sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c375c82f8998c7eae65e534a85d4250376169d07f0350941f9bf44fb7a85e505 | MATLAB | 3,491 | 32 | subjs={
'/m/cs/scratch/networks-pm/pm_denoise/sub-01/sub-01_task-movie_SGdetrend_24HMP-8Phys-4GSR-Spike_HPF_smooth-6mm.nii'
'/m/cs/scratch/networks-pm/pm_denoise/sub-02/sub-02_task-movie_SGdetrend_24HMP-8Phys-4GSR-Spike_HPF_smooth-6mm.nii'
'/m/cs/scratch/networks-pm/pm_denoise/sub-03/sub-03_task-movie_SGdetrend_24HMP-8... |
2fedb96d4fa0bcf6040309ccdc89d50a1ab484ab18c217d8067e26762d3ac365 | MATLAB | 3,493 | 72 | clear
close all
clc
%% Load atlas
% path to MRI template - must include hdr and img files
atlas = niftiread('/Users/jstrohl/Documents/20230908 Pipelines for neural data analysis/Dependencies/ATLAS-MICE 2/2011-10-30_MRI-template3.hdr', ...
'/Users/jstrohl/Documents/20230908 Pipelines for neural data analysis/D... |
b6a8742287f2ecf20f323dbf03ba884159d0c90cb1849bf55a001f6a4a981d04 | MATLAB | 3,493 | 118 | function meg_SFig3_sessionPhaseConsistency
% Polar plot of the fitted phase difference by precue
% Session 1 v Session 2
% Mean phase difference ± 1 SEM
%
% thetaregion, polarregion requires Matlab R2024a or above
%% Load data
% Model fit data
filename = 'figData/ModelFit_SeparatePrecueT1T2_2Hz_session.mat';
% IT... |
303d9520c187cccc2a622bd55206b1da385d606469582b249b1b07b36cc94ad5 | MATLAB | 3,494 | 96 | function perform_rsa_analysis(p)
%
% - This code is written for performing multiple ROI representational similarity analysis.
% - A total of 383 (HCP360, 13 individual ROIs, and 10 subcortical ROIs) are used.
%
%
% called from emotion2020_analysis_BATCH
%
%% settinig
warning off
%% start analysis
for scoritr = 1:lengt... |
26459c132dd86c12b7b8ff9a0fa4a11d6e696f35358b27f15970a1ea31bc715f | MATLAB | 3,495 | 78 | function [GTA] = y_GraphTheoreticalAnalysis_wu(G,RandomTimes)
% function [GTA] = y_GraphTheoreticalAnalysis_wu(G,RandomTimes)
% Perform graph theoretical analysis based on Brain-Connectivity-Toolbox (BCT, http://www.brain-connectivity-toolbox.net)
% Input: G - The weighted undirected connection matrix
% ... |
05a856ed352db1bb4ee45d2c533508b4920da389a8a2e67bb93d76d0d0a1f2c9 | MATLAB | 3,497 | 82 | function build(varargin)
% Build an APT executable.
% Parse optional args
[do_run_test_after, do_compile] = ...
myparse( varargin ...
, 'do_run_test_after', false ...
, 'do_compile', true ...
) ;
% Define things needed for building or running
main_m_file_name = 'APT_deployed.m' ... |
abbe1b35785684899addbf7df066d4208dd18b032ef0762d5eea8190040d3d0f | MATLAB | 3,497 | 102 | %% SCRIPT TO EVALUATE QUALITY OF REGISTRATION
% Uses Dan Goodwin's method from ExSeq paper (Alon et al., Science 2021)
% Accompanies the manuscript by Kang*, Schroeder* et al., 2023
% Last modified by Margaret Schroeder on 12/14/2022
% Image processing up to this point:
% - background subtraction in Fiji an... |
cf19272880ce55529323c92171584e9a0c390fb60424bee2f974d7f9d5f69e09 | MATLAB | 3,497 | 113 | function opts = metamerOpts(oim,varargin)
%
%-----------------------------------------
% opts = metamerOpts(varagin)
%
% generates a structure of parameters for
% metamer analysis and synthesis
% (see metamerAnalysis.m and metamerSynthesis.m)
%
% oim: original image to be used in analysis
%
% opts: structure contai... |
60e6a6b25c7c98d1bad5816cce89536d0fa4d0062e828ff44dc9bff2bc289722 | MATLAB | 3,499 | 87 | % This example recreates the MNIST datasource from
% http://yann.lecun.com/exdb/mnist/
%
% You can load a subsampled version (10k images) from the folder /Tutorials/MNIST_Datasource
% (for instance using the dataspace GUI).
%
% XXXNAT TODO: test
%
%
%<PRE>
% This fil... |
1a616079cfebda9d92defb7225237d6a0cc3dc2f18a113465973268bcb31f7e4 | MATLAB | 3,500 | 99 | function Draw_ROIs_Through_Cortex(Anat,ROI,Conn,params)
%
% This function will draw ROI spheres on a model of the cortical surface.
% The ROI spheres may be connected by tubes that are sized by correlation
% strength and colored by sign. The cortical surface with have a
% transparency.
% Anat is a structure that ... |
611ddf7a74fbc92ad47141154bcf8a923bca598a15efbf0bcbbe7f63d935dd98 | MATLAB | 3,500 | 104 | function mappedX = ltsa(X, no_dims, k, eig_impl)
%LTSA Runs the local tangent space alignment algorithm
%
% mappedX = ltsa(X, no_dims, k, eig_impl)
%
% The function runs the local tangent space alignment algorithm on dataset
% X, reducing the data to dimensionality d. The number of neighbors is
% specified by ... |
4b5319582565203ec98c24b655ebc2f3528686710c560fc242c566c62c124c2d | MATLAB | 3,501 | 105 | % ManualMasking.m
% Sarah West
% 8/23/21
% Is a function that lets you draw masks over mice brains manually. Is
% called by manual_masking_loop.m
% Inputs:
% existing_masks--
% image_to_mask--
% iterator_name -- just for asking user if they're done.
% Outputs:
% masks-- a
function[masks, indices_of_mask]=Manua... |
50b82e96c65d306d3125ca180738830cce71c0cb5d9f261415acb2250fb47bbb | MATLAB | 3,501 | 105 | function motion_corrected_name = FSL_MoCo_batch(filename,tgframe,iframe,fframe)
%======================
% -file input
%======================
fprintf(1,' \n Reading Volume ...');
DYN = load_untouch_nii(filename);
DYN = double(DYN.img);
fprintf(1,' done.');
[inpath, fname, ~] = fileparts(filename);
[~, fname, ~] ... |
ad732cec57d7ca2173eb0322890fadacb64785ee504ef19b28da615849c8edc7 | MATLAB | 3,501 | 107 | function dat = read_egis_data(filename, hdr, begtrial, endtrial, chanindx)
% READ_EGIS_DATA reads the data from an EGI EGIS format file
%
% Use as
% dat = read_egis_data(filename, hdr, begtrial, endtrial, chanindx);
% where
% filename name of the input file
% hdr header structure, see FT_READ_HE... |
30274dda4f79bb48f526c3e25f6b44f5fbf7a08e8034d886fddb079f93bcaf7e | MATLAB | 3,502 | 136 | function [Carotids_mask,Pseudo_TOF_final] = segment_arteries(PET_dyn_path,time_PET,out_path,anatomy,options)
[~,~,~,~, IDIFTemp_path, IDIFVessels_path, IDIFQC_path, ~, ~, COREG_path] = out_path_preparation(out_path);
%loading dynPET
[PET_dyn, PET2D, hdr, NIIdyn] = load_PET(PET_dyn_path);
%cleaning PET...
PET_dyn(:,:,... |
75dab82c670776c818160500bbe5e2f09ce94f381b1efccc5fa5b2dcf921f899 | MATLAB | 3,502 | 124 | %% Multimodal PLS
%
%
% 1. Load data
% 2. Regress out confounds
% 3. Reduce imaging data dimensionality with PCA
% 4. PLS analysis
clear
close all
clc
addpath(fullfile(getenv('CBIG_CODE_DIR')
addpath(fullfile(getenv('CBIG_CODE_DIR','external_packages','matlab','non_default_packages','PLS_MIPlab')))
data_dir = ... |
69248f7e0b3758d8c9ebc6a81e758a7922dd05a1b7fdd0372680ea7acdcdfd91 | MATLAB | 3,503 | 82 | function compile_apt(varargin)
% Build an APT executable.
% Parse optional args
[do_run_test_after, do_compile] = ...
myparse( varargin ...
, 'do_run_test_after', false ...
, 'do_compile', true ...
) ;
% Define things needed for building or running
main_m_file_name = 'APT_deploy... |
2dcb87c7225375fb88ff827debe44a6f0909e5e7bfb5f4b18ed00ac019bf8765 | MATLAB | 3,505 | 70 | function [Epri, Ppri] = bemf3_inc_field_electric_gauss_selective(strdipolePplus, strdipolePminus, strdipolesig, strdipoleCurrent, P, t, Center, dipoleClusterCenter, gaussRadius)
%% Compute model subdivision parameters
% number of integration points in the Gaussian quadrature
... |
9a0a49adf13a5208cb8cbc637b2aec83bec8465ee407a98bf91b090a8bb03539 | MATLAB | 3,505 | 105 | function surr = CBIG_RL2017_get_AR_surrogate(TC,n_surr,order,distribution)
% surr = CBIG_RL2017_get_AR_surrogate(TC,n_surr,order,distribution)
% This function generates autoregressive (AR) surrogates. The three
% mandatory inputs are:
% 'TC' original time course of size (num_timepoints,num_variables).... |
dda3d58c7c11e10df508113ca8660ddf17901e3c9a9b79d916de43fd31f6f8c5 | MATLAB | 3,505 | 70 | function [Epri, Ppri] = bemf3_inc_field_electric_gauss_selective_dipoles(strdipolePplus, strdipolePminus, strdipolesig, strdipoleCurrent, P, t, Center, dipoleClusterCenter, gaussRadius)
%% Compute model subdivision parameters
% number of integration points in the Gaussian quadrature
... |
04a57d3b3e40d02aa547ef7d04d8b25e56677c31a96eeda2dac94b296b731dff | MATLAB | 3,507 | 99 |
function[out] = fit_measure_rois(measure, range, above_SNR_thresh_VTA, above_SNR_thresh, VTA_analysis_out, LC_analysis_out, x_units, grab_laps,range2)
if exist("range2", "var")
LC_range = range2;
LC_x = x_units;
x_units = x_units(21:60);
else
LC_range = range;
LC_x = x_units;
end
if measure == '... |
54619c671c24ba57753ca7d2bfcd236fa933ca3221478ec6904081cef7f2f3bb | MATLAB | 3,507 | 136 | function [B,MSEs]=jisotonic5(A,direction,weights)
% jisotonic5 - isotonic regression (jfm, may 2105)
%
% [B,MSEs] = jisotonic5(A,direction,weights)
% A is the input a vector
% direction = 'increading', 'decreasing', 'updown', or 'downup'
% weights is the optional input weight vector (same size as A)
% B is the ... |
f27e7bc27b36c13402776257b3e232b8a5e3da3e85e2665d0b6b62cc39c1aa0c | MATLAB | 3,507 | 114 | function sources2vtk(mesh,output_fn,varargin)
% SOURCES2VTK Saves sources of a FEM mesh in NIRFAST format into a *.vtk file.
%
% SOURCES2VTK(MESH,OUTPUT_FN) Saves sources (MESH.source.coord) of a FEM
% MESH in NIRFAST format into a *.vtk file. Usefull for visualization
% with e.g. ParaView.
% MESH - mesh struct... |
4690a9ebb56326a59893e0363c62d272c65283bbd5480945b435c93814675dd1 | MATLAB | 3,508 | 112 | %% pxTools_predictPxtFromPx0
% Core method for predicting and output distribution given an input
% distribution.
%
% Assume input distributions are columnwise
%
% Can pass two types of operators to this functions: Transition matrices
% (px) or difference matrices (dpx); If the later, select between two
% different type... |
f7003fa75ae0de0779da95171b924609aeb257534ff722a28574c5bd9227b972 | MATLAB | 3,508 | 111 | function [mappedX, mapping] = laplacian_eigen(X, no_dims, k, sigma, eig_impl)
%LAPLACIAN_EIGEN Performs non-linear dimensionality reduction using Laplacian Eigenmaps
%
% [mappedX, mapping] = laplacian_eigen(X, no_dims, k, sigma, eig_impl)
%
% Performs non-linear dimensionality reduction using Laplacian Eigenmaps.
% T... |
76cee028b153d6116669fbc6b8cbb989501f6e8211b38c90aa988873de84ef45 | MATLAB | 3,509 | 160 | function [A, fH, figNames] = meg_plotDecode(D, I, p, classLabels, classNames, selectedChannels)
% function [A, fH, figNames] = meg_plotDecode(D, I, p, classLabels, classNames, selectedChannels)
%
% ADD doc
%
% Rachel Denison
% March 2020
%% Inputs
if nargin < 1
D = [];
end
if nargin < 2
I = [];
end
if nargin ... |
8fddfca55eb104d90498251317928f8d8bd38ccffcd4cb0505b92d2c3f0c4659 | MATLAB | 3,510 | 106 | function val = ft_getopt(opt, key, default, emptymeaningful)
% FT_GETOPT gets the value of a specified option from a configuration structure
% or from a cell-array with key-value pairs.
%
% Use as
% val = ft_getopt(s, key, default, emptymeaningful)
% where the input values are
% s = structure or cell... |
e43f0cbce9cc885e4593b8f508950cd2d6b42ab69c7276a3055d6d3c1595d06a | MATLAB | 3,511 | 173 | function [xc,good,bad] = centercirclefinder(xt,I,wintx,winty);
%xt = [521.6249 ; 469.9916];
%wintx = 60;
%winty = 60;
xt = xt';
xt = fliplr(xt);
if nargin < 4,
winty = 5;
if nargin < 3,
wintx = 5;
end;
end;
if nargin < 6,
wx2 = -1;
wy2 = -1;
end;
mask = ones(2*wintx + 1,2*winty + 1);
%mas... |
9534aeb603b628befa1899f93c2a69c50d3ca4509fc11460d7f1f1cd461b9dba | MATLAB | 3,512 | 101 | function [XX, XY,Yn,allstim,n,T] = MkSuffStats_BilinReg_Data(Data,includeTerms,variable_name,cntxt,ssm,TrainTrials)
n = length(Data.unit);%number of units in the data set
T = size(Data.unit(1).response,2);
allstim = cell(n,1);
Yn = cell(n,1); % neural responses (each cell has resps for one neuron)
ntrials = zeros(n,1)... |
7e6b1566ce30b6a12575b919d163905351babf542f8b4c993f3df48e0c8b4694 | MATLAB | 3,513 | 94 | loadParameters;
if ~params.DO_DOWNSAMPLE
fprintf('Skipping downsample because the parameter file says not necessary\n');
fprintf('[DONE]\n');
return;
end
t_downsample_apply = tic;
delete(gcp('nocreate'))
conditions = conditions_for_concurrency();
max_pool_size = concurrency_size_in_downsample_apply(condit... |
dce24905242b196e729838559f34af9f85c135118bbffb9c56d976b4abf2a49f | MATLAB | 3,513 | 154 | % Field Trip-related test scripts - Synthetic FT data - Event detection.
%
%
% Includes.
% FIXME - Assume init has already been called.
%
%
% Configuration.
% Select the actual parameter extraction method to use.
paramconfig_chosen = paramconfig_coarse;
if strcmp('amp', param_chosen_type)
disp('.. Using det... |
4266c20cdd9809f084b25c18b3d98d2d9ae58cc0e59b715f0fa96c8715a4dd69 | MATLAB | 3,514 | 124 | function catFAdemoAuto()
% Factor analysis with categorical and continuous data
% We reproduce the demo from
% http://www.cs.ubc.ca/~emtiyaz/software/mixedDataFA.html
% The original source code for this demo is in
% demoFAemt; the results are identical since the underlying
% code (and initialization) is identical.
%[d... |
a70d41a81913d157eaadc1d33af91c87d6b553dc950e15923e5cee8437f69d41 | MATLAB | 3,514 | 116 | function B = pmlGrabBook(includeEx, includeSol)
%% Grab the entire PML book and put it in a cell array
% Each chapter is put in its own subcell so that B{i}{j} is the jth line in
% chapter i. Comments, (including block comments} and blank spaces are
% removed. Does not include, ttl, dummy, preface, or the generated in... |
c6303958eb80e5324f2fc835fd0ed28d79aabf222aa5716e4d67bf6d9f74bbe3 | MATLAB | 3,514 | 92 | function model = svmlibFit(X, y, C, kernelParam, kernelType, varargin)
% PMTK interface to libsvm
% If RBF, the kernelParam is gamma in exp(-gamma ||X-X'||^2).
%
%% Setup
% (1) Download libsvm from
% http://www.csie.ntu.edu.tw/~cjlin/cgi-bin/libsvm.cgi?+http://www.csie.ntu.edu.tw/~cjlin/libsvm+zip
% (2) unzip to e.... |
28ba5a280771c22f790b0dcd6067bc6d2865a7d8c346fa3fb171b392663c034a | MATLAB | 3,517 | 84 | function [postSaccTimes, saccLats] = GetTimesBeforeTriggers(saccCodes, beforeCode, trigLats, trigs, times)
% function [postSaccTimes, saccLats] = GetTimesBeforeTriggers(saccCodes, beforeCode, trigLats, trigs, times)
% Returns boolean matrix of whether each time sample was after the saccade
% trigger codes given, on eac... |
662081491c6c5c2b0491be99e984979324c5fd638dab2902209624a4740b07e5 | MATLAB | 3,520 | 71 | function CBIG_AuthorTopicEM_ReplicateBrainMapResults(seed, K, alpha, eta)
% CBIG_AuthorTopicEM_ReplicateBrainMapResults
%
% Wrapper function to replicate the cognitive components estimated from BrainMap
% from Yeo et al. 2015. Input data is stored in CBIG's HPC server.
%
% The inference was performed with ... |
5a4aec589897a891be38b8920ef7b2f8600fb2cf5111529aff9ae7da9d6900bb | MATLAB | 3,521 | 109 | function [data] = analyze_mExR_5xFAD_abeta_cropped(params,fov,chs)
% Analyzes validation data, with same proteins stained in consecutive rounds
% Outputs
% num_puncta: the number of puncta in each synapse
% punctavol: the total puncta volume for each synapse
% AR: the aspect ratio of the most ellipsoid volume in each ... |
b8d7e179ca8fa3c1632f01278a4e68d0a32fa0078d34a17737323e2c378fdf74 | MATLAB | 3,521 | 122 | function [tev, tsq] = read_tdt_tev(filename)
% READ_TDT_TANK
%
% Use as
% [tev, tsq] = read_tdt_tank(filename)
%
% Note:
% tev file contains event binary data
% tev and tsq files work together to get an event's data and attributes
% sev files contains streamed binary data
% the possible values of the data for... |
20b61a36bc8f272147f52e5987a34da0e0be36a837feec83ae3c7ee250297760 | MATLAB | 3,522 | 92 | % Source-target evaluations on the unit square, Helmholtz kernel.
%
% This is basically the same as MV_SQUARE1 but using the Helmholtz kernel. The
% associated matrix is rectangular and complex.
%
% Inputs (defaults are used if not provided or set empty):
%
% - M: number of row points (default: M = 16384)
% - N: nu... |
34eeda87e8a9179c47345d5e6d07e291e6caee9e83e2d4c0574b497aec26f68e | MATLAB | 3,524 | 92 | function [H, basis] = hessianmatrix(problem, x, basis)
% Computes a matrix which represents the Hessian in some tangent basis.
%
% [H, basis] = hessianmatrix(problem, x)
% [H, basis] = hessianmatrix(problem, x, basis)
%
% problem is a Manopt problem structure with a manifold and cost function.
% x is a point on ... |
9c3d582d64a55d28303871f609fea17ea6896673e96d6893a419f70f6548161a | MATLAB | 3,524 | 92 | % Source-target evaluations on the unit circle, Helmholtz kernel.
%
% This is basically the same as MV_CIRCLE1 but using the Helmholtz kernel. The
% associated matrix is rectangular and complex.
%
% Inputs (defaults are used if not provided or set empty):
%
% - M: number of row points (default: M = 16384)
% - N: nu... |
3a357a8c5744fd9ed1c483b708d98f007abfd010f18161708ea6757224842c60 | MATLAB | 3,525 | 118 | % Author: Birgit Nierula
% nierula@cbs.mpg.de
function esg_prepro_loop10(subject, condition, srmr_nr)
debug_mode = false;
%% set variables
subject_id = sprintf('sub-%03i', subject);
analysis_path = [getenv('ANADIR') subject_id '/esg/prepro/'];
cfg_path = getenv('CFGDIR');
% get condition info
[cond_info] = get_cond... |
04e5d14381cea0eb9905e92fc9ed7193a0a02af97609b34c33410a1e43c452f7 | MATLAB | 3,527 | 91 | function [Error, Cfg]=DPABISurf_RerunWithGSR(Cfg)
% FORMAT [Error]=DPABISurf_RerunWithGSR(Cfg)
% The data has been processed without global signal regression for the first pass. Now re-run it with global signal regression.
% Input:
% Cfg - the parameters for auto data processing
% Output:
% The processed data... |
1dfb20081097ade02cc9af24e731208385079d9854ecc43db24197ec8661c4b8 | MATLAB | 3,527 | 110 | function copy_ctf_files(oldname, newname, deleteflag)
% COPY_CTF_FILES copies a CTF dataset with all files and directories to a new CTF
% dataset with another name.
%
% Use as
% copy_brainvision_files(oldname, newname, deleteflag)
%
% Both the old and new name should refer to the CTF dataset directory, including
% t... |
7eec7dcdbf5ff7bf2f4ab40d46f8303198fc55c822a4f7c97eb0ccf880566655 | MATLAB | 3,527 | 121 | function [path, name, ext] = fileparts_platind(file)
%
% parses paths as in windows, regardless of the os
% renamed by KB 20160803
% experiments directories pathes in .jab files created on windows machines
% are not parsed correctly
% on unix based system because '\' is not a proper delimiter, so this
%... |
95054c2289dc3bc7633794bfa49b90e09451293032c381b250f94d6042ffbf7e | MATLAB | 3,529 | 72 | % This function fits sinusoids of different frequencies to the drift at
% different bump positions (starting and restarting)
function [A_All_Begin, A_All_End, Theta_All_Begin, Theta_All_End, DC_All_Begin, DC_All_End,...
Model_FitToData_Begin, Model_FitToData_End, Model_FitToData_Begin_Plot, Model_FitToDa... |
10d6fc2192707af78bf69811c570d21b519062c89626814d8cb57548a8f3f740 | MATLAB | 3,530 | 104 | function [hdr] = read_nihonkohden_hdr(filename)
% READ_NIHONKOHDEN_HDR reads the known items from the Nihon Kohden EEG
% system header file (*.m00) and returns them in a structure. This reading
% function is an adaptation of get_nkheader.m written by Timothy Ellmore
%
% Use as
% hdr = read_nihonkoden_hdr(file... |
fc11d7d801ea0b87c05fe144e52a484fe80bf61a360d8952f036c470c8fcb510 | MATLAB | 3,530 | 130 | classdef ParameterVisualizationTgtCropRadius < ParameterVisualization
properties
% If true, a prop for this pvObj is currently selected, and we are
% successfully initted/displaying something.
initSuccessful = false;
hRect % scalar line handle. set/created during init
isMA % scalar ... |
15835dcc18b83108985672b6613857d5dd9a545161a97a0da75d4b427ce2ae78 | MATLAB | 3,531 | 103 | function [AllVolumeBrain, GHeader] = y_bandpass_Surf(InFile, ...
ASamplePeriod, ALowPass_HighCutoff, AHighPass_LowCutoff, ...
AAddMeanBack, ...
AMaskFilename,...
AResultFilename,...
CUTNUMBER)
%Ideal Band pass filter
%Algorithm re-written to call y_IdealFilter by YAN Chao-Gan
% FORMAT [AllVo... |
a058cb72bbba5b4e872b562accab452f376e34abbb9006525006eb7e408ff4fb | MATLAB | 3,532 | 120 | function state = randomseed(setseed)
% RANDOMSEED retrieves or sets the random seed, taking into account the different
% MATLAB version specific methods
%
% Use as
% state = randomseed(setseed)
%
% INPUT
% setseed [] does not reset the state, but saves out the state for future use
% intege... |
a59163bf5224a524b2ad796776f40d6639c7318df852ada4baac543951f93711 | MATLAB | 3,532 | 79 | % note: change current folder to figure "number"
clear all;close all;clc;
rawPath=pwd; %displays the current working directory - set it to the figure "number"
savePath=rawPath;
addpath Panels/
addpath Functions/
load("StaticBars_width900_VS_width300_basedOnRF_Population_All")
load('colors.mat')
%% Figure 4
dataPath... |
83cfa8c7d827cfdde73afe52ecad593746612230b8bf30f6c1ee4a1ce2a48bba | MATLAB | 3,533 | 175 | function [H,Hnorm,inv_Hnorm] = compute_homography(m,M);
%compute_homography
%
%[H,Hnorm,inv_Hnorm] = compute_homography(m,M)
%
%Computes the planar homography between the point coordinates on the plane (M) and the image
%point coordinates (m).
%
%INPUT: m: homogeneous coordinates in the image plane (3xN matrix)
% ... |
28a7a17429fd1ac3601197e015817636ef601f6079073a480d8f4cb112301d1c | MATLAB | 3,534 | 144 | %% Demo of group lasso compared to vanilla lasso
% PMTKauthor Mark Schmidt
%%
% This file is from pmtk3.googlecode.com
function linregGroupLassoDemo()
setSeed(1);
%% Make data
% Generate categorical features
nInstances = 200;
%nStates = [10 5 10 5 20 5 10 5 20 5 10 20 10];
nStates = [10 5 10 20 10 20 10];
% Numb... |
386528d145d6f2ae7c6640965363a47a81ca4a2f5c60661a082d9c944265a0e5 | MATLAB | 3,535 | 90 | function [theta_AIC,phi_AIC,reg_id_AIC,cut_id_AIC,AIC_value] = ...
AICfun_ForStepRegression_constrained(Y,phi,theta,ori_reg_id)
% Akaike Information Criterion Forward selection method.
% given Y, phi, and the regulator IDs before AIC
% calculate AIC and output theta_AIC, regulator IDs after AIC, regulator IDs c... |
6b2c2bc535c95d64458805b7c716ab5113b73336b9606e90ee8392b3a0d60fe2 | MATLAB | 3,535 | 97 | %% Code to run sleep-session decoding of Shin et al., 2019 data
% sleep_decode_batch_new.m
%
% This was adapted from exptSleepDecoding.m to run decoding of
% experimental data from Shin et al., 2019 using the decode_events function
% created for simulated preplay events.
%% Set up
% Get data directory
userDir = char... |
7bfb1a721352b430f2dd267a110ee628259e2943d625cb7807dcbc89df6952ac | MATLAB | 3,535 | 81 | function [ gx ] = ObsRecGen(x,P,u,in)
% observation function for k-ToM's bet about her opponent's next move
% [ gx ] = ObsRecGen(x,P,u,in)
% Marie Devaine wrote this function in November 2015 (comments: JD).
% A k-ToM learner bases her decision (a=1 or a=0) upon her prediction of
% her opponent's next move, given the g... |
223f2a40714938323a541c924e87adacfaa119b36c26c9304d1cf0d98456b446 | MATLAB | 3,537 | 106 | function X = ttm(X,V,varargin)
%TTM Tensor times matrix for ttensor.
%
% Y = TTM(X,A,N) computes the n-mode product of the ttensor X with a
% matrix A; i.e., X x_N A. The integer N specifies the dimension
% (or mode) of X along which A should be multiplied. If size(A) =
% [J,I], then X must have size(X,N) = I... |
a889eef2aced865106ec501c180ebe5042d90ce5639286ae923c0056326f6558 | MATLAB | 3,537 | 102 | function [Xdata,ydata,W] = bolassoMakeData(n,d,r,nDataSets,requireConsistent,noise)
%Generate synthetic data as per section 4.1 in
%Bolasso: Model Consistent Lasso Estimation throught the Bootstrap by
%Fracis R. Bach, available at www.di.ens.fr/~fbach/icml_bolasso.pdf.
%
% n - number of examples
% d ... |
5918269eb1bb92f73061725af3888012cdc2a1796626d8818967bb3c3ccafc25 | MATLAB | 3,538 | 131 | function createFromDeeplabcut(dlc_data_file,mov_dir,varargin)
% function convertFromDeeplabcut(dlc_data_file,mov_dir)
% Creates a APT project from Deeplabcut project.
% dlc_data_file is the csv file generated by deeplabcut during training.
% mov_dir is the directory with the movie files used for the deeplabcut
% projec... |
2b170417a243da3f078fb8249551a9180c3cbeae1d602182acd959e9db657d83 | MATLAB | 3,540 | 115 | %% Split Drift/Diff SDOs.
%
% If the Fokker-Planck Equation underlying the stochastic process is an
% appropriate estimation of the underlying Kraymer-Moyals' Expansion, then
% the effects in probability DRIFT and DIFFUSION can be segregated as the
% first and second order approximations.
%
% In the SDO, passive diff... |
4ff1de74c253c719a2d0d0fea07bc6a36ea4d1804dff93d0abec4b5c169f9cda | MATLAB | 3,540 | 106 | function DataStructure=PowerFit3D_ZN(Xdata,Ydata,ZData)
FitBuffer=0.2;
FitDeviations=1000;
beta0 = [1, 1, 0]; % Guess values to start with. Just make your best guess.
modelfun = @(b,x) b(1) * x(:, 1) .^ + b(2) + b(3);
if size(Xdata,2)>size(Xdata,1)
else
Xdata=Xdata';
Ydata=... |
3d6f406ce5f887942c8c20644a0123bf6fb1eac7f18be2e4dcc1267689516c02 | MATLAB | 3,541 | 93 | %% cifReshuffle
% Utility to reshuffle spiketimes based upon the Conditional Intensity
% Function (CIF) generated from the supplied spikes. The number of output
% spikes will equal the number of input spikes.
%
% Used here to generate an arbitrary number of reshuffled timestamps.
%
% INPUTS
% timeStamps - [... |
4fe92a5315ed7f4ef4e895dccd755e7f599ee3dadb9e5ce1195f2e79d72f355e | MATLAB | 3,544 | 115 | function plotmesh_fiducials(mesh)
% PLOTMESH_FIDUCIALS Plots sources and detectors of meshes in NIRFAST format.
%
% SYNTAX:
% PLOTMESH_FIDUCIALS(MESH)
%
% PLOTMESH(MESH) MESH is NIRFAST mesh structure.
%
% Part of NIRFAST package.
%% load mesh
if ischar(mesh)== 1
mesh = load_mesh(mesh);
end
%% plot source... |
5610517fc03207f45c8823e66aa67d3b3e02ce3c50264c489f3f4ace0796d8dc | MATLAB | 3,544 | 136 | % makes the leaderboard
function make(look_here, nerve_name, neuron_name, window_size)
if isempty(look_here)
look_here = pwd;
end
data = crabsort.leaderboard.measure(look_here);
all_exp_id = categorical(zeros(length(data),1));
all_best_snr = (NaN(length(data),1));
all_worst_snr = (NaN(length(data),1));
all_mean_s... |
a8344652c4909d846599e2a3f719c8c09f3aae3a44b4959cd6186bbbb662b6d9 | MATLAB | 3,544 | 102 |
%% refrence and citation
%%%%%%%%%%%This code is a modified version of the the available code in Zajkowski et al 2017 article
%%%Zajkowski, Wojciech; Kossut, Malgorzata; Wilson, Robert, 2017, "A causal role for right frontopolar cortex in directed, but not random, exploration", https://doi.org/10.7910/DVN/CZT6EE
%%... |
a2b86b12775f0b1f45a9fcc9461a29cdd392b7d7d6c6a8ab99ed02408a93b057 | MATLAB | 3,545 | 102 | % DeleteMasks.m
% Sarah West
% 10/7/21
% Plots all the masks you drew with ManualMasking.m and lets you pick some
% for deletion.
function [masks, indices_of_mask] = DeleteMasks(masks, indices_of_mask, bRep)
% Inputs:
% masks -- a 3D matrix (pixels, pixels, mask #) of all the masks you drew.
% bRep -- a representativ... |
a537398ba1e693543796a6d2b6c52662a15585416f7b2f9a7f8de09513dabf84 | MATLAB | 3,546 | 91 | function segmentation = fixsegmentation(segmentation, fn, style)
% FIXSEGMENTATION is a helper function that ensures the segmentation to be internally
% consistent. It is used by ft_datatype_segmentation and ft_datatype_parcellation.
%
% % See also CONVERT_SEGMENTATIONSTYLE, DETERMINE_SEGMENTATIONSTYLE
switch style
... |
d153113176d461d59b0f565a5123362870e2be48feee5619744574519516c2d8 | MATLAB | 3,547 | 102 | %% initialize settings
% This script loads position data from the flytrack_video script, collapses
% data from multiple replicates, and makes a heatmap of where the flies went.
% Jeff Stafford
% How long is the assay (in seconds)? If one of the csv files is shorter
% than this, defaults to the shorter time.
total_t... |
f9f3caebba24197d339de51e0c7cd2b8469347808618a7308fbfdae1886af4ee | MATLAB | 3,547 | 176 | function ignore = ignorefields(purpose)
% IGNOREFIELDS returns a list of fields that can be present in the cfg structure that
% should be ignored at various places in the code, e.g. for provenance, history,
% size-checking, etc.
switch purpose
case 'appendtimelock'
ignore = {
'cfg'
'label'
... |
6041af6ef6f67e3170e6bf7e49661b756ab6a20b43a8e5d90fdf4266243a7a1a | MATLAB | 3,549 | 65 | %G distribution, AUC ratio comparisons.
clear
close all
clc
% Excel_Names_G = ['All_feature_Whole_G_Feb29_Injury2022_Glial_30SB'];%
% raw distribution
% Excel_Names_S = ['All_feature_Whole_S_Feb29_Injury2022_Neuron_30SB'];
% Excel_Names_G = ['All_feature_AUC_G_Feb29_Injury2022_Glial_30SB']; % AUC calibrated for ... |
dbaaa48e144c7c3dddf4da2d2b6596a9c1e2585e8151a51eed3d4458ebea9015 | MATLAB | 3,550 | 101 | function [model, p_lr] = CBIG_ASDf_logReg_clusterBehavAssoc(cluster_idx, id_scoreGrp, ...
sub_info_file, behav_score_file, idx_score)
% [model, p_lr] = CBIG_ASDf_logReg_clusterBehavAssoc(cluster_idx, id_scoreGrp,
% sub_info_file, behav_score_file, idx_score)
%
% Performs logistic regression to compare ASD participants... |
ecb88b3af6b8e6c98fdbdd49746696cb9340cb2736f9b12a21ba33ef5d8b76af | MATLAB | 3,550 | 134 | %% SP-ComBat
% implement ComBat harmonization at the image level with 3D superpixel parcellation
% requirement: MATLAB R2016b and above
% original environment for the implementation:
% MATLAB R2022a, SPM (v7771), and CAT12 (v12.8.2)
pkg_dir = '/path/to/the/pkg_spcombat';
addpath(pkg_dir);
%% Preprocessing... |
c0dbe4c501f5783175eff237ab9daad969be194b5f00f528ab335bb4db20563a | MATLAB | 3,551 | 110 | function X = ttm(X,V,varargin)
%TTM Tensor times matrix for ktensor.
%
% Y = TTM(X,A,N) computes the n-mode product of the ktensor X with a
% matrix A; i.e., X x_N A. The integer N specifies the dimension
% (or mode) of X along which A should be multiplied. If size(A) =
% [J,I], then X must have size(X,N) = I... |
0086e3b9aaa0d8ac573dd89e850eedf3a8570c52afc53da84b38306fefb9cdfc | MATLAB | 3,552 | 139 | %%
%load trnDataSH_Apr18.mat;
load trnData20180503.mat
%%
t = tMain20180503;
id = strcat(t.lblCat,'#',numarr2trimcellstr(t.flyID),'#',t.movID);
idC = categorical(id);
tCats = sortedsummary(idC)
idC = reordercats(idC,tCats.cats);
%%
hFig = figure;
cla;
ax = createsubplots(2,1);
plot(ax(1),tCats.cnts,'.');
grid(ax(1),'o... |
67c4dfd13eca5014ca2d6e506f13687634f58dc106f068ae10bb0a35287b2498 | MATLAB | 3,553 | 111 | % Script for running Enrichment analyses between fc data and behavioral
% data.
% It is assumed that the fc data is organized as ROI-ROI-Subject and the
% behavioral data is a vector with the same order and number of subjects
% in the fc array.
outputdir = 'filepath to output directory/';
addpath(genpath('filepath to ... |
7c2a23fcc604575de6e8141d28b787ee5ad5fb7bd9a889a38ff59e2d49e504e6 | MATLAB | 3,553 | 110 | function event = presentation_log(filename)
% PRESENTATION_LOG reads a NBS Presentation scenario log file and
% represents it as a FieldTrip event structure.
%
% See also FT_READ_EVENT
% Copyright (C) 2018 Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentatio... |
e120426b52f1a80704ff0fdd1825ef25d9d4e15bc99924707fa02766edc493ef | MATLAB | 3,553 | 87 | % Need to test more.
% Compute power in a signal along a frequency trajectory. numel(inSig) has
% to be equal to numel(freqTrajectory). Options to use both multitaper PSD
% (pmtm) or DFT.
% If stim_freq_shift is undefined, then stim_freq_shift is set to the
% geometric mean of the desired freauency trajectory.
functi... |
0af24fa665f8d085d2efe7615913ac0eec8a8e0f47b43805838b10c662189591 | MATLAB | 3,554 | 87 | function [subs,vals,keep] = nonMaxSuprList( subs, vals, radii, ...
thresh, maxn, flag)
% Applies nonmaximal suppression to a list.
%
% See nonMaxSupr for more information. Has the same effect as nonMaxSupr
% except it operates on a list of position/values pairs. Running time is
% n^2 in the number of such pairs. F... |
8c2f20a4709c05744e7940ecde5b6a923246a73d4e10b1840d7e80a364d06745 | MATLAB | 3,554 | 98 | function generateSupportReport()
%% Generate the html table describing packages in pmtkSupport
% and write it to PMTKlocalSupportPath/docs/authors/packageAuthors.html
% You need to commit this modified file in svn.
% Creating the report takes a few seconds.
% PMTKneedsMatlab
%% Setup
% This file is from pmtk3.googlec... |
fa0d982ab49006cfe33afa8a44736cb3127bb3105920b27c57de63cb7fde50db | MATLAB | 3,554 | 114 | %% plot_autocov
%
% Autocovariance plotting utility
%
% <matlab:open('plot_autocov.m') code>
%
%% Syntax
%
% plot_autocov(G,leg,dt,trange,auto,acorr)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% G matrix of autocovariance matrices
% leg ... |
2c54113a9537e1bb1f20666d727f170266a9b17b39e076528900c91f8fd4e0cc | MATLAB | 3,555 | 103 | %% Start by processing the clusters, aligning them
median_W = median(W, 'all');
std_W = std(W,[],'all');
range_max = median_W + 2*std_W; %FIX:consider switching to 3 std dev?
log_range = log(range_max);
log_max = log(range_max +std_W);
for t=1:num_groups
cluster_map = zeros(16,64);
for k=1:length(good_ch... |
7800f1e1c7f7e7627ab77ff93024306b0fb8011715c596894b9e96a9835b5199 | MATLAB | 3,555 | 123 | %% sdoAnalysis_demo (OOP)
%
% Demonstration of the SDO Analysis Toolkit;
% Run an SDO analysis using the Object-Oriented Programming (OOP)
% class-method data wrappers.
%
% This can be used as a framework for designing custom SDO analysis
%_______________________________________
% Copyright (C) 2023 Trevo... |
acbdc148f66aa713c2cfc7d830629646b08c30c3d34ac72272bc185d00ce220d | MATLAB | 3,555 | 104 | %% Plot 2d sigmoid functions for various values of w1, w2.
% i.e. sigmoid(w1*x1 +%w2*x2)
%%
% This file is from pmtk3.googlecode.com
function sigmoidplot2D
% Plot sigmoids with these parameters
w_1 = [-2 ; -2 ; 0 ; 1 ; 1 ; 2 ; 2 ; 3 ; 5 ; 5];
w_2 = [-1 ; 3 ; 2 ; 4 ; 0 ; 2 ; -2 ; 0 ; 4 ; 1];
lowRes = 0; % Set... |
0c9ad672bc4aafec82ccd4578b95db5205c33f827d254ed8dbf3ede4709dc522 | MATLAB | 3,556 | 67 | function Obj=SOFAconvertFHK2SOFA(miroObj)
% OBJ=SOFAconvertFHK2SOFA(miroObj) converts the HRTFs described in miroObj
% to SOFA. miroObj is the miro object saved at the Fach-Hochschule Köln
% provided by Benjamin Bernschütz.
% Reference to the source format: http://www.audiogroup.web.fh-koeln.de/ku100hrir.html
% Referen... |
3f152f644ea4221304b3c964035c3875d2ce4e74ce616f5723490004ff6dacf6 | MATLAB | 3,556 | 159 | function [t,F,p,df,R2,cR2,B,r,aR2,iR2,Bcov] = glm(y,X,c,pflag);
% [t,F,p,df,R2,cR2,B,r,aR2,iR2,Bcov] = glm(y,X,c,pflag);
%
% Generic function for General Linear Model (GLM)
% Note: assumes error is spherical (residuals white)
% Rik Henson, 2004
%
% (Note requires Matlab stats toolbox, or SPM functions to be on path)
%... |
aae04d95fad3727abe2532379a701f5a6c673217f02f2a21c83832ddcb325506 | MATLAB | 3,556 | 94 | function [grid] = mollify(cfg, grid)
% This function does something
%
% Copyright (c) 2006, Jan-Mathijs Schoffelen & Robert Oostenveld, F.C. Donders Centre
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribu... |
6f2dae255957934f0a96d0918658210a74b02cf5b3fdbaf778dea38548b1c721 | MATLAB | 3,557 | 69 | %% SAVE MATLAB FILE
cd(['F:\DataResearch\' PatientName '\Label'])
mri_name = dir(['F:\DataResearch\Brainstorm\' ProtocolName '\anat\CAT\subjectimage*01.mat']);
sMRI = load([mri_name.folder '\' mri_name.name]);
bs_low = load(['F:\DataResearch\Brainstorm\' ProtocolName '\anat\CAT\tess_cortex_pial_20484V.mat']);
bs_headmo... |
bb4a3fae5a5cbb4edb9105aa239102b3775a2bd9cea395aa2bdcbf6d629d368f | MATLAB | 3,558 | 164 |
if ~exist('n_ima'),
fprintf(1,'No data to process.\n');
return;
end;
if n_ima == 0,
fprintf(1,'No image data available\n');
return;
end;
if ~exist('active_images'),
active_images = ones(1,n_ima);
end;
n_act = length(active_images);
if n_act < n_ima,
active_images = [active_images ones(1,n_ima-n_act... |
ea995752ef1fb4d276d9960d636be49b145d7523c404b60c1c7fdb430e7e15be | MATLAB | 3,559 | 115 | %% GSA_FAST_GetSi: calculate the FAST sensitivity indices for multi-output systems
% Ref: Cukier, R.I., C.M. Fortuin, K.E. Shuler, A.G. Petschek and J.H.
% Schaibly (1973). Study of the sensitivity of coupled reaction systems to uncertainties in rate coefficients. I Theory. Journal of Chemical Physics
%
% Max number o... |
20c51ee997bc14b335303f710938ae8b12be46da52e795d8b843ba78c2cb59d7 | MATLAB | 3,560 | 122 | function s1 = mergeconfig(s1, s2, emptymeaningful)
% MERGECONFIG merges the fields of a structure with another structure. The fields of
% the 2nd structure are only copied in case they are absent in the 1st structure.
%
% Use as
% s3 = mergeconfig(s1, s2, emptymeaningful)
%
% See also MERGE_TABLE
% Copyright (C) 20... |
8e82be31f163ae76c7bea358c62041f4390e02dab643b114d606060974b260e9 | MATLAB | 3,561 | 124 | function [ IDX,timestamps ] = bz_INTtoIDX(INT,varargin)
%[IDX] = bz_INTtoIDX(INT) Converts state on/offsets to vector of indices
%
%INPUT
% INT: {nstates} cell array of [nintervals x 2] start and end times.
% (optional) can be TSObject intervalSet
% -or-
% structure with f... |
7ba26bd7e6d0d984d9ee9add46ff59bd534488b520decdb16406487d6afc0a95 | MATLAB | 3,562 | 98 | %-----------------------------------------------------------------------------------------
% Example raster plot of a human piriform neuron responding to odors
%
% Kehl et al. 2024 (DOI:XX)
% Single-Neuron Representations of Odors in the Human Brain
% Figure 1g
% Author: Marcel Kehl
% License: MIT License
%---------... |
b0ee76005681bc32e9f4fe8bf3767b41477fbbab2ac58e583c9c9e83b2be2fda | MATLAB | 3,563 | 90 | %% SAT - app_input ::
%% determineXtFileType
% Name: Phone Kyaw
% Date: 09/19/2024
% Description: Return a xt_cell when a user inputs XT files
% Parameter: None
% Return Value: xt_cell - Nx2 cell array where the {1,1} contains the header
% and the second column contains xt... |
c6d0438e1da2c840b2364bcbeb867121945810cf043c2ec632edd1a9489db723 | MATLAB | 3,563 | 80 |
ind = 1;
data = dir('/DATAPOOL/ERRORMONITORING/SEM_mri_data/P*');
%%
for i = 1:size(data,1)
data_func = dir([data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/func/run*']);
fprintf(data(i).name);
dir_folder = [data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/... |
1a25737ea159e09f46a621ed059b238f3088fa8df00f0cfe3da8a268395a66bc | MATLAB | 3,564 | 93 | function [ simulated_data] = makeSimulatedRound(num_puncta,bases,cross_talk,puncta_positions,puncta_sizes,puncta_variability,outputDims)
%MAKESIMULATEDROUND
% num_puncta: how many puncta are going into this volume?
% bases: what base is each puncta showing
% cross_talk: what percentage of each signal is in each round... |
2d00b979c1d6f388d0389dd2dcfb9fff6c12aec444b686a9f1c1495f340c334d | MATLAB | 3,564 | 95 | % Source-target evaluations on the unit cube, Helmholtz kernel.
%
% This is basically the same as MV_CUBE1 but using the Helmholtz kernel. The
% associated matrix is rectangular and complex.
%
% Inputs (defaults are used if not provided or set empty):
%
% - M: number of row points (default: M = 16384)
% - N: number... |
2ee62afe5ad654e3e76644543393704864c160eed39db11f74d8ae05bff7c0a4 | MATLAB | 3,566 | 123 |
medA = load(fullfile(saveLoc, 'for_plots_mediation_norm_to_se'));
mediatedDimsA = [52 19 27]; dimTin = 27;% ramp, PC1, Tin ('for_plots_mediation_norm_to_se')
tt = medA.leverage(medD).per_session.self_mediated.tt;
tpt = find(round(tt, 3) == 0.40);
allMed = [];
allP = [];
for medD = mediatedDimsA
... |
22a09a7aae20775d514fc87e632e5702433c15a6530350af541046035abca517 | MATLAB | 3,567 | 148 | %% Compare SMLR selecting lambda on grid or on path.
% If path, we use the same kernel basis for all lambda
% If grid, we change the basis depending on the fold.
%
% See also linearKernelDemo
% This file is from pmtk3.googlecode.com
%PMTKslow
% Results: rows = soy, colon
% cols = 'smlrPath', 'smlrNoPath', 'rmlrPat... |
9c78ad5253e3806ba0169eb5b2d5569e2bb82b4095e71abf2645f8fd5d4f16c9 | MATLAB | 3,567 | 103 | function [b,idx,outliers] = deleteoutliers(a,alpha,rep);
% [B, IDX, OUTLIERS] = DELETEOUTLIERS(A, ALPHA, REP)
%
% For input vector A, returns a vector B with outliers (at the significance
% level alpha) removed. Also, optional output argument idx returns the
% indices in A of outlier values. Optional output argume... |
d994663ef89370696a196892dff34f0d449a6c8a918e8304efb62471a86116fa | MATLAB | 3,567 | 119 | function vol = read_asa_vol(fn)
% READ_ASA_VOL reads an ASA volume conductor file
%
% all data is converted to the following units
% vertices mm
% conductivities S/m
% Copyright (C) 2002, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and... |
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