % if to plot xy graphs for ... |
43ca6fb2abcaf56e00117df4d71591cbd6d51fbc9406de35aa52b79265dc0202 | MATLAB | 29,382 | 697 | %% Figure 1 Code
% Fig. 1c: spike-trajectory figure
% Fig. 1d: firing rate map
% Vertex score analysis/Firing field analysis (number, distance, size)
%% Session setting
idx_session = 4 ; % 1: Circle, 2: Triangle, 3: Square, 4: Hexagon
%% Data load
if idx_session == 1
% Spike-trajectory map
... |
be3c7eb8a1d895c84db618f758edc5c06bab99271bb6ccbd2d0265d83499ecc9 | MATLAB | 29,408 | 1,057 | function DATA = aedes_readbruker(filename,varargin)
% AEDES_READBRUKER - Read Bruker file formats (raw FID-files and
% reconstructed 2DSEQ files)
%
%
% Synopsis:
% DATA=aedes_readbruker(filename,'PropertyName1',value1,'PropertyName2',value2,...)
% DATA=aedes_readbruker(filename,'h... |
487d254b95509aea2a25942d87ba686e574bc1083ddeffaddb4414b903a2e935 | MATLAB | 29,612 | 1,154 | % Written by Damien Jullié, feel free to spread.
% Base structure based on Corona
% Code displays 3 channels
% Code allows to select ROIs based on a segmentation in one or two channels of choice
% Quantifies the background subtracted fluorescence at segmented structures
function Puncti(action)
if nargin... |
17b2a11863b38cbb05dd831ebb0d2a7ee373f58242e6f0430f84c6bdc56fdc82 | MATLAB | 29,957 | 971 | %% Code Outline
% This code does the following:
% - loads in both fMRI and behavioural data
% - processing both behavioural and fMRI data
% - removes subjects that don't meet selection criteria
% - normalises amount of trials for each subject
% - checks robustness of random samplin... |
637d1e3b991d0d2ca9fce2322cac8156e4b3d722a5bde13fb788a922bfb77d09 | MATLAB | 30,034 | 916 | function GUI_find_missing_4train_blockwise(video, folder, masks, patch_locations, ...
images_added_crop, masks_added_crop, added_frames, added_weights, update_result)
% constants
global fileName;
global thred_IoU;
global thred_IoU_split;
global thred_jaccard_inclass;
global thred_jaccard;
% global auto_on;
% global... |
cf27012c8471d53866e08847925e2d07fbf82f4a37facc4c117c2d40f2a1e050 | MATLAB | 30,220 | 508 | function R = weightedcorrs(Y, w)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% IF YOU USE THIS FUNCTION PLEASE CITE:
% REFERENCE: the mathematical formulas in matrix notation, together with
% the code, is also available in
% F. Pozzi, T. Di Matteo, T. Aste,
% "Exponential ... |
de52e359fbdfa9f229c643eb73b0bed170c6555aee43e7177e826f6d5dd0a065 | MATLAB | 30,280 | 522 | function [output_UFARSA, opt_out, ROIs_all] = run_UFARSA(opt, fluor, true_spikes)
% [output_UFARSA, opt_out, ROIs_all] = run_UFARSA(opt, fluor, true_spikes)
%
% Applying UFARSA on the given fluorescence trace(s). The trace(s) will be first pre-processed, and then spiking activity trains will be reconstructed,
% p... |
03259263502626d4f4007f4a0a6ed31c78da0e808339209733ecea08a2b3d733 | MATLAB | 30,419 | 866 | function result=robpca(x,varargin)
%ROBPCA is a 'ROBust method for Principal Components Analysis'.
% It is resistant to outliers in the data. The robust loadings are computed
% using projection-pursuit techniques and the MCD method.
% Therefore ROBPCA can be applied to both low and high-dimensional data sets.
% In l... |
3288b6f3e1bef9a7cb600bd61c164c12194acc7eee5777b5c9debe4843235536 | MATLAB | 30,493 | 606 | function fitGLM_lab(fnRaw,neuronsToFit,fitModel)
% Fit GLM models and select best model
%
% fnRaw : ouptut file obtained by running rawDataForGLM
% neuronsToFit : list of neuron numbers to fit.
% fitModel : string specifying specific model to fit, e.g., 'XAOL', according to modelLabels.
% O... |
ffe0054945f31c0c98dc96eaa693804d99ec72f4555217a1d7523efd88ea889d | MATLAB | 30,502 | 819 | function varargout = GUI_environments_fix(varargin)
% GUI_ENVIRONMENTS MATLAB code for GUI_environments.fig
% GUI_ENVIRONMENTS, by itself, creates a new GUI_ENVIRONMENTS or raises the existing
% singleton*.
%
% H = GUI_ENVIRONMENTS returns the handle to a new GUI_ENVIRONMENTS or the handle to
% the ... |
369128c7a6145d7d576612f19c3ed34e1acb496f3501a1131cc6e7569d732815 | MATLAB | 30,537 | 824 | function varargout = GUI_environments(envfile,varargin)
% GUI_ENVIRONMENTS MATLAB code for GUI_environments.fig
% GUI_ENVIRONMENTS, by itself, creates a new GUI_ENVIRONMENTS or raises the existing
% singleton*.
%
% H = GUI_ENVIRONMENTS returns the handle to a new GUI_ENVIRONMENTS or the handle to
% ... |
9007a1cb7b00a8572591851f36b065366a12e926af98c6321c9452a3a108271e | MATLAB | 30,623 | 582 | %%% To run this code you require workspace data. You can generate by
%%% running custom_optotap_stimulus_script or any of its variant. You need to make
%%% sure that when you run that file you mention these variables in
%%% relevant_track_fields = {'BehavioralTransition','Frames',
%%% 'AlignedStimulus','EllipseRatio',... |
794181f71d5420a8dea196e927bb7e060314c62503bb23f75e8666d306c4ebf3 | MATLAB | 30,713 | 648 | function varargout = scan_volume_1p(neur_vol, PSF_struct, neur_act, ...
vol_params, scan_params, noise_params, spike_opts, wdm_params, vessel_mod, pixel_size, exp_level, output_dir)
% mov = scan_volume(neur_vol, PSF, neur_act, scan_params, varargin)
%
% Scan a volume and create a simulated two-pho... |
abe03825727da5ae1247b96824a1bd1cb89aca2849a57c0593f761713fb4f82a | MATLAB | 30,865 | 673 | classdef UpdateSectionImageTest < matlab.unittest.TestCase
% Tests for webupload.updateSectionImage with an injected fake Poster, so
% nothing touches the network (except one test against a refused localhost
% port). All inputs are synthetic temp files.
% Run: runtests(fullfile(<repo>, 'upload_core', 't... |
b623b81d518363fb63973bd1bd2d742435f6a6cde847917de426df4de570f41f | MATLAB | 31,024 | 590 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: OptoDoseResponse_TempWindow_2023
% Cohort: PFC dLight1.3b with opto
% May 2023 - Marie Labouesse, marie.labouesse@gmail.com
% 1- CALCULATE TEMP WINDOW
% loads FP data previously analyzed (with: OptoDoseResponse_DataExtraction then OptoDoseRespon... |
a3cf641df0de0c3ccc1881f248be5080f5e98a8fee7d210b6f2230052f71496b | MATLAB | 31,052 | 705 | classdef Violin < handle
% Violin creates violin plots for some data
% A violin plot is an easy to read substitute for a box plot
% that replaces the box shape with a kernel density estimate of
% the data, and optionally overlays the data points itself.
% It is also possible to provide two s... |
1a50ad705a1d0767896733426dc5e08eca09a8f0b1fd4f2f006269b9853bed35 | MATLAB | 31,382 | 849 | 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... |
5f50625b123c17c6175adcb01cb268370a45e89c93a8cf70656aa7158894136f | MATLAB | 31,402 | 849 | function [SPM,xSPM] = spm_getSPM(varargin)
% Compute a specified and thresholded SPM/PPM following estimation
% FORMAT [SPM,xSPM] = spm_getSPM;
% Query SPM in interactive mode.
%
% FORMAT [SPM,xSPM] = spm_getSPM(xSPM);
% Query SPM in batch mode. See below for a description of fields that may
% be present in xSPM input.... |
a99baf8a27695ba9c32e7699f19c8c6d7b04680aa851cc50d4b93b54eeef3842 | MATLAB | 31,776 | 822 | function varargout = ConfirmCompartmentsMap_60(varargin)
%CONFIRMCOMPARTMENTSMAP_60 MATLAB code file for ConfirmCompartmentsMap_60.fig
% CONFIRMCOMPARTMENTSMAP_60, by itself, creates a new CONFIRMCOMPARTMENTSMAP_60 or raises the existing
% singleton*.
%
% H = CONFIRMCOMPARTMENTSMAP_60 returns the handle ... |
0aa5814c78b9b282f2973131f637bdc320f386c81969e39b3834a4592176b91b | MATLAB | 31,885 | 502 | clc, clear
close all
%% this file is to allocate the temporal signals to the generated sample.
% note there is no noise contaminations here.
% all traces looks perfectly great.
% note the trace is highly related to the neuron volume, so I will send it
% back to the volume dir.
% last update: 8/20/2020. YZ
%% spike p... |
ac8ef6c5e9c1dbaa2a7205f144e0d169bf0dcb77ec2f254a0e10f6ada2a85c77 | MATLAB | 31,896 | 742 | function varargout=spm_XYZreg(varargin)
% Registry for GUI XYZ locations, and point list utility functions
%
% ----------------
%
% PointList & voxel centre utilities...
%
% FORMAT [xyz,d] = spm_XYZreg('RoundCoords',xyz,M,D)
% FORMAT [xyz,d] = spm_XYZreg('RoundCoords',xyz,V)
% Rounds specified... |
b8e2f1692c22bc8ba1ffd2af3f487ca1ff885a0c4d85cbd78717c82d1e988f87 | MATLAB | 31,904 | 592 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: CocaineNAc_PooledGraphs
% Cohort: NAc AllodLightctrl with opto and drugs (DETQ or cocaine)
% Feb 2023 - Marie Labouesse, marie.labouesse@gmail.com
% 1- POOLED DATA
% loads FP data previously analyzed (with: CocaineNAc_DataExtraction) in matlab sp... |
d72eaceedaeceea70afdd7c4d7f69ea82ddd1f7143ecd1dd68d3c3609941bd3f | MATLAB | 31,956 | 501 | function fun_time_trace_generation(vol_out,nt, frate, output_dir)
%% this file is to allocate the temporal signals to the generated sample.
% note there is no noise contaminations here.
% all traces looks perfectly great.
% note the trace is highly related to the neuron volume, so I will send it
% back to the volume... |
3de0e4898f08a1ac075997fc416afa19dcdbfd0a5c033c5639e6ce6e73d58f0f | MATLAB | 32,198 | 894 | function varargout=spm_figure(varargin)
% Setup and callback functions for Graphics window
% FORMAT varargout=spm_figure(varargin)
% - An embedded callback, multi-function function
% - For detailed programmers comments, see format specifications
% in main body of code
%______________________________... |
03ad3d05eeb13eb35e2da5ad6ed9cab270e435e4dd40946799de4c4679e29094 | MATLAB | 32,273 | 833 | function varargout = ConfirmCompartmentsMap_4Q(varargin)
%CONFIRMCOMPARTMENTSMAP_4Q MATLAB code file for ConfirmCompartmentsMap_4Q.fig
% CONFIRMCOMPARTMENTSMAP_4Q, by itself, creates a new CONFIRMCOMPARTMENTSMAP_4Q or raises the existing
% singleton*.
%
% H = CONFIRMCOMPARTMENTSMAP_4Q returns the handle ... |
f8b0171f12fe8cd2bc3a5ce1bb919c17ad0ffd4415d8b5a1b7e45c0110f4b541 | MATLAB | 32,774 | 602 | %function update_unitsTable(Sesname, elec,unit,field, val)
clear all; close all;
globals; initglobals;
DATA_TYPE = 'OF';
DATA_TYPE = 'EM';
PLOT_VARHISTS = 0; % if to plot individual hists for each Var
PLOT_VARSUMMARY = 0; % if to plot summary bar graphs for all Vars
PLOT_CROSS = 0; % if to plot xy graphs for ... |
0568af7a9614aa4171bb00e704af8ea0f8984392c43549764f1642c8e3c1e4ec | MATLAB | 32,804 | 574 | % Marie_FP_PooledData
% Marie Labouesse, marie.labouesse@gmail.com - Dec 2023
% Cohort: NAc dLight1.3b with opto-inhibition (eNPHR)
% 1- POOLED DATA
% load matlab spaces generated in: Marie_FP_IndivData_extraction
% puts individual trials into one big matrix (all mice together): PooledINDIV
% calculates the mea... |
f65fdc38d369d8cb13bc6a3f169ba2ab0b2130c7fc6e43a8c448523578cf72ae | MATLAB | 33,001 | 856 | % F_sig_raster() - Plots 2D (electrode x time/frequency) raster diagram of
% variables that show significant effects according to F-tests.
%
% Usage:
% >> [img, h_ax] = F_sig_raster(GND_GRP_specGND_or_fname, test_id, varargin);
%
% Required Inputs:
% GND_GRP_specGND_or_fname - A GND/... |
a1ad2f2ebde86e680447fa5e902e02857d50bc3d7c005af4647e8911e5379015 | MATLAB | 33,128 | 621 | %%% To run this code you require workspace data. You can generate by
%%% running custom_optotap_stimulus_script or any of its variant. You need to make
%%% sure that when you run that file you mention these variables in
%%% relevant_track_fields = {'BehavioralTransition','Frames',
%%% 'AlignedStimulus','EllipseRatio',... |
205782971ac4701161df3f4e07b08750f347424bfa7a96f03fe779c3d6793d64 | MATLAB | 33,162 | 1,040 | function aedes_headerbrowser(inStruct)
% AEDES_HEADERBROWSER - Browse and search file header information or any
% Matlab structure
%
%
% Synopsis:
% aedes_headerbrowser(DATA) % Open the file format specific header
%
% aedes_headerbrowser(STRUCT) % Browse a generic Matlab structure
%... |
48dc062eee3a559e36d4a302458108fb8a64ac436e2210671d2f0a28fa54af88 | MATLAB | 33,668 | 528 | %% rip conditioning: main content analyses
% focus on post-conditioning, since that's when we have good quality decoding
% relationship between behavior and rips/replay goes here, since we have behavior outputs
animals = {'jaq','roquefort','despereaux','montague','remy','gus','bernard','fievel'};
epochfilter{1} = [... |
bda4b356916c1afbce3888151f115940fa652907ce492b8c10a5df8f5cd57290 | MATLAB | 33,746 | 798 | function hn=arrow3(p1,p2,s,w,h,ip,alpha,beta)
% ARROW3 (R13)
% ARROW3(P1,P2) draws lines from P1 to P2 with directional arrowheads.
% P1 and P2 are either nx2 or nx3 matrices. Each row of P1 is an
% initial point, and each row of P2 is a terminal point.
%
% ARROW3(P1,P2,S,W,H,IP,ALPHA,BETA) can be used to spe... |
be34d1b026b5d032a2445f0e0c1e5b43c9604dad89692d549aa900c7d7ba4edc | MATLAB | 34,214 | 714 | classdef BStimulator < handle
%BStimulator: MATLAB class wrapper to the underlying C++ class BStimulator
% Go to http://www.mathworks.com/matlabcentral/fileexchange/38964-example-matlab-class-wrapper-for-a-c++-class
% for more details on the "handle" implementation here.
%
% The BStimulat... |
2af281ad1ae79541f4c26a2ee09fd88e797aa749464080e8ed89539db1a18547 | MATLAB | 34,332 | 883 | % initScreen.m
%
% $Id$
% usage: myscreen = initScreen(myscreen, randstate)
% by: justin gardner
% date: 12/10/04
% copyright: (c) 2006 Justin Gardner (GPL see mgl/COPYING)
% purpose: init screen parameters (using mgl)
%
function myscreen = initScreen(myscreen,randstate)
% see if passed i... |
73607662fc47f58a040bc3f0387704480c1e5f05ecef8f7ef0030cea9553ab64 | MATLAB | 34,561 | 1,149 | %% TI task
clear all
close all
%%
tic
seed = randi(9999);
rng(seed);
PlotFigures = true;
% Set the network.
Options.NetSize = 100; % Number of units.
Options.Tau = 0.1; % Single-unit decay constant in seconds.
Options.StdJinter = 0.05; % 'g' param of (Stern et al, 2014) and (Sompolinsky et al., PRL 1988).
Ortho... |
026ce35439956cbccc90662dbdf9d95c609f96a286bc04fd348286632a5b92ee | MATLAB | 34,570 | 888 | % initScreen.m
%
% $Id$
% usage: myscreen = initScreen(myscreen, randstate)
% by: justin gardner
% date: 12/10/04
% copyright: (c) 2006 Justin Gardner (GPL see mgl/COPYING)
% purpose: init screen parameters (using mgl)
%
function myscreen = initScreen(myscreen,randstate)
% see if passed i... |
2e6435f537caf2a6f58abcb6d6f919f239bce1fba569d6ed887ff6dd1e9937f4 | MATLAB | 34,725 | 760 | function Params = ExtractKilosortData(KiloSortPaths, Params, RawDataPathsInput)
% Prepares cluster information for subsequent analysis
%% Inputs:
% KiloSortPaths = List of directories pointing at kilosort output (same format as what you get when
% calling 'dir') for all sessions you want to analyze as one session (e.g... |
4122abafe7baba575620d1652a301111432474ab6c521cab65d9c13120370d83 | MATLAB | 34,739 | 648 |
%%
%% BACH ELDERLY MEG - COMMUNICATIONS BIOLOGY - REVISION I
%%
%% Defining the conditions - only for old/new paradigm (in the case of MMN the conditions were defined during epoching)
definecond_l = 1; % 1 = defining conditions; 0 = computing descriptive statistics
xlsx_dir_behav = '/scratch7/MINDLAB2021_MEG-Temp... |
e4b29d8ddb8621cb8334fd80504fff4f04ef8aed65be144484e57b1ca4707697 | MATLAB | 34,795 | 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... |
f95d213a258d9cd46c797d09ef78b8c9e10309f35681e76f5938c8998b67a3d4 | MATLAB | 34,824 | 1,219 | function DATA = aedes_readbruker(filename,varargin)
% AEDES_READBRUKER - Read Bruker file formats (raw FID-files and
% reconstructed 2DSEQ files)
%
%
% Synopsis:
% DATA=aedes_readbruker(filename,'PropertyName1',value1,'PropertyName2',value2,...)
% DATA=aedes_readbruker(filename,'h... |
a9ca6ef787ca47a44f8c682dfa8525257fe84eefc3fbd565531f3f9406c83a75 | MATLAB | 35,012 | 665 | %% LFP_adicht.m
% Author: Jürgen Graf
% date: 21.07.2021
% intended use: extract LFP and Respiration/Movement data from LabChart files (.adicht)
% specifically written for LFP recordings in Gi-DREADD mice
% Prerequisite:
% - import_adicht.m (J. Graf)
% - Simple Data File SDK (from ADInstruments)
% ... |
2c7d92d74e6152365388da225ae7d2d062689383ff3eadac80f898a3975bccf4 | MATLAB | 35,235 | 673 | function print2eps(name, fig, export_options, varargin)
%PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
% print2eps(filename, fig_handle, export_options)
% print2eps(filename, fig_handle, export_options, print_options)
%
% This fun... |
86b405c73a98cdbea00cbde62d95616776e1ea03f4a4509ab6d218e91ad7826c | MATLAB | 35,248 | 1,160 | function aedes_resviewer(Res_in)
% AEDES_RESVIEWER - View and convert Aedes statistics results
%
%
% Synopsis:
% aedes_resviewer(Res)
%
% Description:
% The AEDES_RESVIEWER function opens a graphical user interface (GUI) for
% handling Res-structures or *.res files saved from AEDES. If
% the... |
7a74d10c50187f1caad0f064427d32135d0d39b78bd5c5196e9f7435447bbf67 | MATLAB | 35,730 | 1,072 | % This script analyzes the virtual murine cohort from the OCHiPerGator.m
% output and generates figures 3-6 in Anderson et al. "Optimal control
% of combination immunotherapy in a glioblastoma-immune dynamics model"
% (code does not generate the pi charts, which were created using
% PowerPoint)
% Uses output from OC... |
6876d5224de90c3477e7da34f053cf4f4d27aada182d97ee9cf42b29c72fb1cd | MATLAB | 35,766 | 685 | %% LFP_adicht.m
% Author: Jürgen Graf
% date: 21.07.2021
% intended use: extract LFP and Respiration/Movement data from LabChart files (.adicht)
% specifically written for LFP recordings in Gi-DREADD mice
% Prerequisite:
% - import_adicht.m (J. Graf)
% - Simple Data File SDK (from ADInstruments)
% ... |
95aa2c5151474fa6ee0a8d0ab39688c3e9b8bcdfd7264d671d97598fa38f9c55 | MATLAB | 35,863 | 649 | % modified from analyze_unitsTableEM 10.6.2023
% added bootstraping
% The probability that the two observed distributions (y1 and y2) were pulled out of one common distribution was tested using permutation analysis.
% Two vectors were randomly (uniform) selected out of the common vecor [y1,y2].
% The difference b... |
36cccd099fbd5a68f2b82690fa6fc27e95600fa6a02ab0acb8f9d999272f6060 | MATLAB | 35,897 | 1,061 | function [done,msg] = aedes_write_nifti(DATA,filename,varargin)
% AEDES_WRITE_NIFTI - Write data in NIfTI or Analyze 7.5 formats
%
%
% Synopsis:
% [done,msg] = aedes_write_nifti(DATA,filename,prop1,value1,prop2,value2,...);
%
% Description:
% The function writes "DATA" to a file "filename" in NIfTI
% ... |
7cf770284e7df31674c36c26d7fe426001b16eefb7d36bddbe347aa1eeb71dde | MATLAB | 35,915 | 650 | % modified from analyze_unitsTableEM 10.6.2023
% added bootstraping
% The probability that the two observed distributions (y1 and y2) were pulled out of one common distribution was tested using permutation analysis.
% Two vectors were randomly (uniform) selected out of the common vecor [y1,y2].
% The difference b... |
c4f5984469143fdce3d8f8b669a7cb00193aa2e128eaeba7c42c0145af8775ca | MATLAB | 36,527 | 813 | function ComputeFunctionalScores(SaveDir, saveFig, recompute)
if nargin < 2 || isempty(saveFig)
saveFig = 0;
end
if nargin < 3 || isempty(recompute)
recompute = 0;
end
SigThrs = 3; % Threshold for number of standard deviations away from mean
load(fullfile(SaveDir, 'UnitMatch.mat'), 'MatchTable', 'UMparam', ... |
c84eb5eb5ca15e2d97fca1707fa128c81150721b0cf76ba6a6636a2a26fcd087 | MATLAB | 37,056 | 660 | % The "qmri-ald" program provides automated image-processing pipelines for
% structural MRI images primarily acquired in pediatric healthy controls
% and pediatric patients with cerebral adrenoleukodystrophy. The program
% provides preprocessing, processing, quantitative, and statistical analysis
% of MRI images such a... |
8091b98e51bdff5eb34189ed5b424c9b809cabc78c88e64bfa34e3738d21c47f | MATLAB | 37,158 | 828 | %% Author: Jiri van Bergen and Xu Li
% Affiliation: Radiology @ JHU - Kirby Center
% Contact via xuli@mri.jhu.edu
% Updated by Xu Li, 2019-07-09
% Updated by X.L., add in msSFCR for ARIC processing, 2019-08-21
% Updated by X.L., removed msSFCR, added NDI & TFI & FANSI for testing
% Updated by X.L., 2021-05-26, ... |
50345d9bc3ab693533b2edce5f2e4ce1870676a4b6f689066cdaf1456ea51f95 | MATLAB | 37,203 | 950 | function [] = analyze_BehavioralData_SIF_HC_SCZ()
close all;
flagExludeSCA = 1;% = 1 = exclude SCA patiens (i.e., only SCZ patients included)
flagComputeFromBCIPredictions = 0;% = 1 = compute BCI model predictions from parameter file
subjIDinAna_SCZ_SCA = {'K01','K02','K03','K04','K05','K06','K07','K08','K09','K10... |
3348ba063b0fd2faa61cf0714790b08d5b7ee6c36d9b1b70c9fa27704d1cbf06 | MATLAB | 37,284 | 1,068 | classdef ExperimentGroup < network_project_superclass2
% Class instance for a unique physical coupled learning network.
%% Properties
properties (Constant)
ObjName = 'group';
SaveFolder = network_project_superclass2.GroupFolder;
end
properties (SetAccess ... |
19100e41615ce823a9cf8fcf13c06e837870ba985b4ab5d2f9777cc6f88c46b6 | MATLAB | 37,547 | 1,020 | classdef RefineSeg
% set of function for the analysis of segmented 3d axons from EM
% 31-Jan-2022 by Ricardo Coronado-Leija
methods (Static)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
55b41f0e371880f547a0bb36d32fddf82fef0562b7e3a98df48eb5b27156f394 | MATLAB | 38,189 | 1,038 | % Performs resampling under the null hypothesis and computes p-values for
% (multiple) comparisons among independent samples in a one-way layout.
%
% -- Function File: boot1way (DATA, GROUP)5
% -- Function File: boot1way (..., NAME, VALUE)
% -- Function File: boot1way (..., 'bootfun', BOOTFUN)
% -- Function File: boot1... |
61e0284d816f4944badb9b21f58e0712e3e6b5a9ea9887a8408b8a14f1cc1c32 | MATLAB | 38,607 | 519 | %% rip conditioning: main content analyses
% focus on post-conditioning, since that's when we have good quality decoding
% relationship between behavior and rips/replay goes here, since we have behavior outputs
animals = {'remy','gus','bernard','fievel'}; %,'jaq','roquefort','despereaux','montague','gerald'
epochfil... |
21386b24712640244a3b295124ac9ee271e7acc60b0bdf4f5104584beb296225 | MATLAB | 38,954 | 900 | classdef ImagingRetinotopy < types.core.NWBDataInterface & types.untyped.GroupClass
% IMAGINGRETINOTOPY Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of responses to specific stimuli and a combined polarity map from which to... |
fe0464480fe98f9bd0153b012d24a638ba72dc2a96fa5b232ad877bc1bb3ef4f | MATLAB | 39,017 | 724 | %aspikes
%plot STA for units, only those whose Mdep has p<0.05 by bootstrap
% odd/even by spike
% Unit names:
% elecName - true electrode number (apperas in goodElectrodes)
% elec - the index of elec in goodElectrodes)
% elec = find(goodElectrodes==elecName);
% unitName - [elecName,unit];
% ShowUnits - by elec... |
bce0c5dbadebf8ec5612369f70ede60da5e604207a8d05d88c14e7c6f1e983d8 | MATLAB | 39,142 | 1,448 | function [filename,filepath,filterindex] = aedes_juigetfiles(filefilter,ftitle,defaultdir)
% AEDES_JUIGETFILES - A Java based file browser for selecting multiple files in
% non-sorted order from different folders.
%
%
% Synopsis:
% [FILENAME, PATHNAME, FILTERINDEX] = AEDES_JUIGETFILES(FILTERSPEC,TITLE, DEFAUL... |
9f9bea4d0a80ee92e0d7e4784eed6296b233ab2c320b18b84bebd2b2ee7ec427 | MATLAB | 39,160 | 916 | % Advanced bootstrap confidence intervals: Performs bootstrap and calculates
% various types of confidence intervals from the resulting bootstrap statistics.
%
% -- Function File: CI = bootci (NBOOT, BOOTFUN, D)
% -- Function File: CI = bootci (NBOOT, BOOTFUN, D1,...,DN)
% -- Function File: CI = bootci (NBOOT, {BOOTFU... |
3601be529e41b5962f70e030f19e8dffdbd01f61b457363679d1b992f06da784 | MATLAB | 39,446 | 737 | %aspikes
%plot STA for units, only those whose Mdep has p<0.05 by bootstrap
% odd/even by spike
% Unit names:
% elecName - true electrode number (apperas in goodElectrodes)
% elec - the index of elec in goodElectrodes)
% elec = find(goodElectrodes==elecName);
% unitName - [elecName,unit];
% ShowUnits - by elec... |
3b9e99225fc1dedb3ab684c80f662f87e98831678c6e55a6acdafadf70345dd5 | MATLAB | 39,522 | 714 | %amap. ehud,Feb 2016. analyze response maps for pairs of variables. can
%plot or save to data base
%
% run:
% a loop over Sessions (SesList = {'ses1';'ses2';,...})
% a loop over varaibles (VarList = {'var1';'var2';,...})
% analyze Nmeasures (MeasureList = {'Ree';modp2p}
% WAS - For each Session save an array of ... |
3c3c0410bcb0df5732cdfba295799a769610757f648d5987d78bbc5176ccce01 | MATLAB | 40,156 | 991 | function varargout = biceps(varargin)
% BICEPS MATLAB code for biceps.fig
% BICEPS, by itself, creates a new BICEPS or raises the existing
% singleton*.
%
% H = BICEPS returns the handle to a new BICEPS or the handle to
% the existing singleton*.
%
% BICEPS('CALLBACK',hObject,eventData,handles,... |
32bbc7c649816eedc092ca51c3d6778fd21cb483c09b3282525e81e319af91c8 | MATLAB | 40,469 | 1,013 | 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... |
eef4c91227c81513985714ec2dde426216baf7477d02d1b940c30e03f8978d51 | MATLAB | 40,652 | 806 | function [] = simseq_fitAveragePRFTemporalModelPredictionsToPreprocData(subjnr,projectDir,spatialModel,temporalModel,varargin)
% simseq_fitAveragePRFTemporalModelPredictionsToPreprocData(subjnr, projectDir, spatialModel, temporalModel)
%
% Function to fit generated spatiotemporal model predictions using pRF of
% sing... |
d791812c6f65d7b79868a736818c1baaad6c62d5a5f7bab7497b64c35e30bd28 | MATLAB | 40,925 | 1,024 | function [dt, b0, list] = RobustDKIFitting_onDlWl_proxyInput(dwi, grad, mask, DlWlproxy,alpha_tuning)
%
% THIS CAN BE MADE FASTER, JUST NEED TO WRITE THE DERIVATIVES OF THE OBJ
% FUNCTION
%
% [dt, b0, DlWlpred, list] = RobustDKIFitting_onWl(dwi, grad, mask,alpha_tuning)
%
% This is a modification of Jelle's... |
ed2bd001ad8167ffc8dd76f26f6f6b6ed5c45c9ea32884024b1ffc5f113d248c | MATLAB | 41,065 | 789 | function Depth2Area = alignatlasdata(histinfo,AllenCCFPath,sp,clusinfo,removenoise,surfacefirst,LFPDir,treeversion,trackcoordinates)
% Enny van Beest, based on AP_histology from AJPeters & IBLAPP from Mayo
% Faulkner
%% Important
% This tool is purely to align ephys-data (functional) to histology data,
% as obtained b... |
ff4e29214d3b1749b636ab33f88fe5389feae33f8074f243b719e65c21538aa1 | MATLAB | 41,848 | 728 | % mglEditScreenParams.m
%
% $Id:$
% usage: mglEditScreenParams()
% by: justin gardner
% date: 07/17/09
% purpose: This function can be used in conjunction with initScreen in the
% task directory to set your monitor parameters. You will first get
% a dialog box whic... |
d614ca279fe0a3b2a125130cd263f6dd13d037b1be946565759f1210184f4005 | MATLAB | 42,161 | 1,049 | clear all
close all
% WBDataRawExp1 = readtable('Y:\niels\Jianfeng\WesternBlotResults\WB_raw_26wells12wells-1_AllAnimals.csv');
% WBDataRawExp1 = readtable('Y:\niels\Jianfeng\WesternBlotResults\WB_raw_26wells12wells-1.csv');
WBDataRawExp1 = readtable('Y:\niels\Jianfeng\WesternBlotResults\WB_raw_26wells12wells-1_N... |
9ae695943b9cb2a2be8488e884e50ba7415843f401c12981f6594a4913c2763c | MATLAB | 42,169 | 731 | % mglEditScreenParams.m
%
% $Id:$
% usage: mglEditScreenParams()
% by: justin gardner
% date: 07/17/09
% purpose: This function can be used in conjunction with initScreen in the
% task directory to set your monitor parameters. You will first get
% a dialog box whic... |
b958dcd9dfaf52fa10146aaadd3a30c0e57fc180fe26d157d2e4331b2996757d | MATLAB | 42,200 | 1,149 | %--------------------------------------------------------------------------
%Pseudo line-scanning particle image velocimetry (p3LSPIV)
%--------------------------------------------------------------------------
%Used to calculate blood flow in individual blood vessels where the blood
%lumen has been labelled with a... |
b59ba53689b20153ed8001054a2921ab290fa9edf640d7298508e71169c38781 | MATLAB | 42,233 | 1,174 | function varargout = VideoSync(varargin)
% VIDEOSYNC MATLAB code for VideoSync.fig
% VIDEOSYNC, by itself, creates a new VIDEOSYNC or raises the existing
% singleton*.
%
% H = VIDEOSYNC returns the handle to a new VIDEOSYNC or the handle to
% the existing singleton*.
%
% VIDEOSYNC('CALLBACK',hO... |
ef9a31f3adb9c851b9adacb14cf498e2615227a0f8eeac480fdba610a5550b00 | MATLAB | 42,492 | 1,136 | %% User Input
Datadir = '\Path\To\Data'
Scriptsdir = '\Path\To\Scripts\' %Path to all the (sub)scripts of this analysis
storepath = '\Path\To\Store\' %Main storage --> Will contain all processed data & model of the brain
miceopt ={'Faraday','Galilei','Haydn','Jemison','Karlsen','Lully','Mahler','Sebald'}
mousegen = {'D... |
ffaed22cf556baa737a2152ba6a2111ad29dece12bea673eda723158845555a5 | MATLAB | 42,822 | 923 |
% Segment foreground pixels into wings and legs, and disambiguate body
% orientation based on: a) wing positions, b) velocity, c) consistency
%
% To segment detections, use:
%
% trks = track_segment(trks, calib, [show progress], [chamber_str])
%
% where [] denotes an optional parameter and:
%
% trks ... |
c23c26b68e6838db2de21985afa0ba3b0af59285503c3390bbbd091b5ae68dc3 | MATLAB | 42,955 | 1,146 | classdef dat %< hgsetget
% DAT continuous-time AND discrete event data storage object
%
% PROPERTIES
% 'data' - matrix of numeric data, 1 row per sample, 1 column per
% channel. Can be measurement values (continuous) or event times
% (discrete)
% 'chanlabel' - strin... |
9e73f5fdd335e9c3eaf1174301663f566f754442bd4d59f9a8cca55ceabee322 | MATLAB | 43,120 | 1,102 | % Performs balanced bootstrap (or bootknife) resampling of clusters or blocks of
% data and calculates bootstrap bias, standard errors and confidence intervals.
%
% -- Function File: bootclust (DATA)
% -- Function File: bootclust (DATA, NBOOT)
% -- Function File: bootclust (DATA, NBOOT, BOOTFUN)
% -- Function File: boo... |
b62974a50da6822e327d6055e982f76d43d9be1370173607f3c01c1d5cd222fb | MATLAB | 43,340 | 1,143 | function varargout=spm_help(varargin)
% SPM help and manual facilities
% FORMAT spm_help
%_______________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/s... |
075ce95b2bf1d02c47362a9630aa12f6774272085bb0a271604a0e49e79c1715 | MATLAB | 43,724 | 1,102 | function [dt, b0, list] = RobustDKIFitting_onDlWl_proxyInput(dwi, grad, mask, DlWlproxy,alpha_tuning)
%
% THIS CAN BE MADE FASTER, JUST NEED TO WRITE THE DERIVATIVES OF THE OBJ
% FUNCTION
%
%
%
% [dt, b0, DlWlpred, list] = RobustDKIFitting_onWl(dwi, grad, mask,alpha_tuning)
%
% This is a modification of Jel... |
690906fdf7ad9e2dd4b0b9d47107e22fc5c6cf1b85956df0c7f186a957a78d5c | MATLAB | 43,733 | 785 | %amapOF - modified from amap to analyze OpenField data. Oct 2016, ehud.
%
%amap. ehud,Feb 2016. analyze response maps for pairs of variables. can
%plot or save to data base
%
% run:
% a loop over Sessions (SesList = {'ses1';'ses2';,...})
% a loop over varaibles (VarList = {'var1';'var2';,...})
% analyze Nmeasur... |
e6f64d0feca94060787f15fd79c8e00cffa03c87cb869d15bfbcaa20325a2c3b | MATLAB | 43,785 | 855 | function [] = simseq_fitTemporalModelPredictionsToPreprocData(subjnr,projectDir,spatialModel,temporalModel,varargin)
% simseq_fitTemporalModelPredictionsToPreprocData(subjnr, projectDir, spatialModel, temporalModel)
%
% Function to fit generated spatiotemporal model predictions using pRF of
% single vertex from toono... |
5a5da08015063ff2a95beb464dcc3a627fb84369a4001eb20ff43f3176787295 | MATLAB | 44,318 | 1,001 | function [V,C,XY]=VoronoiLimit(varargin)
% --------------------------------------------------------------
% [V,C,XY]=VoronoiLimit(x,y,additional_variables)
% Provides the Voronoi decomposition of a set of (x,y) data, but with all
% vertices limited to the boundary created by the data itself.
% V contains the verti... |
36e54c9f04704c7249fc5726d73b090762242d8224894446ef74109c4680b107 | MATLAB | 44,626 | 1,191 | % initTask - initializes task for stimuli programs
%
% usage: [ task myscreen ] = initTask( task, myscreen, startSegmentCallback, ...
% screenUpdateCallback, <trialResponseCallback>, ...
% <startTrialCallback>, <endTrialCallback>, <startBlockCallback>,...
% <randCallback>);
% $I... |
00678a4fc748f94612a9883324d8d9a65c3679464be8f45bc55ffc0558c32f75 | MATLAB | 44,873 | 1,172 | function varargout=spm(varargin)
% SPM: Statistical Parametric Mapping (startup function)
%_______________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/... |
8623cc1dc53d4981cc9b90e14cbc0fedd2aafe64d0d37091cc7d9058944114d8 | MATLAB | 44,877 | 1,201 | % initTask - initializes task for stimuli programs
%
% usage: [ task myscreen ] = initTask( task, myscreen, startSegmentCallback, ...
% screenUpdateCallback, <trialResponseCallback>, ...
% <startTrialCallback>, <endTrialCallback>, <startBlockCallback>,...
% <randCallback>);
% $I... |
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