sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0bc45047cf1f1144963651292224732bcf693f5b15e8b734eb1175f151e06539 | MATLAB | 6,695 | 172 | function append_pdfs(varargin)
%APPEND_PDFS Appends/concatenates multiple PDF files
%
% Usage example:
% append_pdfs(outputFilename, inputFilename1, inputFilename2, ...)
% append_pdfs(outputFilename, inputFilenames_list{:})
% append_pdfs(outputFilename, inputFilenames_cell_or_string_array)
% append_pdfs ... |
9bfb3cbf97dd2ff30e29a899fca8bf65bd26d02b361747b52a2cd9b0ef8bd9d3 | MATLAB | 6,699 | 178 | function homo_with_weight = CBIG_ParcellationHomogeneity_FS_meantimecourse(lh_labels,rh_labels,mesh,...
lh_input_filename,rh_input_filename)
% This modified version computes per-parcel homogeneity as the mean of
% correlation between the parcel's average time course and each vertex's
% time course in that parcel... |
53e1168e532e3163da88f6f92650bb23268305c88fdc7e22a7d723ab8dafdc79 | MATLAB | 6,700 | 173 | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for futur... |
a720bcf81481b6b53e8be989d73062d6c8eec668f4ff1c6fd3eb141c036d5890 | MATLAB | 6,709 | 215 | %% Prepare data files
% BLOCK 1
% ---------------------------------------------------------------
% Establish that images are on path
% if not, you'll get an empty variable basedir
basedir = fileparts(which('con_00810001.img'));
% Load behavioral data
% "Reappraisal success", one score per person, in our example
b... |
2ce3f8abfc0e2fec187ea42c0036f93efb2615264df8f790f4dc7c10f7c1e45b | MATLAB | 6,712 | 166 | % loadtxt() - load ascii text file into numeric or cell arrays
%
% Usage:
% >> array = loadtxt( filename, 'key', 'val' ...);
%
% Inputs:
% filename - name of the input file
%
% Optional inputs
% 'skipline' - number of lines to skip {default:0}. If this number is
% negative the program will only sk... |
c9e1ebd69bc41c43c6647fd8572f8b532924eed0384754eac1fcee1ffa8b76c8 | MATLAB | 6,712 | 201 | % openbdf() - Opens an BDF File (European Data Format for Biosignals) in MATLAB (R)
%
% Usage:
% >> EDF=openedf(FILENAME)
%
% Note: About EDF -> www.biosemi.com/faq/file_format.htm
%
% Author: Alois Schloegl, 5.Nov.1998
%
% See also: readedf()
% Copyright (C) 1997-1998 by Alois Schloegl
% a.schloegl@ieee.org
% Ver ... |
a8ac2629d41d054e73463b6059edc5a878bc26751754c4cee7c721082bd721b5 | MATLAB | 6,715 | 162 | % Name: Robert Kim
% Date: 03-10-2024
% Email: robert.f.kim@gmail.com
% S15_16.m
% Description: Script to compare number of trials and 1-modality DMS performance
% b/w one-layer and two-layer models. Used for Supplementary Figure 15.
clear; clc;
%% Directories
% Put the directory containing helper functions here.
co... |
079143164b26551f8d80b0be690d453fb87734c38572f8c95ffbe8f3536be292 | MATLAB | 6,723 | 171 | % eeg_regepochs() - Convert a continuous dataset into consecutive epochs of
% a specified regular length by adding dummy events of type
% and epoch the data around these events. Alternatively
% only insert events for extracting these epochs.
% Ma... |
bdb2f4efbcdf909f51af578a2794c00270a46e26303de3a4cda82ab9c0ce07cc | MATLAB | 6,726 | 143 | %% Efficient subpixel image registration by cross-correlation.
% Registers two images (2-D rigid translation) within a fraction
% of a pixel specified by the user. Instead of computing a zero-padded FFT
% (fast Fourier transform), this code uses selective upsampling by a
% matrix-multiply DFT (discrete FT) to d... |
5640a67f01270953dfc4d1118e34b36282e42c82687f69329ad874b40f035b9e | MATLAB | 6,729 | 165 | function p_behavior = CBIG_ASDf_clusterBehavAssoc_wrapper(outputDir)
% p_behavior = CBIG_ASDf_clusterBehavAssoc_wrapper(outputDir)
%
% Wrapper function to perform 4 sets of behavioral analyses (only those significant in
% factor behavioral analyses) on k-means clusters for comparison to behavioral associations in f... |
844d83ac863ac729551d326cc92b9c92385091affe5f87f2480ed666b4f7108c | MATLAB | 6,730 | 253 | clc
clear all
close all
set(0,'defaultfigurecolor',[1 1 1]);% set figure background color
addpath('/Users/guofanhua/Desktop/gfh/tools/MatlabTools/BrainConnectivityToolbox/2019_03_03_BCT')
addpath('/Users/guofanhua/Desktop/gfh/work/experiment/ASL_Mesoscopic2025/reference/2019PNAS_FCSC/code')
addpath('/Users/guofanhua/De... |
be16ffdec8745ea65c19591cac6208486b2f20b6e55a27276498c3458e52cf87 | MATLAB | 6,730 | 180 | function Save_SingleData_bin(handles, f_wait, ifhold)
if nargin == 1
f_wait = waitbar(0.2,'Saving');
end
if nargin < 3
ifhold = 1;
end
moviedir = fullfile(handles.filepath, handles.filename);
im_norm = handles.im_norm;
Feature_parameters = handles.defaultPara;
Feature_parameters.BitsPerSample = handles.BitsPerS... |
2a3ca9c5f72821cbe0504df62b87edc6be502c8a8393271f797348a12a868dd1 | MATLAB | 6,732 | 98 | % +IOSR
%
% Contents file for +IOSR and its subfolders.
%
% +IOSR
% iosr.install - Set search paths, and download and install dependencies
%
% +IOSR/+ACOUSTICS
% iosr.acoustics.irStats - Calculate RT, DRR, Cte, and EDT for impulse response file
% iosr.acoustics.r... |
7dce0b6d47057ca15f12c938bc125bae5c11192ce325412997b60cd4358fb3c2 | MATLAB | 6,734 | 190 | function ts = run_absorbing(topology,homparam,hetparam,stim)
% RUN with ZERO TRIVIAL CONDITIONS: phi(r,0) = phi_t(r,0) = 0;
% Absorbing boundary conditions - by adding absorbing layer over Omega
% Layer has width L/2, and has effective gain ranging from nu0 to 0
% Takes in input of model parameters, timesteps and leng... |
a848193a196cdf828a0dcfcecea3f454b339089b168499349617cf27457f6403 | MATLAB | 6,738 | 149 | function [roll_out] = ea_diode_manual_main(options)
%% Determine Orientation for BSCI directed leads from postoperative CT
% has an unsupervised and a supervised version
if strcmp(options.subj.postopModality, 'MRI') % check for electrode type and postoperative imaging
msg = sprintf(['Rotation detection works only... |
db796af2452e89c07d9bf4ea99277859ccaf142828b7cb5ce44691ab07b5a1bc | MATLAB | 6,738 | 174 | %WAVE_SIGNIF Significance testing for the 1D Wavelet transform WAVELET
%
% [SIGNIF,FFT_THEOR] = ...
% wave_signif(Y,DT,SCALE,SIGTEST,LAG1,SIGLVL,DOF,MOTHER,PARAM)
%
% INPUTS:
%
% Y = the time series, or, the VARIANCE of the time series.
% (If this is a single number, it is assumed to be the va... |
c4fd6085f6f920f05edd0445574c07a0865f4d597ef3a8a6c113338673972416 | MATLAB | 6,741 | 197 | function [fitresult, figtitle, fmodel, xx, value_g] =...
FitstampResp_v2(trace_stamp, framestamp, stampsel, stampinfo,...
glist_all,varsel,...
fmodel_input, fmodel_Independent,fmodel_startpoint,...
funcsel, xvalue, handles, ttlabel, figiniID, datatitle)
N = size(trace_stamp,2);
stampinfo_t = table2arra... |
b08fe42830f9a2bad5c5fe6f361d7ec717994c60aa5d591a3464fabb6ebd92f2 | MATLAB | 6,743 | 172 | %% symbolicdata2states - converts data to states using ranking symbols
% Converts raw data to states using rankings of data values, similar to the
% symbolic entropy techniques applied in Staniek and Lehnertz, PRL 100,
% 2008, 158101. Note, wordstates will reduce the total number of time bins.
% Trial based data will b... |
a7479c6b4a37134604c238c001a9c82ac500ec59029fb2d1249e7baf14c616af | MATLAB | 6,747 | 237 | function [EigenVal, eigVect, M_error, sqErr, kurtParams, kurtTensor] = do_calculation(DEscheme, singleSliceDWI_set, matrix,threshold,kurto)
if exist('kurto') ~= 1
kurto = false;
end;
if length(size(DEscheme)) == 2,
for k = 1:size(DEscheme,1),
B_tensor(:,:,k) = DEscheme(k,:)'*DEscheme(k,:);
end;
e... |
51771c6cd902634d7c38bbe81e8ff33103ee10c1b47f04d388666e40c7ec303d | MATLAB | 6,755 | 237 | function [ cvx_optval, success ] = quad_form( x, Q, v, w )
%QUAD_FORM Internal cvx version.
%
% Check sizes and types
%
narginchk(2,4);
tol = 16 * eps;
tolLDL = 4 * eps;
if nargin < 4,
w = 0;
if nargin < 3,
v = 0;
end
end
sx = size( x );
if length( sx ) ~= 2 || all( sx ~= 1 ),
error( 'The f... |
870a77122a84dce95d8952eda5aa86764a12ae14e2d2bb43599f2eb029e63163 | MATLAB | 6,766 | 156 | %
% This is a calling routine to test & check out the power spectrum &
% spectrogram routines for unequal segment lengths. In addition, use it
% to compare with Chronux routines when segments are of equal length.
%
clear all;
gram = 0 ; % 0=spectra, 1=coherence
chronux = 0; % 1=compare, 0=don't
line = 0;
... |
1df3a432f83754c4789b6b64b22e3381dc872f3cdc2de948f4819ff141d8fd48 | MATLAB | 6,767 | 124 | %Single Unit Data Analysis
%% Generate Binary Files for Kilosort
%See Kilosort Protocol in google drive for info about workflow and how to
%install kilosort - some information may be out of date.
%LV used Kilosort 2.5 for all analysis, others in the lab may have tested
%later versions.
%Manually decide what... |
099b45388489e844436ff74383fc7186df0ec74276eb05b68d4cb4a094b4f045 | MATLAB | 6,770 | 165 | function ea_showisovolume(resultfig,elstruct,options)
% __________________________________________________________________________________
% Copyright (C) 2015 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
set(0,'CurrentFigure',resultfig);
isobar=getappdata(resultfig,'isobar');
if isempty... |
cf4bafaaacb0a4a7a1e196bb27b6cbeaf8ac2b99a7ba618966469083000c042d | MATLAB | 6,771 | 230 | function motionGrid = stepGenerator(sampleNum,sampleStep,mode,dMatrix,orient,holeDepth)
% Mode: 1 - cylinder
% 2 - Flat circle
% 3 - Triangular prism
% 4 - Cube
% % -- Debug --
% sampleNum = 11;
% sampleStep = 0.08;
% mode = 3;
% dMatrix = [1,1.2,1;
% 1,0.2,3;
% 1,0.1,... |
ae4227e4a744b5be51859b9ba6962ccb407bdf29ee2932fa31bd800f6a7429d4 | MATLAB | 6,774 | 195 | % anova2rm_cell() - compute F-values in cell array using repeated measure
% ANOVA.
%
% Usage:
% >> [FC FR FI dfc dfr dfi] = anova2rm_cell( data );
%
% Inputs:
% data = data consisting of PAIRED arrays to be compared. The last
% dimension of the data array is used to comput... |
3d44cd6b25ef28fbe47d97aae29f8654d6ef4132422b0d8c9ae826c565532269 | MATLAB | 6,778 | 113 | %%Post Processing - LFP Data
%Once data is pre-processed for all animals, channel assignments have been
%manually checked and input into a spreadsheet, and start and end times of
%desired analysis windows have been set (excluding any obvious issues or
%artifacts that occurred on recording day) - these next steps... |
b9c6216f1c93f1457dfe18f965a2b121f91f0803c8e159060e59305c13d3c154 | MATLAB | 6,778 | 195 | %% RUN_GLM_STEP (group orchestrator version)
% Uses pipeline.run_group_glm (which calls pipeline.run_subject_glm) to:
% - preprocess + GLM per subject (HbO/HbR and ΔOD optional)
% - collect per-subject arrays
% - save the same files your previous script produced
%
% Outputs to SAVE_DIR:
% <DATE>_GLM_Betas... |
ef22f313cc1024e2288596f4cdf63d5ac97ae9dbbf59de763ff33c3575e7395c | MATLAB | 6,778 | 260 | % Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_folder is... |
b64c96501513e9bf1f0c54c060cb37e44dcf8b0b293c89bf291cd0880fc88704 | MATLAB | 6,780 | 182 | function [f, pp] = make_violin_plot(plot_an, plot_aw, colL, colR, markerSize, markerAlpha, violinAlpha, jitterWidth, figure_index)
% if nargin < 6 || isempty(markerSize); markerSize = 80; end
% if nargin < 7 || isempty(markerAlpha); markerAlpha = 0.7; end
% if nargin < 8 || isempty(violinAlpha); viol... |
6201c231006d14cdd05e7356250a7d810eb4f009869156d5c2e04b695573e4e6 | MATLAB | 6,785 | 154 | function [Obj,Dims] = NETCDFload(filename,flags,varargin)
%% NETCDFLOAD
% Obj = NETCDFload(filename,'all') reads the SOFA object OBJ with all data from
% a SOFA file.
%
% Obj = NETCDFload(filename,'nodata') ignores the Data. variables while
% reading.
%
% Obj = NETCDFload(filename,[START COUNT],partia... |
0be6a0b07db6feea627cb5b478c39bf43ca2aa7b7561849ef47474c240a9ef18 | MATLAB | 6,789 | 147 | %% Overview
% A brainpathway object is a CANlab object designed for connectivity and
% computational model-based analysis of fMRI data. It holds an atlas (defining
% brain regions), voxel-level time series data, and derived node and region
% averages. In addition, it contains connectivity matrices and graph metrics
% (... |
684d3a9cf2da1ca39c23a75ec2a9663e7a19a1083f57b39afc9fd713c2e1bc15 | MATLAB | 6,799 | 128 | function ClincFreq_AffVolume(INDIR,OutAffVoldir,SetUpPara,Para,AtlasTempU)
[V,D,namelist] = Dynamic_read_dir_NIFTI_sparse(INDIR);
D(isnan(D)) = 0;
D(isinf(D)) = 0;
D = D>0;
% Dvol = sum(D)';
% Dvole = sum(D,2);
% IgV = Para.IgP;
% indexs = find(Dvole>=(size(D,2)*IgV/100));
% Dmasked = zeros(V.dim);
% Dmaske... |
187f3b2cb714054fa5c05b2ed4fc78d2641b166e1b09b5099e51e3d09b15d2b4 | MATLAB | 6,803 | 230 | % vararg2str() - transform arguments into string for evaluation
% using the eval() command
%
% Usage:
% >> strout = vararg2str( allargs );
% >> strout = vararg2str( allargs, inputnames, inputnum, nostrconv );
%
% Inputs:
% allargs - Cell array containing all arguments
% inputnames - Cell arra... |
79018b8847156eda34ad22df2adc6ace82aaa6a9b6e1f27353a9874f3342d6e1 | MATLAB | 6,804 | 136 | % std_movecomp() - Move ICA component(s) from one cluster to another.
%
% Usage:
% >> [STUDY] = std_movecomp(STUDY, ALLEEG, from_cluster, to_cluster, comps);
% Inputs:
% STUDY - STUDY structure comprising all or some of the EEG datasets in ALLEEG.
% ALLEEG - vector of EEG structures in t... |
ff30f7e2e84b72eabbcad1fe6c99ff278cc1c05970d1ce67d3f4caf644a612a2 | MATLAB | 6,807 | 180 | function nptype24_imro
% imro files for 24 npix begin with (24, 38) and then (channel ID, shank
% ID, bank ID, reference ID, electrode ID), eg (1 0 0 1 1) is electrode 1 on
% shank 1 (channel is a n integer that goes from 0 to 384), (2 0 0 2 1)
% see https://billkarsh.github.io/SpikeGLX/help/imroTables/
% Build im... |
c74b5b54c25ac76ad5253ba510a5263adcc34ad29eac9e2415ca86b2183cd83c | MATLAB | 6,810 | 163 | % Example replay and relationship between weighted corr. and
% sequence likelihood for all candidates
load('result_example_5_cw.mat'); % Example: clockwise direction in the 5th block
load('no_replay.mat'); % no. of replays (real and shuffled for cw,ccw directions, for Fig.I)
load('result_non_pc.mat'); % results ... |
dfe7821b59550d38315dac1d2e150b04b6a3e23ae85c4578d79b1382533314b7 | MATLAB | 6,810 | 183 | function[fluordata,fluordata_red,fluordata_diff,ROIs,redtemps]= pooldirections3(headpath,fileexpnum,imskip,expskip,deltamode,FrameRate)
% point towards wherever the experiment data for matlab
%control is and then pool across experiments for all ROIs
%then will be able to average across individual ROIs for multiple t... |
95901d29bc25105a24fe551e038544a391e6219e71958e20813b3b64a6202ed9 | MATLAB | 6,811 | 123 | function mris_SD_register(input_surface, atlas_name, output_surface, disp_iter)
% mris_SD_register(input_surface, atlas_name, output_surface, disp_iter)
% Example call:
% <When in the same directory as mris_SD_register.m>
% mris_SD_register('../../example_surfaces/OAS1_0001_MR1/surf/lh.sphere', 'lh.DW.Atlas1... |
d78050561db007eb50af813951f4e2fba43ea9cfb546632510e30b780b8e8307 | MATLAB | 6,816 | 182 | %% QUICKMI - quick mutual information calculation
% Calculates the mutual information between two variables. The data can be
% continuous or discrete. If the data is single trial, the mutual
% information is calculated through time. If the data is trial based, the
% mutual information is calculated at each time point i... |
9a2875be299b4e089c4201cb0b72f3eba7419eeea8cf3e79da5b1e524042d794 | MATLAB | 6,817 | 175 | function [t,rcdx] = stepdif(d,R,y0,x,y,z,dy0,dx,dy,dz,b,mint,tpmtd)
% [t,rcdx] = stepdif(d,R,y0,x,y,z,dy0,dx,dy,dz,b,mint,tpmtd)
%
% STEPDIF Implements Primal-Dual Step-Differentiation for self-dual model
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by I... |
a06d90c026e3ac0413dcae44919ea395dff7b1144e0c19672b4553be65555a66 | MATLAB | 6,817 | 151 | function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
% Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes
%
% Usage:
%
% [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
% ... |
34c7aa396cdeeea675c8f76b02cac4f0b232ea1a00012ac354f5dc2fd0739ac1 | MATLAB | 6,818 | 189 | function [cT, cNull] = colocalMeasureBlob2Blob(refSeg,tarSeg,cellMask,threshold,numRandomizations)
%COLOCALMEASUREBLOB2BLOB measures colocalization between two sets of segmented objects
%
%SYNOPSIS: [cT, cNull] = colocalMeasureBlob2Blob(refSeg,tarSeg,cellMask,threshold,numRandomizations)
%Function uses nearest neighbo... |
7292ce31aec604896055c6da2848f4ba2029fde84f81c3fbcbe27c3153789983 | MATLAB | 6,823 | 137 | function settings = ea_get_stimProtocol(options, S, settings, activeSources, source_index)
% Get stimulation settings for particular source
% By Butenko and Li, konstantinmgtu@gmail.com
arguments
options % Lead-DBS options for electrode reconstruction and stimulation
S % Lead-DBS stimulat... |
48374334221a87a08e3a234f047308278d64561c1fae09b69722fe59b70feb21 | MATLAB | 6,830 | 159 | function [ChannelsPerGroupSuperficialToDeep,SpatialChannelXY,NumChansPerProbe,GroupsPerChannel] =...
bz_ReadProbeGeometryFiles(probemaplist,extrachannelgroups)
% USAGE
% [ChannelsPerGroupSuperficialToDeep,SpatialChannelXY,NumChansPerProbe,GroupsPerChannel] =...
% bz_ReadProbeGeometryFiles(probemaplist)
%
% INP... |
b3d19e71ed60ffb4e676f22a2114da6b7e7d0e4c1617c12b43651ee25e2644e0 | MATLAB | 6,840 | 226 | function ea_computeGM(options,modes,finas,threshs,fs)
expfolder=[options.root,options.patientname,filesep,'connectomics',filesep,options.lc.general.parcellation,filesep];
for mode=1:length(modes)
load([expfolder,finas{mode},'_CM.mat']);
X=eval([modes{mode},'_CM']);
% Ensure threshold is a scalar double (GU... |
859cebb39a0c0df49889b0d7a25951b53d4f37282417dcf6ca5bb177cedeba60 | MATLAB | 6,842 | 224 | % mapcorr() - Find matching rows in two matrices and their corrs.
% Uses the Hungarian (default), VAM, or maxcorr assignment methods.
% (Follow with matperm() to permute and sign x -> y).
%
% Finds correlation of maximum common subset of channels (using
% channel location... |
3e503613fe6a40dbab01e884ff0d97164fa4456d86d7c45bf71986b3094e195b | MATLAB | 6,846 | 177 | function [p,boundary_plot,BOUNDARY] = plotSurfaceROIBoundary(surface,vertex_id,data,boundary_method,cmap,linewidth,climits)
% This script is a wrapper for findROIboundaries and makeFaceVertexCData so
% that they smoothly work together and you don't have to spend a lot of
% your own time making them work together. ... |
3574a12225d4cdcac1f8e34389b204a61d4ab17d4987017be9ad97dbc0cc3361 | MATLAB | 6,849 | 256 | % Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI fil... |
83e3c289624a52827e2d7c3a874d1cbfc1fd862122f89d422afdd4c09447b8c5 | MATLAB | 6,850 | 194 | function [ts,phi] = run_init_absorbing(topology,homparam,hetparam,stim,init)
% RUN with Initial Conditions, or zero trivial conditions if init = NaN;
% Absorbing boundary conditions - by adding absorbing layer over Omega
% Layer has width L/2, and has effective gain ranging from nu0 to 0
% Takes in input of model para... |
6f4d3bf1860a5e0fca5a3a3e63275f1401d1bf4e52ab420f66c8027c5fd5f2df | MATLAB | 6,851 | 180 | %% Check whether contrasts are defined
% ------------------------------------------------------------------------
if ~isfield(DAT, 'contrasts') || isempty(DAT.contrasts)
% skip
disp('No contrasts specified. Skipping contrast estimation');
return
end
%% Specify which montage to add title to. This is ... |
1aa7343895c06b80930af705983f72b59176273687d1586b5f0a8b037a61c210 | MATLAB | 6,852 | 256 | % Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI fil... |
25bc1f62a26a7f27b574e1592ab427368db7ff3f0a31499ef7a77213f1f8f466 | MATLAB | 6,856 | 124 | % Help for file Mat2NlxTS
% Version 4.1.1
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is used to ext... |
bae9863fdaf30e4657f06246b19dd6a77963ec3972d9eab4c75886fb92a97753 | MATLAB | 6,862 | 198 | function [pTR,nullTR] = simulateBlob2BlobColoc(segmentation,numTarObj,cellMask,colocFraction,varargin)
%SIMULATEBLOB2BLOBCOLOC simulate object positions to be used for blob2blob coloalization
%
% Function sets up simulated positions and runs blob2blob colocalization analysis.
%
%INPUT
% Required
% segmentation: binar... |
fccfe5652d52af5828386a91f599c78809bf6099be479db892cb6628935346d6 | MATLAB | 6,863 | 178 | classdef select_or_exclude_top_k_features_FP
% select_or_exclude_top_k_features_FP is a feature preprocessing (FP) object
% that uses an ANOVA to find the k features with the lowest p-values using data
% from the training set. The algorithm either uses only these features
% (i.e., removes all other featur... |
0f51eb167df62b1218b1631fcb1c0cf00826e0457185f5f24e1333ccebe9b7ba | MATLAB | 6,864 | 200 | function [f_intrins, theta_index, modelstruct] = IntrinsicFrequency2(self, cel, varargin)
% Intrinsic frequency of a unit
%
% ARGUMENTS
%
% cel [tetrode index, cell index] in Session object root
% params (see below)
%
% RETURNS
%
% f_intrins scalar, frequency of ... |
867d578f0c38e635dcf1233a79ad5799f52c95eadad677f71fe11ca4c5b3ac3e | MATLAB | 6,867 | 169 | function [fibsvalBin, fibsvalSum, fibsvalMean, fibsvalPeak, fibsval5Peak, fibcell, connFiberInd, totalFibers] = ea_discfibers_calcvals(vatlist, cfile, thresh)
% Calculate fiber connection values based on the VATs and the connectome
disp('Load Connectome...');
load(cfile, 'fibers', 'idx');
prefs = ea_prefs;
if ~exist(... |
c2d93bcd3e07771f12db501656f523da270f4d173a7fb153bfdc52a17f0676a7 | MATLAB | 6,867 | 150 | function [specific_binned_labels_as_numbers string_to_number_mapping] = convert_label_strings_into_numbers(specific_binned_labels_as_strings, ignore_case_of_strings, string_to_number_mapping)
% This function takes specific binned labels (i.e., binned_labels.specific_binned_labels) where labels for each site are cell
%... |
881d74f4500068fbd465ae4d295663b3df51b54541be0fe5507709da6f2c1abe | MATLAB | 6,873 | 211 | function ea_ftr2trk(ftrfile, specs, LPS)
% export FTR matrix to TrackVis trk format
%
% specs can also be the path of the nifti file which defines the space. If
% not specified or empty, MNI space T1 will be used as reference.
%
% If the trk is going to be visualized in Surf-Ice, LPS should be set to 1
% to fix the ori... |
0a69b440d3b09a82384cbab3343ea9f256141018adfe8e1569e0d8fd1bdf1d68 | MATLAB | 6,874 | 188 | function [coherogram,phase,t,f] = bz_MTCoherogram(lfp1,lfp2,varargin)
%MTCoherogram - Compute LFP coherogram by multi-taper estimation.
%
% USAGE
%
% [coherogram,phase,t,f] = MTCoherogram(lfp1,lfp2,<options>)
%
% lfp1,lfp2 wide-band LFPs (one channel each).
% <options> optional list of property-val... |
f3bd807b31cb8f57670def688fb8fe9b3756678993563007bab8bd610e7f7f05 | MATLAB | 6,874 | 177 |
%% ======================= step 01-00 for disposal all data
% input all the basic data
%% set parameters
% input parameters
subjs = {'S01','S02','S03','S04','S05','S06','S07','S08','S09','S10',...
'S11','S12','S13','S14','S15','S16','S17','S18','S19','S20',...
'S21','S22','S23','S24','S25','S26','S2... |
60d93dc9a459c53852c32ab5cb01dd643bfed4dc3f697d711f6e6d7d97efcfeb | MATLAB | 6,877 | 191 | function [map,data] = PhaseMango(spikes,phases,varargin)
%PhaseMango - Compute phase as a function of spike rate and acceleration.
%
% Compute spike phase as a function of spike rate and acceleration, as in
% Harris et al. (2002). The name of the function refers to the aspect of
% the resulting phase plot.
%
% USAGE
... |
5003184f34de09b992d1c877535d19e3054ef24021976d4cbf1e6a1fffad1785 | MATLAB | 6,885 | 189 | function condColocGeneralWrapper(MD,paramsIn)
%CONDCOLOCGENERALWRAPPER applies conditional colocalization described on condColocGeneral to a MovieData file
% movieData = condColocPt2Pt2BlobWrapper(movieData, paramsIn)
%
% Applies colocalization method described in condColocGeneral to three
% channels. All channels can... |
ea9f30afa23520be15d7013d87d4c9b2ff7659d9a1ab68cb2cc5bc8a86751699 | MATLAB | 6,888 | 197 | function ts = run_init_periodic(topology,homparam,hetparam,stim,init)
% RUN with Initial Conditions, or zero trivial conditions if init = NaN;
% Periodic boundary conditions
% Takes in input of model parameters, timesteps and lengthsteps.
% Returns timeseries at each point.
% List of step-size inputs (topology)
... |
343e68ba9b80b8471ca03307ffcc305739f19478a4622f6161e731b996883903 | MATLAB | 6,890 | 182 | function ea_connectome_filter_downsample_flip(connectome_path, ROI_file, factor, fixed_N, N_threshold, flip)
% This function allows to prepare large connnectomes for simulations:
% 1) Optionally, filter OUT fibers that do NOT pass the ROI
% 2) Optionally, downsample the connectome either by factor (integer,
% default o... |
5b72d13c016b3903ae251430a3dd7371681940f3ca5d71fda9e2684df597589f | MATLAB | 6,890 | 216 | function [f_peak, power_ratio] = IntrinsicFrequency(self, cel, print_to_screen, speed_thresh, varargin)
% Intrinsic frequency of a unit
%
% ARGUMENTS
%
% cel [tetrode index, cell index] in Session object root
% print_to_screen 0 or 1 (0) plots analysis
% speed_thresh ... |
e4ccec1260caf1a998d40a248af0dcd05fd25bb625758d65970c7860085347a8 | MATLAB | 6,891 | 203 | function ea_anatomyslices(resultfig,togglestates,options,controlhandles)
% input xyz in mm coordinates.
% this function plots an anatomical slice to the 3D viewer of lead-dbs.
% __________________________________________________________________________________
% Copyright (C) 2015 Charite University Medicine Berlin, Mo... |
3287708a033a861c62b6c8d20e54534e4bcfbed2182ec00be41556160848364b | MATLAB | 6,894 | 176 | function [spl, f, params] = iso226(phon,fq,sq)
%ISO226 ISO 226:2003 Normal equal-loudness-level contours
%
% [SPL,F] = IOSR.AUDITORY.ISO226(PHON) returns the sound pressure level
% (SPL) (dB) of pure tone frequencies F (Hz) at the loudness level(s)
% PHON. The values are calculated according to ISO 226:2003 us... |
d0fc878358afcf90d9e581fec65f6e7875a9d729026396c843b0db6692bc1304 | MATLAB | 6,898 | 234 | function y = pow_cvx( x, p, mode )
%POW_CVX Internal cvx version.
%
% Expression type matrices
%
persistent remap_pos remap_p remap_abs remap_pwr remap_uniq
if isempty( remap_uniq ),
remap_x1 = cvx_remap( 'real' );
remap_x1c = cvx_remap( 'complex' );
remap_x2 = cvx_remap( 'log-valid' ) & ~remap_... |
0a1ed06c621b2a5ed182e594bc43a9603f704f52df07e819123185d9be303ca0 | MATLAB | 6,901 | 199 | % Name: Robert Kim
% Email: robert.f.kim@gmail.com
% svm_decoding.m
% Description: Per-neuron SVM decoding of the instruction signal (pro vs.
% anti) for the INTACT two-layer one-modality (instr) RNNs. For each unit
% and each sliding time window, train a linear SVM to discriminate the two
% instruction classes from th... |
7100a83823859e910cb3d5e2f9c031cd033f29ed67a6852d2c445306a1d21c40 | MATLAB | 6,911 | 148 | function outstruct = cifti_read(filename, varargin)
%function outstruct = cifti_read(filename, ...)
% Read a cifti file.
% If wb_command is not on your PATH and you need to read cifti-1
% files, include the extra arguments ", 'wbcmd', '<wb_command with full path>'".
%
% >> cifti = cifti_... |
a29ab898228e2443fcdbe940a5a7c217714c3b7b276c4262e3c3a9415fbb7d57 | MATLAB | 6,924 | 190 | function [logReg_wMeanStd, num_pVal] = CBIG_ASDf_logReg_compareSex(k, sub_id, ...
sub_info_file, factorLoading_file, factor_order, output_name)
% [logReg_wMeanStd, num_pVal] = CBIG_ASDf_logReg_compareSex(k, sub_id,
% sub_info_file, factorLoading_file, factor_order, output_name)
%
% This function performs logistic r... |
7719f7b8a732eafaed1f8cf5eb55f7c64b81e58a7b933296c1e57dd41bea4d21 | MATLAB | 6,926 | 209 | %%*****************************************************************************
%% checkdepconst: compute AAt to determine if the
%% constraint matrices Ak are linearly independent.
%%
%% [At,b,y,idxB,neardepconstr,feasible,AAt] = checkdepconstr(blk,At,b,y,rmdepconstr);
%%
%% rmdepconstr = 1, if want to rem... |
6b689a9e2c91c23d79b1172c7c0a32cc6fdc635d3de306014e05c4b114b2ebdf | MATLAB | 6,928 | 145 | function [refinedTrackSpan, measurementsSpan, numBigSpan] = basicTransientTrackChopBySpan(refinedTrack, measurements, spanRadius)
%BASICTRANSIENTTRACKCHOPBYSPAN divide tracklets (from refinedTrack) that span long distance into spatially localized tracklets within an input acceptable span (by max pairwise distance) and ... |
29fb8c53d376b491148d3a06d8bc06d0d3f400bbe54960221e463979a0725c8b | MATLAB | 6,935 | 186 | function M=SOFAplotHRTF(Obj,type,ch)
% SOFAplotHRTF(OBJ, TYPE, CH) plots the CH channel of HRTFs given in OBJ.
% The following TYPEs are supported:
% 'EtcHorizontal' energy-time curve in the horizontal plane (+/- 5 deg)
% 'EtcMedian' energy-time curve in the median plane (+/- 2 deg)
% 'MagMedian' m... |
1c67ccd792a0c9252cde4e6b9fafa7870efc33ac71cc99e604b6e9f4a7ae137d | MATLAB | 6,938 | 154 | function [ data_ica, Cmp_to_remove_all, comp] = RFT_EEG_ICA( data, cmp_nr, range, layout, data_aux, ICs_to_remove_auto )
%%
% This script runs ICA on EEG 'data' using the FT's functions.
% A number of ICs (='cmp_nr') is computed only for EEG channels (other
% channels in the dataset are ignored - although plotted).... |
8e2e10f479368cdec615042b1c31227887bdc04d59d1d9819e2cee168f68ce2d | MATLAB | 6,938 | 189 | function CBIG_brain2doc(vol4D, concatOrder, mask, refListOrParams, nuisanceVars, outDir, varargin)
% CBIG_brain2doc(vol4D, concatOrder, mask, refListOrParams, nuisanceVars, outDir, varargin)
%
% This function converts registered, modulated GM images into documents
% that can be analyzed by LDA. It will first take log1... |
e977847a4c9eff59b7e55c015e3380a3fab8a4466f87a30f05135c70988aac3b | MATLAB | 6,941 | 150 | function [] = doBayesianLasso(cfg,outputDir,T,intervene_matrix,perturbations,data,species_names,BMD,experimentBlocks)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically ... |
bae608bd7936c915ed63c4f1f268618d217c37b69229032bf9ec5599eb34bbd3 | MATLAB | 6,942 | 241 | function [EigenVal, eigVect, M_error, sqErr, kurtParams, kurtTensor] = do_calculation(DEscheme, singleSliceDWI_set, matrix,threshold,kurto)
if exist('kurto') ~= 1
kurto = false;
end;
if length(size(DEscheme)) == 2,
for k = 1:size(DEscheme,1),
B_tensor(:,:,k) = DEscheme(k,:)'*DEscheme(k,:);
end;
e... |
6e1e227d2e54c6bbd0b45a19241b6a28faa5597bd3fe4838b4be1a2e30431b62 | MATLAB | 6,949 | 279 | function bestpp = createModelModelLUT(ten,Pstruc,fixedTissuePrior,fid,verbose)
ordermax = Pstruc.ordermax(1);
kappa = Pstruc.ordermax(2);
alpha = Pstruc.alpha;
% get the likelihood norm we are optimiznig for
W = createWeightingScheme(ten,Pstruc.b_weighting);
% the grid of diffusion values we are optimizing on
n ... |
aa6e03cd3d2ba486b71ab4f7c9794d6dd30715923201d8ffd9faca1e6512b946 | MATLAB | 6,949 | 201 | function [Y,maskstruct,Yisvol,Yissrf,Ykindstr,Ytmp] = palm_ready(Yfile,maskstruct,opts,removecte)
% An intermediate function to read input data (-i) and
% voxelwise EVs (-evperdat).
%
% Usage:
% [Y,maskstruct] = palm_ready(Yfile,maskstruct,opts)
%
% Inputs:
% - Yfile : Filename to be read.
% - maskstruct : Mask st... |
1512c5aa1217ba261013ce01e59c8d8a29c2ea53e3dc353ab2a0151a3d6e56d8 | MATLAB | 6,951 | 208 | function segmentBlobsPlusLocMaxMLMD(MLMD,blobChannel,varargin)
%SEGMENTBLOBSPLUSLOCMAXMLMD runs segmentation process SegmentBlobsPlusLocMaxSimpleProcess
%
%Synopsis segmentBlobsPlusLocMaxMLMD(MLMD,varargin)
%
%INPUT
%Mandatory:
% MLMD: MovieData or MovieList to be segmented
%
% blobChannel: scalar or vec... |
481518e116269ad6ad22d01a2841ef6b6512566417c1dd1aceb26f032f9c9cb7 | MATLAB | 6,952 | 188 | function varargout = sleepStatistics(varargin)
% SLEEPSTATISTICS MATLAB code for sleepStatistics.fig
% SLEEPSTATISTICS, by itself, creates a new SLEEPSTATISTICS or raises the existing
% singleton*.
%
% H = SLEEPSTATISTICS returns the handle to a new SLEEPSTATISTICS or the handle to
% the existing si... |
b7a6a3d5d02af48fc0dc452bcb6d248512088585ea5f8e5af44c16fefbfd283c | MATLAB | 6,952 | 184 | function varargout = palm_metrics(varargin)
% Compute some permutation metrics:
% - For permutation trees, return the entropies.
% - For sets of permutations, return the average Hamming distance.
%
% Usage:
% [lW,lW0,C] = palm_metrics(Ptree,X,stype)
% [Hamm,HammX,Eucl,EuclX,Spear] = palm_metrics(Pset,X)
%
% Inputs:
%... |
589484582a4703f69e5a0da4997c3a21af3522e0e7bc7eb01bd7694a3769e799 | MATLAB | 6,955 | 183 | function [ s ] = xml2struct( file )
%Convert xml file into a MATLAB structure
% [ s ] = xml2struct( file )
%
% A file containing:
% <XMLname attrib1="Some value">
% <Element>Some text</Element>
% <DifferentElement attrib2="2">Some more text</Element>
% <DifferentElement attrib3="2" attrib4="1">Even more t... |
01ea81c9dc721ea3acf99c534fd53131c2af342cfe9273e836c5c3ba84bf849d | MATLAB | 6,956 | 157 | function [roll_out] = ea_diode_main(options)
%% Determine Orientation for BSCI directed leads from postoperative CT
% has an unsupervised and a supervised version
if strcmp(options.subj.postopModality, 'MRI') % check for electrode type and postoperative imaging
msg = sprintf('Automatic rotation detection works on... |
359072ef8e6c4ba65b40c6f7210b99dc0f1062855156df32b06b6a49e141568c | MATLAB | 6,956 | 148 | function [edgeClass, gridClassInfo, imgErodedMask] = classifyMaskGridByErosion(mask, gridSize, numErosion, se, nBorder, senseCheck)
%CLASSIFYMASKGRIDBYEROSION: grid mask into boxes and classify those boxes into edge class and center class based on iterative erosion
%
%SYNOPSIS: [edgeClass, gridClassInfo, imgErodedMask]... |
82e725f6f7dc771be03de6cf2c64c64950eea8e00bc7029eda443d3b8a37dca4 | MATLAB | 6,963 | 125 | function varargout=ea_normalize_spmshoot(options)
% This is a function that normalizes both a copy of transversal and coronal
% images into MNI-space. The goal was to make the procedure both robust and
% automatic, but still, it must be said that normalization results should
% be taken with much care because all recons... |
3a774de3a884eaf6a4dc00a4e3d2a977a66db6062921dd69b29d67c73726c972 | MATLAB | 6,968 | 151 | function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
% Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes
%
% Usage:
%
% [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscor... |
b9c5aca306fca7b2a78e42fe7e8b4ba629cf69b10e2112eefb315cca010cb517 | MATLAB | 6,971 | 176 | function RATIO = cal_RATIO_dosl_acquired(R1a, R2a, R1b, MPF, R, T2b, T1d,dw, w1, TSL, B1, B0, SNR)
% COMPUTE_ACQUIRED_RDOSL Calculates the Rdosl.
% Simulates magnetization evolution under ihMT pulse sequences.
%% 1. Model Initialization (Two-pool model)
M0b = MPF; % Macromolecular pool fraction
M0a = 1-... |
8034b08052fb1d821253e64752130d129914f61a86ebff4b492868f8c303ee12 | MATLAB | 6,974 | 274 | function [vol, M, mr_parms, volsz] = load_mgh(fname,slices,frames,headeronly)
% [vol, M, mr_parms, volsz] = load_mgh(fname,<slices>,<frames>,<headeronly>)
%
% fname - path of the mgh file
%
% slices - list of one-based slice numbers to load. All
% slices are loaded if slices is not specified, or
% if slices is emp... |
8690ca62fad920a8e6a33e01ab58db38a57d978720e068a7d61c7f60bf07b605 | MATLAB | 6,977 | 199 | function [Theta_samples_lasso] = MDSINELassoMCMC(X,F_hat_prime,growth_mean_p,growth_std_p,self_reg_mean_p,self_reg_std_p,perturb_std_p,numPerturb,node,params)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-... |
1e5e9f321573c474d31ddc0ae7fae4e7c7e7f6dffe201ef99e8d8563a21674e2 | MATLAB | 6,983 | 200 | % pop_plotdata() - Plot average of EEG channels or independent components in
% a rectangular array. Else, (over)plot single trials.
% Usage:
% >> avg = pop_plotdata(EEG, typeplot, indices, trials, title, singletrials, ydir, ylimits);
%
% Inputs:
% EEG - Input dataset
% typeplot - Type d... |
c6f83528c396f887ddb3554be5d9a379bedd2693f9d293d4bf3083f13e4079e6 | MATLAB | 6,984 | 190 | % THIS SCRIPT RUNS SVMs for WITHIN-PERSON CONTRASTS
% Specified in DAT.contrasts
% -------------------------------------------------------------------------
% USER OPTIONS
% This is a standard block of code that can be used in multiple scripts.
% Each script will have its own options needed and default values for
% t... |
9ea7245c47110c7a9c36bdfe12b4c3d316f403a61e5e91a296c52816dc89f7d3 | MATLAB | 6,987 | 188 | function [coherogram,phase,t,f] = MTCoherogram(lfp1,lfp2,varargin)
%MTCoherogram - Compute LFP coherogram by multi-taper estimation.
%
% USAGE
%
% [coherogram,phase,t,f] = MTCoherogram(lfp1,lfp2,<options>)
%
% lfp1,lfp2 wide-band LFPs (one channel each).
% <options> optional list of property-value ... |
dff97798abe9c48acaaac83c719460e58796c5712e65c8cbc562a0729db3d7f4 | MATLAB | 6,987 | 207 | function [result, M] = warp_pnt(input, target, method);
% WARP_PNT determine intermediate positions using warping (deformation)
% the input cloud of points is warped to match the target.
% The strategy is to start with simpelest linear warp, followed by a more
% elaborate linear warp, which then is followed by the non... |
76997b1bd82667d59814614847f28cf139c09e6ed65b49cff10cb4feca497f1d | MATLAB | 6,996 | 154 | function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)
% Multi-taper time-frequency coherence,cross-spectrum and individual spectra
% continuous process and binned point process
%
% Usage:
%
% [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingw... |
a8033d30ebeb8ea9102349a5ae4f741e1da0b43ad429bcb1205304c252d15f09 | MATLAB | 7,001 | 173 | % epoch() - Extract epochs time locked to specified events from continuous EEG data.
%
% Usage:
% >> epocheddata = epoch( data, events, timelim);
% >> [epocheddata, newtime, indices, rerefevent, rereflatencies ] = ...
% epoch( data, events, timelim, 'key1', value1, ... );
%
% Inputs:
% data ... |
9c9cee1ebdba434c7e4b4869c04f4d4f516896e42033dc7c5a6336e91c7a5df7 | MATLAB | 7,004 | 165 | % 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,ar... |
495f267d3ef41aef151e3dcb260a77207aea775922aded7f7131a8b3731b2ca8 | MATLAB | 7,010 | 249 |
% Version 26/06/2026
% Authors: Alessandro Petrini and Davide Pierangeli
% -------------------------------------------------------------------------
% This script is provided as a reference implementation of the experimental
% procedure described in the manuscript. It documents the acquisition logic
% and computation... |
5adc0e23b21a2d0d03b016f4571205477b0019748c6111d8b2c73bf80ec814bd | MATLAB | 7,010 | 165 | function SOFAcompileConventions(conventions)
%SOFAcompileConventions
%
% Obj = SOFAcompileConventions(sofaconventions) compiles the specified
% SOFA conventions. For every convention a CSV file has to exist which
% will be compiled to a .mat file used later by SOFAgetConventions().
%
% The CSV file must... |
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