sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
48697c92c15d887fa14516bd60721dce19a56dfe33fc49d50fc7c77de9f7594a | MATLAB | 2,393 | 83 | function BackgroundSubtraction(animal,probetype)
%Averages signal across all channels for a given shank and subtracts this average from each
%channel on that shank
%Inputs: Animal ID, Probetype, raw data files in LFP\Full folder.
%Outputs: Background subtracted data files to be used for spiking sorting
%and... |
f33062c37bdeaed00b769c9de09552f00dc8ce5f8efbbae2f7ad91cf3de12579 | MATLAB | 2,395 | 66 | function parcel_components = CBIG_ArealMSHBM_compute_components_general(lh_labels,rh_labels,mesh,num_parcel)
% parcel_components = CBIG_ArealMSHBM_compute_components_general(lh_labels,rh_labels,mesh,num_parcel)
%
% This script will compute the number of components for each parcel of a given parcellation <lh_labels>
% ... |
026ac30bda188f62773a65c22120dc95b0b7e0f98a6861928c39aebd3dfa215a | MATLAB | 2,396 | 80 | function [ux,ispos] = psdfactor(x,K)
% [ux,ispos] = psdfactor(x,K)
%
% PSDFACTOR UX'*UX Cholesky factorization
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (s... |
3c4acc68f221b97be94c7b935eb946b13c94bb31c4da8b955729d012bcacd806 | MATLAB | 2,396 | 89 | function [freq_range, time_range, rect_img, clust_size, b] = G_Outline_Range( img2plot, varargin)
% range of clusters
%
% Usage
% [freq_range, time_range, rect_img] = G_Outline_Range( img2plot, varargin)
%
% Input
% img2plot, binarmized matrix
%
% key-value pairs
% 'xaxis', e.g. time vector
% 'yaxi... |
3d1ff2158636d566f79f91224bb499c42852815c04680b4219f42f9ba808c7a5 | MATLAB | 2,396 | 59 | % scanfold() - scan folder content
%
% Usage:
% >> [cellres textres] = scanfold(foldname);
% >> [cellres textres] = scanfold(foldname, ignorelist, maxdepth);
%
% Inputs:
% foldname - [string] name of the folder
% ignorelist - [cell] list of folders to ignore
% maxdepth - [integer] maximum folder dep... |
3ddab2632efdb559b8095ae10cc9666a4d3e5caac1532f17f326a6853acd009c | MATLAB | 2,396 | 86 |
function [data] = cleanPulses(ts, varargin)
% [data] = cleanPulses(ts, varargin)
%
% Find square tsses
%
% INPUTS
% ts - List of artifacts that will be removed from data (in seconds)
% <OPTIONALS>
% filename
% basepath
% correctDC - Logical variable to indicate if DC is corrected, default
% ... |
a2fb08f01575c40915ce2be76fdb16ddf2084e0376d0a64a01799483702c0f94 | MATLAB | 2,398 | 69 | function rid_icv_vol = CBIG_getVol(ridList, structNames)
% rid_icv_vol = CBIG_getVol(ridList, structNames)
% Get baseline structure volumes from FS stats
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
imgDir = '//share/users/imganalysis/yeolab/data/ADNI_mert/';
ri... |
899da8eac1a0e96d37acca9b38258c0d6cfc05f5a0ae84f859828a254e596142 | MATLAB | 2,399 | 101 | function [y,dimage,header]=readOIS(fname,im)
% Usage ... y=readOIS(fname,im)
%
% If a range of images is selected, a 3D set is returned
verbose_flag=0;
fid=fopen(fname,'rb','l');
if (fid<3), error('Could not open file!'); end;
if (fname(end-5:end)=='oldraw'),
verinfo=' ';
dateinfo=' ... |
e79257699003f1b98919aa7eb3693e587ce3b18ccd3b039e907aa1369f050440 | MATLAB | 2,399 | 76 | % readeetraklocs() - read 3-D location files saved using the EETrak
% digitizing software.
% Usage:
% >> CHANLOCS = readeetraklocs( filename );
%
% Inputs:
% filename - [string] file name
%
% Outputs:
% CHANLOCS - EEGLAB channel location data structure.
% See hel... |
459c127009869d9818bfcec94b89f99705b2441fb34c26f7cc692f8de4648772 | MATLAB | 2,400 | 67 | function obj=stat_qq(obj,varargin)
% stat_qq Makes a quantile-quantile plot from the data in x
%
% 'distribution' is used to provide a custom distribution
% constructed with Matlab's makedist(). Default is
% makedist('Normal',0,1). Use 'y' instead of a custom
% distrubution to plot the distribution of y against the
% d... |
58a3b0b52b40a871f45f26bd238602adab6e79f0383ea8f94e4c5bb63c8b464d | MATLAB | 2,400 | 66 | % std_findsameica() - find groups of datasets with identical ICA decomposiotions
% (search identical weight*sphere matrices)
%
% Usage:
% >> clusters = std_findsameica(ALLEEG);
% >> clusters = std_findsameica(ALLEEG,icathreshold);
% Inputs:
% ALLEEG - a vector of loaded EE... |
761f1f31b9f54e51deb4d29602739492aeccc28d7628788466ef3cdd135c776e | MATLAB | 2,402 | 92 | function allenMapSMc(dorsalMaps, axLims, alpha)
% allenMapSMc(dorsalMaps)
%
% Produce a dorsal-view Allen atlas map using polygons, centered on the
% sensorimotor cortex.
%
% Input "dorsalMaps" should be from allenDorsalMap.mat.
%% Parameters
lineWidth = 0.9; % Line width for area outlines
lineWidthBox = 0.... |
2d473add482842cb5308f01cef6485553430275f80218117c51b9c3796c41a63 | MATLAB | 2,403 | 49 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
38c6bb6c076d5a5a074089cb8af0d6f8e248b6451cbccef799e303860ac2a136 | MATLAB | 2,403 | 64 | function id=ea_unifiedmapping_method2methodid(obj,efm)
obj.compat_statmetric; % old compatibility for old statmetric notation (used to be stored as integers).
obj=ea_unified_discfibers_compat_statmetrics2statsettings(obj);
if ~exist('efm','var')
efm=obj.statsettings.efieldmetric;
end
switch obj.calcsettings.conn... |
d77adeb72aa73fcb6e511bccf0d5fa567a3d170332f06f75f931a79d2d63fc99 | MATLAB | 2,403 | 77 | function [ynew2,tmpi]=myTBfix1(y,ref,thr,off1)
% Usage ... [y_new,ii]=myTBfix1(y,ref_tb,thr,aoff)
%
% Uses REF and THR to correct changes in Y
if nargin<4, off1=[]; end;
do_many=1;
if prod(size(y))==length(y), do_many=0; end;
if do_many,
if size(ref,2)==1, ref=ref(:)*ones(length(ref),size(y,2)); end;
end... |
2ec7f7d53554509ccee50f06b780f20e5f396e6b78c5b6c32606aa4d96aca610 | MATLAB | 2,404 | 66 | %% Plot line&shadow
for i = 1:numel(power_log)
% power_log_pre{i} = power_log{i}(:, 1:xx, :);
% power_log_post{i} = power_log{i}(:,xx:xx, :);
end
power_fre_log = cellfun(@(x) squeeze(mean(x(roi_band, :, roi_trial), 2)), power_log_stim, 'UniformOutput', false);
power_fre_base_log = cellfun(@(x) squeeze(m... |
ad7743f8bc9e5d39524794b44cc2a7e3f05a53f90b98a56f8f6ceca22c009b98 | MATLAB | 2,405 | 62 | % demo file for applying the NoRMCorre motion correction algorithm on
% 1-photon widefield imaging data using low memory (good for long datasets)
% Example file is provided from the miniscope project page
% www.miniscope.org
clear;
gcp;
%% read data and convert to double
name = 'msCam13.avi';
if ~exist(name,'file') ... |
1d95e37964ead35399d2706071c6d1e34fa63156ebf4bded395b2009764e07f9 | MATLAB | 2,406 | 62 | function permSet = CBIG_ASDf_genPermSetForNBS(id_factor, id_con, sub_info_file, Nperm)
% permSet = CBIG_ASDf_genPermSetForNBS(id_factor, id_con, sub_info_file, Nperm)
%
% This function generates the within-site permutation set using PALM package.
% ASD and control subjects from the same site are permuted.
%
% Input:
... |
1a90eaf8c67ee37442a36d3aa5d715638cdd699fe2c49af6e8c7ce15343acf94 | MATLAB | 2,407 | 60 | function [Dr_pos_file, Dr_neg_variable_file, Dr_neg_constant_file] = calculate_Dr(input_nifti_path, angle_nifti_path)
% Define output file paths
Dr_pos_file = 'data/maps/Dr_positive.nii.gz';
Dr_neg_variable_file = 'data/maps/Dr_negative_variable.nii.gz';
Dr_neg_constant_file = 'data/maps/Dr_negative... |
51202819da39447d2789fa7897d3a8f3618264008d1cbb67ae227e75b3409796 | MATLAB | 2,407 | 21 | %EEGLAB time-frequency functions (timefreqfunc folder):
% <a href="matlab:helpwin angTimeWarp">angTimeWarp</a> - Given two event marker vectors, angTimeWarp computes a...
% <a href="matlab:helpwin bootstat">bootstat</a> - Accumulate surrogate data to assess significance by permutation of some...
... |
716c24c3ae18e0fbd74c1507e382343dcb5bab64548a081f1e84abe3558b6801 | MATLAB | 2,407 | 78 | % DENDPLOT: Plots a dendrogram given a topology matrix.
%
% Usage: dendplot(topology,{labels},{fontsize})
%
% topology = [(n-1) x 4] matrix summarizing dendrogram topology:
% col 1 = 1st OTU/cluster being grouped at current step
% col 2 = 2nd OTU/cluster
% ... |
815afd831e4499b423a7aa3c2ce210ae6a2ee2c524f255a27f595db0045a77bc | MATLAB | 2,407 | 49 | function ClincFreq_Norm2MNI_withT1_clinc(indat,inroi,indatT1,outdir,outname,voxelsize,pth)
try
[patdat,namdat,extdat] = fileparts(indat);
% [patroi,namroi,extroi] = fileparts(inroi);
[patdatT1,namdatT1,extdatT1] = fileparts(indatT1);
%%
[patdat,namdat,extdat] = fileparts(indat);
% [patroi,namroi,extroi] = fileparts(in... |
8eea2103dbb2505d3d0bec33cbecf1599d02fe6b0d0234f0a219385aa31c792a | MATLAB | 2,407 | 66 | function d=edit_distance_levenshtein_keylist(s,t)
% Calculate the Levenshtein edit distance for cell arrays of (string)
% keys, e.g.
% edit_distance_levenshtein_keylist({'the','quick','brown','fox'},{'the','lazy','dog'})
%
% @author B. Schauerte <schauerte@ieee.org>
% @date 2010
% Copyright 2010 B. ... |
904f88e88919dc2d34ce3b18f02fead9a8a7bb21672c317b17a625b29056c19b | MATLAB | 2,407 | 79 | function CBIG_IndCBM_create_surf_gifti(mesh, output_dir, varargin)
% CBIG_IndCBM_create_surf_gifti(mesh, output_dir)
%
% This function will create .func.gii files of different meshes for cifti
% templates creating.
%
% Input:
%
% - mesh:
% Mesh name. Can be 'fsaverage5', 'fsaverage6', 'fsaverage',
% ... |
9c3101bf9287152a7dabb43360c5f9ab5b4f16c764c0f0b80f8ca822efc4fedc | MATLAB | 2,407 | 57 | % Logic: Identify a set of "good" subjects for which no condition images are marked as outliers
% If a subject has one condition image that is an outlier, any contrast
% involving that image is also likely to be an outlier.
%
% Use fmri_data.outliers( ) to get outlier status for combined set of
% condition images. (Co... |
32706606504d00e1ba18c8098e9ed827d3f653b62a9d9f06ea8c416dab27d399 | MATLAB | 2,408 | 76 | %% Generate the average map across all participants (in fsaverage space)
clear all; clc;
% Set environment
setenv('FREESURFER_HOME','/tools/freesurfer');
% Setup paths
p.Home = '/egor2/egor/MovieProject2';
p.FS_subDIR = fullfile(p.Home, 'bids_data', 'derivatives', 'freesurfer');
p.SamSrf = '/egor2/egor/MovieProject2/... |
6c29188ca5e7eefcfecdcd8d28f9653a0dae3fff31d5efb25d94b15f9f643f95 | MATLAB | 2,408 | 67 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
9ac3fe72e1ad9adbd8053fbdabf7900673b8179145dc80d0d74629040d5e2217 | MATLAB | 2,410 | 48 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
10dd22bf09eae66e718bd375d37824fbcff259bde992b7f2ca338b45f7453b38 | MATLAB | 2,411 | 56 | % SOFA API - demo script
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "License")
% You may not use this work except in compliance with t... |
80fafc62ae011924fee790b91668956913047cf18b292ea172af5ba0cd9ebdd1 | MATLAB | 2,411 | 75 | % std_indvarmatch - match independent variable value in a list of values
%
% Usage:
% indices = std_indvarmatch(value, valuelist);
%
% Input:
% value - [string|real|cell] value to be matched
% valuelist - [cell array] cell array of string, numerical values or
% cell array
%
% Output:... |
6cbaaae1ab5eea3b497f7104bf2a798aaae65761ee4cc693510426fee6a1a9d0 | MATLAB | 2,412 | 80 | %%***************************************************************************
%% blkeig: compute eigenvalue decomposition of a cell array
%% whose contents are square matrices or the diagonal
%% of a diagonal matrix.
%%
%% [d,V] = blkeig(blk,X);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. ... |
8a06d33a62f0a49d889910c1f73a5db0fc75575d909f50a1092b10d62e8b4733 | MATLAB | 2,412 | 94 | function [ftr lens] = saveFTR(finame,P,I,offset,info,saveit)
if nargin == 5,
saveit = true;
end;
cc = {};
csc = {};
lens = [];
if isempty(offset),
warning('Empty field offset: guessing');
offset = eye(4);
offset(1,1) = 2; offset(2,2) = 2; offset(3,3) = 2;
end;
vox = [offset(1,1) offset(2,2... |
b91f6811a03e55ca9ef844c2597d25a0a0c580d1d1c98f2cac3d84b41e63be5f | MATLAB | 2,412 | 78 | function filter = makeGaborFilterGBVS(gaborParams, angle, phase, varargin)
% makeGaborFilter - returns a 2d Gabor filter.
%
% filter = makeGaborFilter(gaborParams, angle, phase, makeDisc)
% Returns a two-dimensional Gabor filter with the parameter:
% gaborParams - a struct with the following fields:
% filte... |
06c26f432b6bf3ad51efb50a655d9de8d71ce06d3e94563dae4035a776d2d7b8 | MATLAB | 2,414 | 47 | function SANDIinput = ProcessAllDatasets(SANDIinput)
StudyMainFolder = fullfile(SANDIinput.StudyMainFolder,'derivatives','preprocessed');
SubList = dir(fullfile(StudyMainFolder,'sub-*'));
SANDIinput.DatasetList = SubList;
%SANDIinput.report = [];
for subj_id = 1:numel(SubList)
SesList = dir(fullfile(StudyMai... |
df6b2cd907856d77df0637f53ae565f49ee9acb8650249b844604160c775ea44 | MATLAB | 2,414 | 63 | function [I,idx] = bfGetPlaneAtZCT( r, z, c, t, varargin )
%bfGetPlaneAtCZT Obtains an image plane for the Z, C, T
%
% I = bfGetPlaneAtZCT(r, z, c, t) returns a specified plane from the input
% format reader. The indices specifying the plane to retrieve should be
% contained between 1 and the number of planes for... |
48520362f711704d85b9e9377c5ac1f1ccef449952528381121d17c63c2210ad | MATLAB | 2,415 | 45 | function cvx_begin( varargin )
%CVX_BEGIN Starts a new CVX specification.
% CVX_BEGIN marks the beginning of a new CVX model. Following this command
% may be variable declarations, objective functions, and constraints, and
% a CVX_END to mark the completion of the model.
%
% If another model has already bee... |
7b0a55b06afa98faf6f378b22cf0c8fe339af008140da1bdd86995c49458ab7e | MATLAB | 2,415 | 61 | %% applyANTSTransformToPoints - transform points in world coordinats of a sourceRefImage to
% world coordinates in targetRefImage applying a ANTS affine transformation
%
% Parameters: transPoints - Nx3 matrix of points in world cooridnates
% antsTransformFileStrings - '[antsTransformFile, useInverseFlag]'... |
a59caabb7c056df90d4f1a60978df3e1122f663cc8c63b63aa897764d879839e | MATLAB | 2,415 | 66 | function dataOut = dan_field_search(specData, thingy, stages)
% Search a specData struct for spindles or so (thingy) in a particular
% sleep stage
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
specDataFields = fieldnames(specData);
fieldIndex = ~cellfun('isempty', regexp(specDataFields, thingy));
if any(fieldIn... |
d86b2fd38cbe33455e89464e6433f1d9e99cfa650e753db0229bcb8149a483e9 | MATLAB | 2,415 | 80 | function stats = CBIG_fitLME_4t(subInfoFile, GMICVFile, q)
% stats = CBIG_fitLME_4t(subInfoFile, GMICVFile, q)
% What is the subtype order?
% Offset by 1, the RID column
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
SUB_COL = 1+2;
FRO_COL = 1+3;
PAR_COL = 1+1;
fpri... |
14de3fd4ec15137464ff24cf9ecd49071f5a55c8ccd98122102fce3913eafbb2 | MATLAB | 2,416 | 52 | %% sleepDanalyzer montage.
% Montage scripts provide a conveinient way to control how the data looks
% when sleep scoring.
% chanList. A list of channel names and (optionally) channel coordinates.
% This should be an EEGLAB chanlocs struct. Alternatively you can read in a
% .txt file using the readlocs function (EE... |
6792b60eb8bf4bc0966a271537a34e38bac49a956ecce5b5416476d6d429efe5 | MATLAB | 2,416 | 72 | function newname = decodevarname(name,varargin)
%
% newname = decodevarname(name)
%
% Decode a hex-encoded variable name (from encodevarname) and restore
% its original form
%
% This function is sensitive to the default charset
% settings in MATLAB, please call feature('DefaultCharacterSet','utf8')
% ... |
28034b58c6879a28e1f3c255eb9da20e83852b99016d8ae77eb8f8b84a970ba8 | MATLAB | 2,417 | 71 | function CBIG_ASDf_getBootstrappedSamples(output_dir, N)
% CBIG_ASDf_getBootstrappedSamples(output_dir, N)
%
% Wrapper function to perform bootstrapping on ABIDE-II+GENDAAR ASD
% participants.
%
% Input:
% - output_dir:
% Absolute path to output directory where the results will be
% saved
% ... |
5999658cae74e7f5d8bb9a8289218cb81647e01f9696b015a267f28a4e4493d0 | MATLAB | 2,419 | 68 | %% Running LDA model on bag of words data from stream for use with
% SWR model
%%
% Choose the dataset
dataset = 2; % 1 = psych review abstracts 2 = NIPS papers 5 = NYTimes
if (dataset == 1)
load 'psychreviewbagofwordsfromstream'; % WO DS WS ORIGWSPOS;
T = 50; % Set the number of topics
BE... |
8ca17484ed96a7a1e778bd347a180d78e9c645c2ae80e6ccb39986dc4e20439a | MATLAB | 2,419 | 61 | function [params, results] = CBIG_hMRF_generate_parcellation_for_diff_rand_inits(params)
% [params, results] = CBIG_hMRF_generate_parcellation_for_diff_rand_inits(params)
%
% This function runs the clustering algorithm based on the input parameter structure.
%
% Input
% - params: (struct)
% The structure that c... |
a476ccb9cfa5c6b4851f1420d703555201ea5b27da8163fd9c85f3e3438b5d78 | MATLAB | 2,420 | 52 | %% sleepDanalyzer montage.
% Montage scripts provide a conveinient way to control how the data looks
% when sleep scoring.
% chanList. A list of channel names and (optionally) channel coordinates.
% This should be an EEGLAB chanlocs struct. Alternatively you can read in a
% .txt file using the readlocs function (EE... |
f346167278cc60f2a387b12c93dfb8765ba81d07ac85364ceed881eb02f34957 | MATLAB | 2,420 | 74 | % Exercise 4.60: Log-optimal investment strategy
% Boyd & Vandenberghe "Convex Optimization"
% Joëlle Skaf - 04/24/08
% (a figure is generated)
%
% The investment strategy x that maximizes the long term growth rate
% R = sum_{j=1}^m pi_j*log(p_j^Tx)
% is called the log-optimal investment strategy, and c... |
b93fdd8363e9b1e25283f8adc2ed3c43f9c625dd2320f6c8a789eaccb55f090a | MATLAB | 2,422 | 79 | % pop_delset() - Delete a dataset from the variable containing
% all datasets.
%
% Usage: >> ALLEEG = pop_delset(ALLEEG, indices);
%
% Inputs:
% ALLEEG - array of EEG datasets
% indices - indices of datasets to delete. None -> a pop_up window asks
% the user to choose. Index < 0 -> i... |
d0d128284deef1a121888ed3a09901525aa5afd5f897bb59bd9b44dcd5641342 | MATLAB | 2,422 | 66 | function bfUpgradeCheck(varargin)
% Check for new version of Bio-Formats and update it if applicable
%
% SYNOPSIS: bfUpgradeCheck(autoDownload, 'STABLE')
%
% Input
% autoDownload - Optional. A boolean specifying of the latest version
% should be downloaded
%
% versions - Optional: a string sepecifying the ver... |
da1b97d87d2578955b115becbefacd9e4a5294ccdb8d46700ed1f7e8c85a274c | MATLAB | 2,422 | 75 | % <Insert fig_rates and gnd_rates as 3d matrices containing figure vs. ground data (channels, trials, times)>
% <These matrices should be extracted directly from the Kirchberger et. al, 2021 VIP dataset>
x = cat(2,fig_rates(1).vals,gnd_rates(1).vals);
y = [ones(size(fig_rates(1).vals,2),1) ; zeros(size(gnd_rates(1).... |
daa2563c6bbfc3637b52c68e60250a657bac9447a2862b05593b6beacf7c5bff | MATLAB | 2,423 | 62 | function [V,F,nF,T,nT]=collapse_edge(V,F,nF,T,nT,Volume_Original,Options)
% Make list with all vertices which have not collapsed yet
Vind=make_left_vertice_list(V,F,nF,Options) ;
collapse_possible=false;
vs=0;
while(~collapse_possible)
% Select the first vertice
vs=vs+1;
if(vs>length(Vind)), return,... |
4c954030eb72121a53be1c110350547f0ef107e95d61e39e67e997f07501440e | MATLAB | 2,424 | 63 | % std_clustmaxelec() - function to find the electrode with maximum absolute projection
% for each component of a cluster
% Usage:
% >> [STUDY, ALLEEG] = std_clustmaxelec(STUDY, ALLEEG, clustind);
%
% Inputs:
% STUDY - STUDY set structure containing (loaded) EEG dataset structures
% ... |
09b341c2741373b4baad37f0b4a5bfa160dfa163a2c4567922dcd1952b719e10 | MATLAB | 2,426 | 62 | function z = qjmul(x,y,K)
% z = qjmul(x,y,K)
%
% QJMUL Implements Jordan product for Lorentz cones
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
... |
0bd7ef7a9fdf17d32bb86dad7b0516e7e94f58c8242a26284e312db4c4c86aa8 | MATLAB | 2,426 | 97 | function handles = dan_edit_montage(handles)
% Pull up an inputdlg to change montage parameters on the fly
%%
% Authors: Dan Denis
% Date: 2021-07-14
%%
montage = handles.montage;
if ~isempty(montage.scaleLine)
scaleChan = montage.scaleLine{1};
else
scaleChan = '';
end
scaleLineStr = ['[' sprintf('%g;'... |
1361d237a9aac99124f65201ed31e25e110026109e0b5e12b1022a468db38881 | MATLAB | 2,426 | 78 | function [F,V]=solveInterSections(F,V)
FV.faces=F; FV.vertices=V;
nInter=inf; nInterOld=inf;
while(nInter>0)
[FV,nInter]=solveInterSectionsSub(FV);
if((nInter>0)&&(nInter==nInterOld))
error('solveInterSections:process','Mesh intersections not solved');
end
nInterOld=nInter;
end
F=FV.fa... |
b6c534252aa68f616fab04fff0bec09bd9c48d57b0f2714076eef61e8d07ee1b | MATLAB | 2,427 | 3 | function cmap=canlabCmap
%create colormap from yellow to dark blue/purple
cmap=[0.0201307199895382,0,0.986666679382324;0.0402614399790764,0,0.973333358764648;0.0603921599686146,0,0.959999978542328;0.0805228799581528,0,0.946666657924652;0.100653596222401,0,0.933333337306976;0.120784319937229,0,0.920000016689301;0.140915... |
68fbaa4bdf8403a5efbc798638b121419c1445cbfdfa12b7d2dcfe9709af6740 | MATLAB | 2,428 | 78 | %% Compare pain-related brain patterns
%% About this script
%
% This script compares several pain-related 'signature' patterns developed in the
% CANlab over the past years. It uses a test dataset of N = 270
% participants from Kragel et al. 2018 to test the patterns' sensitivity
% and specificity to pain.
%
% it col... |
77e3f1d689ac256b3c899016d9373050a875a217ace72e1a5e76326ee062f5dd | MATLAB | 2,428 | 69 | function [mlnS, mlnSneuman, mlnSnp, bardelta, b] = my_murdaycotts(Delta,delta,r,D0,bb)
%
% [mlnS, mlnSneuman, mlnSnp, bardelta] = murdaycotts(Delta,delta,r,D0,g)
%
% calculates diffusion attenuation, mlnS = - ln(S/S0),
% inside a perfectly reflecting sphere of radius r, free diffusion
% coefficient D0, bvalue b ... |
f7303dfd82f91d9365d3cc11bf916f9e8eaf69abe9786a5cb491b5cf44248b1c | MATLAB | 2,429 | 70 | function [ind,peak,cor,lag] = b_thetaIndex(self,cel,varargin)
% Calculates thetaindex per Ulanovsky
%
% [ind,peak,cor,lag] = b_thetaIndex(self,cel,varargin)
%% Constructed from the methods from
% Grid cells without theta oscillations in the entorhinal cortex of bats
% Michael M. Yartsev, Menno P. Witter & Nachum Ula... |
643926140d75a3ff9ecfe9b173eaad82cb8e73fd8b86ae72a464d4ddbb9adba2 | MATLAB | 2,431 | 54 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
bf5074aa8bb09a99d4f664ef8619843f607e98a8beb80c5e74a2ffa700a06670 | MATLAB | 2,431 | 61 | function ncopies = checkworkspace(obj);
stack = dbstack;
stack(1:2) = [];
stack = rmfield(stack, 'line');
ncopies = 0;
if ~isempty(stack)
% empty stack means the base workspace
% check if we are in a different workspace
if ~isequal(stack, obj.workspace)
% is the current stack a subset of the o... |
cb3dae90ce0c2c2925c636b1d4366d4f31aca15fcb0574b664a4c8d52b91bd1a | MATLAB | 2,432 | 57 | function [handles, refreshflag] = addDendrites(handles)
flagadd = 1;
refreshflag = 0;
im_norm = handles.im_norm;
while flagadd == 1
handles.current_dend_pixel = [];
handles.current_dend_outline = [];
handles.current_pt_all = [];
handles.current_cspoints = [];
handles.current_dend_trace = [];
han... |
cddb68bfd997d93865889c6607063df55dc9d922493e0569b417a37063142d65 | MATLAB | 2,432 | 93 | function [res, errStr]= maskstruct_istype(dataIn, maskType)
%function [res, errStr]= maskstruct_istype(dataIn, maskType)
%
% test function returns 1 if dataIn is a valid maskStruct of
% the version specified in maskType.
%
% dataIn: arbitary data .. may be a ftrStruct or a fiberStruct
% fiberType: {'Ver1' ... |
d389da1f195c2f0980040bedadfadc482e6c04d7cebb2569d01ec99f7a6d867c | MATLAB | 2,432 | 74 | %% Trajectory - represents a (straight line) trajectory by two Point3D (entry and target) objects
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2013 - 2017
% mail@andreashusch.de
classdef Trajectory < handle & matlab.... |
382325d6fc2bff900519aacb7147e803857034c75e1e81fe894cd3bf65def948 | MATLAB | 2,435 | 81 | % Polynomial discrimination
% Section 8.6.2, Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX by Joelle Skaf - 10/23/05
% (a figure is generated)
%
% The goal is to find the polynomial of degree 3 on R^n that separates
% two sets of points {x_1,...,x_N} and {y_1,...,y_N}. We... |
6f41f2b7d5acf615c96611b0caa0c591f34a3a885ae267ce985e2ace18c80510 | MATLAB | 2,435 | 48 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
0be81bb07eb67ba25e7db1847312cda29a1e3b5d1d20b13ec46b35de74c0f3df | MATLAB | 2,436 | 61 | function tree = xmltree(varargin)
% XMLTREE/XMLTREE Constructor of the XMLTree class
% FORMAT tree = xmltree(varargin)
%
% varargin - XML filename or XML string
% tree - XMLTree Object
%
% tree = xmltree; % creates a minimal XML tree: '<tag/>'
% tree = xmltree('foo.xml'); % creates a t... |
7f5680b0140566402817e9b92f49635a0da2af876b9d9e4d594a53b710a427e3 | MATLAB | 2,436 | 90 | function [H] = traditionaldipfit(f);
% TRADITIONALDIPFIT creates the homogenous spatial transformation matrix
% for a 9 parameter traditionaldipfit "Talairach-model" transformation
%
% H = traditionaldipfit(f)
%
% The transformation vector f should contain the
% x-shift
% y-shift
% z-shift
% (in length-units ... |
146f9909c6a43362d036d40cd73d5f91e753f994b72cab690fc1dc63c42c1e6f | MATLAB | 2,437 | 103 | function sim = type2_SDT_sim(d, noise, c, c1, c2, Ntrials)
% Type 2 SDT simulation with variable noise
% sim = type2_SDT_sim(d, noise, c, c1, c2, Ntrials)
%
% INPUTS
% d - type 1 dprime
% noise - standard deviation of noise to be added to type 1 internal
% response for type 2 judgment. If noise is a 1 x 2 vector then t... |
c959b513d584ba64b6c59331fdc7a1108f8569ac2ea0a19b1da9d0e8abb339da | MATLAB | 2,437 | 109 | function [borderness, Cm, Dm] = Borderness(self,cel,plotIt)
% Calculates the borderness score, as in Solstad 2008
% Bill 2012.10.26
% METHOD:
% Dm = Mean Distance to wall:
% Firing Field: FR >= 0.3*Max(FR).
% Area of field > 200cm^2
%
%
%
% Cm = Max coverage of a wall
% (Number of pixels in wall also in field) / (... |
ac8da426305772f1dc588fe444230cfe6110dc3a52a24373752729f4851e12ea | MATLAB | 2,439 | 88 | function NSxToHL(fname)
% NSxToHL
%
% Opens and reads an NSx file without the header information and saves
% the binary data into a .dat file with the same name. This can be used for
% specific applications that require this type of data, e.g. Klusters.
% Works with File Spec 2.1, 2.2 and 2.3.
%
% It does not suppor... |
13e014052cc59619bc1f8f65b6bd3ab9ea3ad986924c8b607ab970678f45a84c | MATLAB | 2,441 | 64 | function CBIG_IndCBM_write_cerebellum_dlabel(surf_labels, cbm_labels, template_file, colortable, output_name)
% CBIG_IndCBM_write_cerebellum_dlabel(surf_labels, cbm_labels, template_file, colortable, output_name)
%
% This function write parcellation labels into a dlabel file. Including the
% cerebral cortical parcella... |
7ab9891785b0d9683e9d0d8265c39cb14d015c025014793fc31a57806ad3f6c2 | MATLAB | 2,441 | 77 | function [m,ll,ul,llj,ulj]=den_jack(X,family,varargin)
% Function to compute smooth estimates of the mean of x using locfit,
% the corresponding confidence intervals, and jackknife estimates of
% the confidence intervals
% Usage: [m,ll,ul,llj,ulj]=den_jack(x)
%
% Inputs:
% X: data in the form samples x trials
% family... |
da8b30d0b318ffe9420bba62066273022c6190b938f2446681fd9069c09d0fcf | MATLAB | 2,441 | 63 | % std_rmalldatafields - remove all data fields from STUDY (before saving
% it for instance.
%
% Usage:
% STUDY = std_rmalldatafields(STUDY, type);
%
% Input:
% STUDY - EEGLAB study structure
%
% Optional input:
% type - ['chan'|'clust'|'both'] remove from changrp channel loc... |
9fe4397ad07995c9f405a31f3c59bca2642af03f47bf8135d6b8b6e94391d1ec | MATLAB | 2,444 | 65 | % written by Yiyuan Han, Essex BCI-NE Lab, 11/12/2019
% Inter-subject classification
% interISPCBinclass: Using ISPC as the feature to create SVM classfier for
% classifying conditions in the binary mode
% Input:
% -datatrial: the segmented EEG data with same length
% -trailtag: confition tags of the input data trials
... |
a0f7dbfe6d3f38aee23b4672a3c0fdcedba64004205c2fa5dfa3de205c7586d6 | MATLAB | 2,444 | 66 | function [err, err_O, err_R, err_rat, dHb_opt, dmu_a_opt] = muA_ls_obj_HbT_rel( ...
x, mean_mu_a760, mean_mu_a850, thres_HbO, thres_HbR, ...
epsilon_mm_uM, J_chrom_brain, meas_HbO, meas_HbR, lambda, relative_beta_SNR)
%MUA_LS_OBJ_HBT_REL HbO/HbR LS fit + 3:1 ratio regularization (+ optional SNR weig... |
5a4509c68e6086bc7a57bd28aafdd4e09ccfb2f18e137672c9a21c81f4da1010 | MATLAB | 2,448 | 78 | % get holdout set for SVM contrasts, 2nd-level batch scripts
% hard-coded options
% 'fivefold_leave_whole_subject_out' : 5-fold cross-validation, leaving
% whole subject out (all images from subject across all conditions)
% 'leave_one_subject_out' : leave one whole subject out
% holdout_set_type = 'fivefold_leave_who... |
c54d0220358cbb64aa53033b5cdf734b70334a38798bfb153b39e18265f60e1f | MATLAB | 2,448 | 60 | function handles = spineROI_regmater(handles, t_points, R_points, roi_seed_master, dendID_master)
roi_seed = R_points*[roi_seed_master'; 1*randn(1,size(roi_seed_master,1))];
roi_seed = bsxfun(@plus, roi_seed, t_points);
roi_seed = roi_seed(1:2,:)';
im_norm = handles.im_norm;
d1 = handles.size(1);
d2 = handles.size(2); ... |
fdc98838a85cf407f60f96fcd1756c5ea52a0b0811a29cc07e5e551599540c0b | MATLAB | 2,449 | 52 | function [p, s] = fit_prf_V7(p,s,ApFrm,apsFile,Hemis,WhichFolder)
% [p, s] = fit_prf(p,s,subnr)
Ecc = Visual_Angle(s.ScreenWidth, s.totdist); % diameter
Ecc = Ecc/2; % radius
prfFolder= char(fullfile(p.FS_subDIR, p.subNames, WhichFolder));
FS_surfDir = char(fullfile(p.FS_subDIR, p.subNames, 'surf'));
disp(prfFolder... |
346741dd476a0494f4631ad436fe6403f99c0d61e328efae120661317da3a362 | MATLAB | 2,450 | 73 | function [trans_mat,elfv,xg,yg,zg] = get_trans_mat(electrode,electrode_patient,grid_vec,side,electrode_native)
% inputs:
% electrode: is the electrode model
% electrode_patient: is the location of the patient's electrode in mni
% space
% grid_vec: is the standard grid points, on whihc the standard efield is
% calculate... |
3125bf59079590d4c85d644ec499619234747c88bd14702af9a2dbf512551b13 | MATLAB | 2,451 | 67 | function [counts,t_inds,x_inds] = histxt(x, varargin)
%HISTXT Column-by-column Histograms.
% COUNTS = HISTXT(X,D), where X is an M x T matrix returns a D x T
% matrix COUNTS in which each column contains the histogrammed (with D
% bins) values from the corresponding column in X. If D is not
% specif... |
d306cf114ee7d8db573c779e5e2f820dd396137deb9363bedc447b96776ed721 | MATLAB | 2,451 | 62 | function [C_calc] = LCN_calc_model_2T4k_vasc2k(params,midscantimes,frameduration,CA_FINETIMES,CA_WB_FINETIMES,FINETIMES,calc_option,STEP)
%
% calculates the output value for the LCN_calc_model_2TCM_K1.m (with parameters params)
% FORMAT C_calc = LCN_calc_model_2TCM_K1(params, midscantimes, frameduration, calc_option)
%... |
a284d488714a003f209cb910d1851b6f02b4f4d8870c7b116873451e870f0309 | MATLAB | 2,452 | 60 | ccc;
% RAWDATAPATHs = dir("..\MAT Data\pre (granger)\single\**\*Active\**\Prediction Data_*.mat");
RAWDATAPATHs = dir("..\MAT Data\pre (granger)\single\**\*Passive\**\Prediction Data_*.mat");
MATNAMEs = {RAWDATAPATHs.name}';
AREAs = cellfun(@(x) x(strfind(x, '_') + 1:end - 4), MATNAMEs, "UniformOutput", false);
RAWDAT... |
4e7328eee88716fe773e45865f0e569aedf500b0373526db87ef44fdf47ab415 | MATLAB | 2,453 | 82 | function [slice,slicebw,maskslice,maskslicebw]=ea_prepare_slice(nii,mask,sliceno,imgsliceno,options)
% this function binarizes each axial slice (resulting in plane slicebw) by
% thresholding the variable slice by x times the standard-deviation of its
% intensity values. x here refers to the sum of a factor defined in t... |
2c0285b69d3a258f15652015d083ab922b13877a0656d1733d4a25c8578f8ec4 | MATLAB | 2,454 | 87 | function h=ea_checkgenesim(map,smooth,geneidx,cols)
prefs=ea_prefs;
if ~iscell(geneidx)
geneidx={geneidx};
end
load([prefs.genetics.dbdir,'geneinfo.mat'],'geneinfo');
for g=1:length(geneidx)
id{g}=[];
tableheaders=fieldnames(geneinfo);
for header=[2,4,5]
id{g}=ismember(geneinfo.(tableheaders{he... |
61cfe975ee9b9bd2d2f0313551edf78dab4dec8b48267cc40006d55f94cc81a3 | MATLAB | 2,454 | 65 | function param = loadParameters_balloon_func
%% loadParameters_balloon_func.m
%
% Contains all the parameters of the model and the
% computational parameters for the simulations/calculations. It is
% necessary to make an instance of the class before you can use the
% parameters.
%
% Example:
% >> param = loadPar... |
76f28e7fb064f74cee1d326f53be9e94e1c1f91245658bdfd099279670236090 | MATLAB | 2,455 | 55 | function Lden = symbcholden(L,dense,DAt)
% Lden = symbcholden(L,dense,DAt)
%
% SYMBCHOLDEN Creates Lden.{LAD, perm,dz, sign, first}
%
% ******************** INTERNAL FUNCTION OF SEDUMI ********************
%
% See also sedumi, dpr1fact
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright ... |
a41cb85e09890ee70587bb6d0d272df7514b3000e7ade23a66c022c40867b93a | MATLAB | 2,457 | 55 | function CBIG_MMLDA_visualize_factors_wrapper(mmlda_dir, visualize_dir)
% This wrapper visualize factors after MMLDA estimation
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
unit_test_path = [getenv('CBIG_REPDATA_DIR') '/stable_projects/disorder_subtypes/... |
4c6bf12f1b07d68605e5d4f0da3d378124eb15396398d8bf6093980e006ce428 | MATLAB | 2,458 | 70 | function out = rotoball_fileimporter(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as a matrix.
% E9CLDATA20201002162310 = IMPORTFILE(FILENAME) Reads data from text file
% FILENAME for the default selection.
%
% E9CLDATA20201002162310 = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads
%... |
0097038fb00c8f41590cf647bd6f8589961fa96785a5166c12d90030d4fc2f22 | MATLAB | 2,459 | 49 | % std_itcplot() - Commandline function to plot cluster ITCs. Either displays mean cluster
% ITCs, or else all cluster component ITCs, plus the mean cluster ITC, in
% one figure per cluster and condition. ITCs can be visualized only if
% component ITCs were calculated a... |
1eb5cef26289e635b9887774cbfa2cead9aa3768ecb04c2af3c934bddde6a9bb | MATLAB | 2,462 | 87 | %USER_STRING Get/set a user specific string
%
% Examples:
% string = user_string(string_name)
% saved = user_string(string_name, new_string)
%
% Function to get and set a string in a system or user specific file. This
% enables, for example, system specific paths to binaries to be saved.
%
% IN:
% string_name - ... |
9062fb6def186b854f378cea2f70f4d0b1ca7572b95904118fc339c043044bdc | MATLAB | 2,462 | 87 | function Par = LoadPar_SleepScore(FileName, varargin)
% LoadPar(FileName)
% loads the specified par file and returns a structure with these elements:
%
% .FileName -> name of file loaded from
% .nChannels -> number of total channels
% .nBits -> number of bits of the file
% .SampleTime -> time, in mi... |
df041c0a3f1e25b25b734f5c7f219cb539ba83d84db4a2227e1a5fcdca2e0c80 | MATLAB | 2,462 | 81 | function [z, r, tp] = fsLR2roizmat_ciftidat_giftinode(cii, roiL, roiR)
% DESCRIPTION:
% Extract node time series from 32k by 32k fsLR saved in CIFTI dtseries.
% Outputs correlation matrix (r), fishers-z-transfromed corr matrix (z),
% and node-by-timepoint matrix (tp).
%
% Node... |
eb62c45fbe840ec51937eb82f8b406398fc087f7174201ccc139637c33dcd2f2 | MATLAB | 2,462 | 58 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
3b7874805b6ac04de3d014c2c3d256dadc2d55eba211b68c8f95d6ac6a9d7dc6 | MATLAB | 2,463 | 50 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
8c2a864d1d879abde99856d60fdb92fd21424aba2d32bc7965ce5f7c6e4625e4 | MATLAB | 2,464 | 85 | function p = PlotSamples(X,varargin)
%PlotSamples - Plot samples (multiple time series).
%
% Plot columns 2...M of a matrix as a function of its first column.
%
% USAGE
%
% p = PlotSamples(X,<options>,<options2>)
%
% X list of (t,x1,x2...xN) data to plot (N variables)
% <options> optional l... |
072ae71d32e71904e4d310b243832a3e5447d7d3da98d726ae8d58153fb8ddab | MATLAB | 2,465 | 78 | % gettext() - This function prints a dialog box on screen and waits for
% the user to enter a string. There is a cancel button which
% returns a value of [].
% Usage:
% >> out = gettext(label1,label2,...,label7);
%
% Author: Colin Humphries, CNL / Salk Institute, La Jolla, 1997
% Copyright ... |
9597f87924683f071b43d33e6d81d18f9c1f16449bee97d914d019e0e2031885 | MATLAB | 2,465 | 48 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
14e3067cb35cf0eb64a69dad995440066edd2230df5b81aae930aeb721881920 | MATLAB | 2,466 | 68 | function mem_ef = CBIG_get_mem_ef(rid, predementedOnly)
% mem_ef = CBIG_get_mem_ef(rid, predementedOnly)
% Fetch MEM and EF scores from .csv files
%
% Input:
% - rid: the RID's of subjects of interest
%
% Output:
% - mem_ef: 1st col is RID, 2nd is VISCODE, 3rd is EXAMDATE, 4th is MEM,
% 5th is EF
%
% Written... |
9b2d98ae893549b04f49d2670be18a0483dad4cf45cb052f61d1e703f200d91a | MATLAB | 2,466 | 80 | function VisualizeTopics( DP , ALPHA , S , VIZMODE );
%% Function VisualizeTopics
%%
% Visualizes topics in a 2D map
%%
% |visualizetopics( DP,ALPHA,S,VIZMODE )| takes the topic strings in |S| and
% the document-topic count matrix |DP| where |DP(i,j)| contains the number of
% times a word in document |i| has bee... |
8715384807cb8b3cea9c906fafe61f612776c4bfeadb4d7673d5decb08e8c1a2 | MATLAB | 2,467 | 63 | function lambda = CBIG_hMRF_initialize_lambda_in_vonmises_partition_func(lambda_init, dimension_for_bessel_func)
% lambda = CBIG_hMRF_initialize_lambda_in_vonmises_partition_func(lambda_init, dimension_for_bessel_func)
%
% This function determines the initial value for lambda in the partition function of von Mises dist... |
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