sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
72848d8bac69cd0cecb15743bdd87e03d47b5b3a9f417e5d97136d0950e6bb50 | MATLAB | 16,892 | 371 | % POP_REJCONT - reject continuous portions of data based on spectrum
% thresholding. First, contiguous data epochs are extracted
% and a standard spectrum thresholding algorithm is
% applied. Regions of contiguous epochs larger than a
% specified size are ... |
e53d92c0d517cc65b93711ffb33412830a32e2ec808fb2a4651978afd8c56be9 | MATLAB | 16,942 | 438 | function figureHandles = plot(this, varargin)
% Different plot modalities for Roi data, including time series & box plots
% showing a couple of statistics for time series or volume ROI data, e.g.
% mean +/- sd,
% min/median/max
% boxplot/histogram (distribution over voxels)
% All plots can show statistics either ... |
345ada2f36c0282a76118415ec182c680f28b92ec9381b3f81d13ecdc7435f1d | MATLAB | 16,982 | 567 | %% Figure 5
%% 1.1 Correct CT for covariates: HCP
clc; clear; close all
load dataHCP
load data
clearvars -except dataHCP labelsGlasser*
dataHCP_Temp = dataHCP(:, {'ID' 'Age' 'IQ'});
CT_CorrectedHCP = dataHCP(:, labelsGlasserCT);
CT_CorrectedHCP = [dataHCP_Temp CT_CorrectedHCP];
CT_CorrectedHCP_Array = nan(height(C... |
03b5c653e3ff889841709b9f1f704ae2d97ba1b681c05685728cd74cae178de3 | MATLAB | 16,990 | 376 | function [FB_y, S, freqAxis, timeAxis] = effectConnect_plot(subjTag)
% standalone script for plotting effective connectivity results (DTF)
% called by: effectConnect_plot_avgOverSubj.m
% WARNING: quick-fix exploratory script (to get mean DTF over subj)
% (c) Jiri, Sep22
%% batch job (uncomment function and use as a s... |
a55b46dad6fa381a6fe1fb7588f87628ee907bb467a92af0bb6d3e3f3e721fb4 | MATLAB | 16,999 | 401 | function [outImg] = mrAnatAverageAcpcNifti(fileNameList, outFileName, alignLandmarks, newMmPerVox, weights, bb, showFigs, clipVals)
%
% outImg = mrAnatAverageAcpcNifti(fileNameList, outFileName, [alignLandmarks=[]], [newMmPerVox=[1 1 1]], [weights=ones(size(fileNameList))], [bb=[-90,90; -126,90; -72,108]'], [showFigs=t... |
3d0d4d0b1b464e10dcdc1cea741f24f14297aa5be36b221490d95e5a597f9082 | MATLAB | 17,025 | 472 | %% Expand wildcards for files and directory names
%
% Pattern matching of file and directory names, based on wildcard
% characters. This function is similar to wildcard expansion performed by
% the Unix shell and Python glob.glob function, but it can handle more
% types of wildcards.
%
% [LIST, ISDIR] = glob(... |
a753b0d3c03fcf5385cc07aa67b04ec9dcbcf1ec760a19d42018c84b14b2f863 | MATLAB | 17,030 | 746 | function vImageGUI(params, mov)
close all;
if isempty(mov)
mov = 100.*rand(20,20,100);
end
h.mov = mov;
clear mov;
h.Nframes = size(h.mov, 3);
h.params = params;
h.cmapstrings = {'parula'; 'gray'; 'hot'; 'cool'; 'bone'; 'copper'; 'pink'; 'flag'; ...
'prism'; 'jet'; 'hsv'; 'green'; 'red'; 'blue';... |
e4a7f572a4148d2029d801eec19ed3657f2feae8e5774f5850d6da3f94f7aa7f | MATLAB | 17,047 | 310 | function res = arg_subswitch(varargin)
% Specify a function argument that can be one of several alternative structs.
% Spec = arg_subswitch(Names,Defaults,Alternatives,Help,Options...)
%
% The correct struct is chosen according to a selection rule (the mapper). Accessible to the
% function as a struct, and visible in t... |
9b9f5b25e4d0aa4665d6f9573c24b4b25dbcc55b58316c78e4c98220c8134656 | MATLAB | 17,067 | 346 | %% jobP_MEGA_Example.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, struc... |
6a57a573bb7adb0d679c28b63b6c2b5acb7ad226d8631986aa7eb6d9c380d5d2 | MATLAB | 17,077 | 442 | % check the dSTR for all epochs, and also compare decoder types
%% load code path and data.
%location of analysis codebase
codepath = '~/projects/constantinoplelab/Analysis/';
% add code paths
addpath(genpath(codepath))
addpath(genpath(codepath + "david"))
addpath(genpath(codepath + "maggie"))
%for saving pds corre... |
01ade5eb09f5739f1ce48e5dcfa0939e78bddb082dcdf5ddde1b87658efb8930 | MATLAB | 17,116 | 387 | % POP_BIOSIG - import data files into EEGLAB using BIOSIG toolbox
%
% Usage:
% >> OUTEEG = pop_biosig; % pop up window
% >> OUTEEG = pop_biosig( filename, 'key', val, ...);
%
% Inputs:
% filename - [string] file name
%
% Optional inputs:
% 'channels' - [integer array] list of channel indices
% 'blockrange' ... |
8f1cc82188c94575d9897dc881e295f76e199905722ca6f40c0c63f310e32713 | MATLAB | 17,133 | 380 | %% extract the beta parameters in each clusters.
% use each mask - mt, mst, hMT on tactile motion Localizer
% take the avg of beta values from the roi
% (1)lmst- motion_beta and (2) lmst -static_beta
% across two runs
clear
subjectList={'sub-001','sub-002','sub-003','sub-004','sub-005','sub-007','sub-008'...
's... |
5afbe1a0081e3f62aa234de81e414882bceacbb5dd9ca36cccb328d8e8a6bb8b | MATLAB | 17,134 | 469 | %% MakeAFMmap_RectangularGrid_standard.m 17/07/2019 Julia Becker
% This script allows the user to tailor a rectangular AFM measurement grid.
% Based on three landmark points for which the stage coordinates are known,
% this script establishes conversion variables between the stage and the
% overview imag... |
a7f403fc18d06f5aa0165b186632312abe3ad1528137b4cc1052efa5aa36bf9a | MATLAB | 17,141 | 471 | function [c, r, t, cpulse, acq_codes, verbose] = ...
tapas_physio_read_physlogfiles_bids(log_files, cardiac_modality, ...
verbose, varargin)
% Reads in 3-column tsv-file from BIDS Data (cardiac, respiratory, trigger),
% assuming log_files-meta information to be in an accompanying .json-file
% Note: if a JSON fi... |
cd5f3db2d2ac6700e95eb1e1e2c05c57a6b37a5d66419244e9165d9c39f296b8 | MATLAB | 17,166 | 406 | function [h_old,h_new] = vis_artifacts(new,old,varargin)
% vis_artifacts(NewEEG,OldEEG,Options...)
% Display the artifact rejections done by any of the artifact cleaning functions.
%
% Keyboard Shortcuts:
% [n] : display just the new time series
% [o] : display just the old time series
% [b] : display both time s... |
5a0765caf1c36e23276dcd872d606f8b58c467bb52db90f54591afa0ac466659 | MATLAB | 17,169 | 406 | function [h_old,h_new] = vis_artifacts(new,old,varargin)
% vis_artifacts(NewEEG,OldEEG,Options...)
% Display the artifact rejections done by any of the artifact cleaning functions.
%
% Keyboard Shortcuts:
% [n] : display just the new time series
% [o] : display just the old time series
% [b] : display both time s... |
60b3fce1634bd8932945c625c0448b9c79dba6e700d14c6a1e4fd814df3959a0 | MATLAB | 17,194 | 424 | function PlotIndvNetMet(expData, Params, Info, originalCoords, originalChannels, oneFigureHandle)
%PLOTINDVNETMET Creates network plot for individual recordings
% Parameters
% ----------
% expData : struct
% Params : struct
% Info : struct
%
% Returns
% ----------
%% electrode specific half violin plots
lag... |
9621d416168464027121921576acbd6664e79f0a9f507c4101d1d70e77d71458 | MATLAB | 17,220 | 553 | function H_BrainNet = BrainNet_MapCfg(varargin)
% BrainNet Viewer, a graph-based brain network mapping tool, by Mingrui Xia
% Function to draw graph from commandline
%-----------------------------------------------------------
% Copyright(c) 2013
% State Key Laboratory of Cognitive Neuroscience and Learning, Beiji... |
61e38975d3b6b984dcf96addd50b9a8e22129c04aa9828c2f53b1a1d60f71d9c | MATLAB | 17,229 | 618 | %% Figure 2
%% 1.1 IRI-PT ~ SA
clc; clear; close all
load data
clearvars -except data*
data.IRI_PT = zscore(data.IRI_PT);
DV = 'IRI_PT';
measure = '_Area';
covariates = '~ Age + IQ + eTIV + ';
measureOfInterest = strfind(data.Properties.VariableNames, measure);
measureOfInterestID = find(~cellfun(@isempty, measu... |
61e0ea6c4b87225211e9a2cf621eff82f510c6351d4d38cf4c4fe1aac13069ed | MATLAB | 17,262 | 425 | function simHandMuscleSystemVariation()
clear all
close all hidden
global mdl mdlWks sampFreq triggerTime
aGainRate = 0.5; % aGain is fiexed to be 0.5 times bGain
evalParamDiffSP =1; % Evaluate results of "set point" variation
evalParamDiff1b =1; % Evaluate results of "1b gain" variation
evalParamDiff1a =1; % Evalu... |
e07182611c211ccce52a447964afe65ee9ad9e8e3c2cab3554e0007cc5f1061f | MATLAB | 17,312 | 337 | function [MRSCont] = osp_combineCoils(MRSCont, kk, ll, ref_ll, w_ll)
%% [MRSCont] = osp_combineCoils(MRSCont)
% This function performs a the receiver coil combination of multi-array
% data. All coil-combination procedures are performed using the ratio of
% the maximum signal in each receiver to the square of the ... |
9473eab60302698da924c532bae4e08fcb7d8b271523d6183b7a6c8ce57558a0 | MATLAB | 17,334 | 463 | % HELP2HTML - Convert a Matlab m-file help-message header into an .html help file
%
% Usage:
% >> linktext = help2html( filein, fileout, 'key1', val1, 'key2', val2 ...);
%
% Inputs:
% filein - input filename (with .m extension)
% fileout - output filename (if empty, generated automatically)
%
% Option... |
6d62e05e9c060eaa75100ea3e9fa4eae5079d22f714fc48b168a7642a2289764 | MATLAB | 17,339 | 440 | function out = MF_FitSubsegments(y, model, order, subsetHow, samplep, randomSeed)
% MF_FitSubsegments Robustness of model parameters across different segments of a time series
%
% The spread of parameters obtained (including in-sample goodness of fit
% statistics) provide some indication of stationarity.
%
% Values of ... |
82f5eef9a46393dd6b3c17609f2f669bd6a59391271439ae593c6f9a498fdc1b | MATLAB | 17,362 | 417 | function varargout = TMStargetSC(varargin)
% TMSTARGETSC M-file for TMStargetSC.fig
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help TMStargetSC
% Last Modified by GUIDE v2.5 08-Nov-2020 22:38:50
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struc... |
5304a231f2436286a327d28b525ce4b99a2ee242958d5b2e46c5ba1ff4fd8aea | MATLAB | 17,371 | 530 | function [] = PlotNetMet(ExpName, Params, experimentMatFileFolder, oneFigureHandle)
% Plot network metrics for MEA data
%
% Parameters
% ----------
% ExpName : cell array
% cell array where each entry is the name of the recording to
% plot network metrics (file extension should NOT be included)
% Params : st... |
362d4e8a7073568cf51c8be3e072787fcd751ec40f2e514e71761d094805157d | MATLAB | 17,375 | 464 | function [ subject ] = nmri_canonical_hdm_suma(subject, data, params)
%[ subject ] = nmri_canonical_hdm_suma(subject, data, params)
%
% This function will use a canocical / atlas headmodel for later source
% processing,
%
% subject = subject structure, see nmri_read_subject
% could be a struct or .... |
4eb8c7879def69e6e7a512a0bba724782691f4d8349d364136b5a34d25b81597 | MATLAB | 17,375 | 411 | function regenerate_reference(varargin)
%% regenerate_reference('confirm', true, 'tier', 'tier1', 'filter', '*')
%
% Description: (re)generates saved reference outputs used by the
% regression comparisons in test/tier1_smoke, test/tier2_matrix (all
% methods, synthetic phantom) and test/tier3_matrix (all methods, real
... |
941c99c6648c071126935005255acdbfaa1ae6686691c72e131d02bc56a9b19a | MATLAB | 17,381 | 452 | function [fitParamsStep1] = fit_Osprey_PrelimReduced(dataToFit, basisSet, fitRangePPM)
%% [fitParamsStep1] = fit_Osprey_PrelimReduced(dataToFit, basisSet, fitRangePPM)
% Performs the first step of the LCModel preliminary analysis
% analogous to the LCModel algorithm. The algorithm is described in:
% S.W. Prov... |
9d9a1b4cf2e7ff7ed2a4d91f8dd1aee8df7631c215ec80ec4a25316c2fdaa213 | MATLAB | 17,389 | 343 | %% jobTwix.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imag... |
c7c4a0a1d9a0c627159375f1dfa47c511926093166ffa8f852995c71054e2404 | MATLAB | 17,393 | 359 | %% jobSDAT.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imag... |
3efa606a05068c898d04c9b93cf41afc29023617e9237d2a382c123212b93673 | MATLAB | 17,397 | 430 | % pop_loadset() - load an EEG dataset. If no arguments, pop up an input window.
%
% Usage:
% >> EEGOUT = pop_loadset; % pop up window to input arguments
% >> EEGOUT = pop_loadset( 'key1', 'val1', 'key2', 'val2', ...);
% >> EEGOUT = pop_loadset( filename, filepath); % old calling format
%
% Optional inputs:
% 'f... |
4cc6894c8c538225ea582d3fa616b2b42ebdb848d9e1e74de506abe0841be465 | MATLAB | 17,418 | 345 | %% jobTwix_MEGA_Example.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, st... |
dadd0469465dfc1c6e2bb467c076a3b79aeb61e4866b328e6f8769d682317461 | MATLAB | 17,468 | 424 | function PlotFigure1(datadir, codedir)
%PlotFigure1 - Plots Figure 1. Must be run after ProcessData_Figure1.
% INPUTS:
% datadir - Local directory where ProcessData_Figure1.mat was saved after running ProcessData_Figure1
% codedir - Local directory where code (e.g., published/EstrousRPE/) was saved
%% Set up paths... |
91d410d998e64b5e87a9b50349234efac20f97a60c63d91dc7e77244bb74d217 | MATLAB | 17,470 | 428 | function [SPM] = spm_fmri_spm_ui_lqc(SPM)
% Setting up the general linear model for fMRI time-series
% FORMAT [SPM] = spm_fmri_spm_ui(SPM)
%
% creates SPM with the following fields
%
% xY: [1x1 struct] - data structure
% nscan: [double] - vector of scans per session
% xBF: [1x1 struct] - Basis functio... |
44e4d6f84699dc0c6a0cc4dc8d87891f69308c4f502ff1f832c65f33ebdd3f55 | MATLAB | 17,506 | 358 | function plotSpectralTrials(params, resp, triggers)
% given cell array resp{sess} of 2D data: [samples, ch] computes the STFT
% normalizes spectra to baseline time to compensate for the 1/f decay
% for each class & channel extracts + plots mean of trials
% the trials are cutted from triggers{1}.sampleSessLabel
% furth... |
310f9a8a7f509a6f839f39e4c2f193e5dd0148eb0955d402cbcbee2fa4d9cf69 | MATLAB | 17,568 | 350 | %% jobIMA.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imagi... |
3fb3e1e85877d21d795c580a0b92d2b2ba7c491a4c1ddbf61d73d05f5b2b3c24 | MATLAB | 17,568 | 466 | function varargout = ica_selection(varargin)
% ICA_SELECTION MATLAB code for ica_selection.fig
% ICA_SELECTION, by itself, creates a new ICA_SELECTION or raises the existing
% singleton*.
%
% H = ICA_SELECTION returns the handle to a new ICA_SELECTION or the handle to
% the existing singleton*.
%
% ... |
ed88a0d11473de174998a99c304a03371d526bc7ec7ac54cd2560245263e4b96 | MATLAB | 17,570 | 584 | function classificationResults = doClassification(recordingLevelData, Params, subset_lag, plotSaveFolder, oneFigureHandle)
% Do classification of genotype based on network features
%
% Parameters
% ----------
% recordingLevelData : table
% Params : struct
% figSaveFolder : str
% subset_lag : int
% which lag to u... |
29433a7259e8694a1f0b8a608bab7f962ad7f160381f47767476385a987afa88 | MATLAB | 17,606 | 434 | function SuppFigure_BroadWeight(varargin)
%SUPPFIGURE_BROADWEIGHT Generate supplementary figure for broad weight distribution analysis
%
% Purpose:
% Creates a comprehensive figure showing the effects of broad weight distributions
% on network dynamics, including weight distributions, balance indices, normalization... |
d33e007443481ce8dab7bc9ab8dfb238ba03ddfec903ad5431f94c0d86a45d94 | MATLAB | 17,644 | 312 | function GRUP = ch2roi_load(params, groupInfo)
% pools results from trigger analysis over:
% - freq. bands
% - ROIs (regions of interest): anatomic areas, ...
% - subjects
% spectra are evaluated based on significance criteria of the last FB specified (typically hiGamma)
% returns: GRUP struct
% (c) Jiri, Nov21
... |
df380a445b04fdfb4afe4731948bf9003aa617709077e8ce17b4529808fd4fd5 | MATLAB | 17,655 | 335 | set_up_paths_and_data_directories;
stim_names = {
'After_The_Rain', 'Between_Viewings', 'Big_Buck_Bunny', 'Chatter', 'Damaged_Kung_Fu', ...
'First_Bite', 'Lesson_Learned', 'Payload', 'Riding_The_Rails', 'Sintel', 'Spaceman', ...
'Superhero', 'Tears_of_Steel', 'The_secret_number', 'To_Claire_From_Sonny', 'You_Again'
};... |
c91dfd32b4fd3ec5c8309b154c02b9de33e90630651e4be26a31cb91337ae36d | MATLAB | 17,662 | 524 | function res = vl_simplenn(net, x, dzdy, res, varargin)
%VL_SIMPLENN Evaluate a SimpleNN network.
% RES = VL_SIMPLENN(NET, X) evaluates the convnet NET on data X.
% RES = VL_SIMPLENN(NET, X, DZDY) evaluates the convnent NET and its
% derivative on data X and output derivative DZDY (foward+bacwkard pass).
% RES... |
a6afae6f5e3366ad19995d13d4e837abffc7626deb44bcf54ea34192c7d03385 | MATLAB | 17,668 | 558 | function [hout,T,perm] = dendrogram2(Z,varargin)
%DENDROGRAM Generate dendrogram plot.
% DENDROGRAM(Z) generates a dendrogram plot of the hierarchical binary
% cluster tree represented by Z. Z is an (M-1)-by-3 matrix, generated by
% the LINKAGE function, where M is the number of objects in the original
% datas... |
78f1836db8ab92f5194ab5b149ec7716171ce89513fbbcb910d110f6284d0cb9 | MATLAB | 17,670 | 349 | % POP_SPECTOPO - Plot spectra of specified data channels or components.
% Show scalp maps of power at specified frequencies.
% Calls SPECTOPO.
% Usage:
% >> pop_spectopo( EEG, dataflag); % pops-up interactive window
% OR
% >> [spectopo_outputs] = pop_spectopo( EEG, dataflag, tim... |
89f9fe316a75632b5491a11e5fa8f43793dbec7990018ba153f6013b7ff88a0d | MATLAB | 17,697 | 372 | %% ms SEI fig - anatomy area (AA): 3D brains + spectra + FBs, Yeo7 + Yeo17
% (c) Jiri, Oct23
% small known bugs:
% 1) FDR should be done for all P values at once (now fragmented in ch2roi_load)
% 2) bip. channel B8 can be assigned to DAN (B7-B8) & DMN (B8-B9)
%% settings: v1 - relaxed conditions (p-level, length of s... |
fa2c805c21bf5febd89f8a179a4b3a375002c93ae6a5b2097bbfce344d6ba3b5 | MATLAB | 17,698 | 361 | %% jobP_MEGA_LCModel_Example.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionall... |
008eb9577c24a2c6ad8e3225401526601da658fea60f2f8608ddb41030a1f1aa | MATLAB | 17,712 | 422 | function [out] = osp_editSubSpecAlign(varargin)
%% [varargout] = osp_editSubSpecAlign(varargin)
% Aligns sub-spectra of (multiplexed) edited MRS data to minimize
% subtraction artefacts.
%
% USAGE:
% [outA, outB, outC, outD] = osp_editSubSpecAlign(in, seq, target,unstableWater);
%
% INPUTS:
% in ... |
6e4c187840e5e91a403cd9fdc46e30593aa887fcc0d7d994ff787cb3e019ad17 | MATLAB | 17,735 | 502 | function read_cat(cat12_path, input_img, num_sources, num_cortex_verts);
%
% Input: cat12_path <string> fullpath to cat12 installation.
% input_img <string> fullpath to T1 MRI image to be segmented by
% CAT12.
% num_sources <integer> number of sourcemo... |
c4d8f0bf18e70e0a820cec59917016e8b5cff65e1327465fc3f5f821599737f7 | MATLAB | 17,745 | 491 | %
% Transform fNIRS data from .txt to .nirs format for use with HOMER
% processing package.
%
% Prerequisite
% ----------
% To use this script, the user must first create an .SD file which matches their Shimadzu
% probe layout using the SDgui function of Homer2 (or AtlasViewerGUI/Make Probe).
% Refer to Aas... |
f3e797643c919c7c786dfac1242a3f4b37ad721370ce608c7ec7df3b18e9caaf | MATLAB | 17,753 | 348 | %% jobSDAT.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imag... |
09553770f92612d0fbea9df9a4d8beb4a325c0d191b167ce957024b4b545fff5 | MATLAB | 17,756 | 401 | function alignLandmarks = TMSviewer(fileNameList, outFileName, alignLandmarks, newMmPerVox, weights, bb, showFigs, clipVals)
%
% outImg = mrAnatAverageAcpcNifti(fileNameList, outFileName, [alignLandmarks=[]], [newMmPerVox=[1 1 1]], [weights=ones(size(fileNameList))], [bb=[-90,90; -126,90; -72,108]'], [showFigs=true],... |
69ac5d5f2b2238b9c67f6e1df97b36f8da3436a2d8307c7c86f4ab145418e269 | MATLAB | 17,772 | 387 | function label_subject_and_write_json(input_img, atlas_dir, num_vertices, out_json, opts)
% LABEL_SUBJECT_AND_WRITE_JSON
%
% Input:
% input_img <string> Full path to a subject T1 (or any NIfTI in the CAT12 output
% folder). Its folder is used to locate CAT12 surfaces and its
% ... |
b7f8ae869bd879d363c118b15312196bc2471bd5e9f03dce72c59356831eb6b7 | MATLAB | 17,782 | 360 | %{
# masks created manually
-> reso.Segmentation
---
%}
classdef SegmentationManual < dj.Computed
properties
popRel = reso.SummaryImagesAverage
end
methods(Access=protected)
function makeTuples(self, key)
images = ne7.mat.normalize(fetch1(reso.SummaryImagesAverage & ... |
b3df6fbff34c770f16864cf228ac9ccb706cbe4a96ffa86f6bb0047a4e25124c | MATLAB | 17,820 | 435 | % code for improved 1/f fit of mouse LFP data
% requires the following in the path: the Chronux package and the following
% called upon functions: improved_LFP_fit.m,st_fit_LFP.m,
% plot_spectrum_two_groups.m, fg_bootstrap_two_groups.m
% fg_bootstrap_two_groups_seed.m, and makeseed.m
% requires the following in ... |
7afec7cf18415851c6893e82961017a84be18ffdae106d3cda6ff1b3d57036ff | MATLAB | 17,837 | 594 | function coactPaper_figureS11()
labelWeight=true;
labelCase=false;
labelSize=9;
letGapX=5;
letGapY=6;
fontsize=6;
close all
fh=initFig('width',18.6,'height',15,'font','Arial','fontsize',fontsize);
x=8;y=4;
panel_01(x,y,fontsize);
panelLetter2(x-letGapX-1,y-letGapY+5,alphabet(1,labelCase),'fontSize',labelSize,'isBold'... |
d38f4ffb79239c0d5d44416f76e52696d808aebba0ac5fc8286357a0e77eb798 | MATLAB | 17,853 | 329 | % POP_CHANCORESP - define correspondences between two channel locations structures
% (EEG.chanlocs) automatically (by matching channel labels)
% else using a user input gui.
% Usage:
% >> [chanlist1 chanlist2] = pop_chancoresp(chanstruct1, chanstruc2, 'key', 'val', ...);
%
% In... |
d5dfff08e5e07527bcdc5c04831af93e559731eeb1838f8392a9101d609b9ea4 | MATLAB | 17,857 | 352 | %% jobSDAT.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imag... |
7068645b3afd0abd954486037a7c0ec077cd59b9e3128515c1f0789b3e1f35da | MATLAB | 17,862 | 664 |
% Author: Tayfun Tumkaya
% Display the Temperature Preference of Fly in Multiple Experiemnt.
%
clc
close all;
clear all;
% Last_Data=42000;
% Basket for Experiments.
% file_list = {
%
%
% {'w1118-UAS-TrpA1(Or65c)_I-n.mat'
% 'w1118-Or65c-Gal4_III-n.mat'
% 'w1118-Or65c-Gal4_II-n.mat'
% 'w1118-Or65c-Gal4_I-n.m... |
6e533ec69db2cdbd880973efb62b35b1f73a765ff750f256accb4331dda81995 | MATLAB | 17,896 | 450 | function [fitParamsStep2] = fit_OspreyPrelimStep2MMGaussians(dataToFit, resBasisSet, fitRangePPM, fitParamsStep1)
%% [fitParamsStep2] = fit_OspreyPrelimStep2MM(dataToFit, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM)
% Performs the second step of the LCModel preliminary analysis
% according ... |
f22261fdfd78c13a8ee3f5326af6c4be9aa84aa1b1ffa7937cc2d34e2ad60d9e | MATLAB | 17,899 | 516 | function json=savejson(rootname,obj,varargin)
%
% json=savejson(rootname,obj,filename)
% or
% json=savejson(rootname,obj,opt)
% json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
% Object Notation) string
%
% author: Qianqian Fa... |
2d0d961b2717fc334e5e9773b4fd246504b44b0d7d58c95bf15db7c55b028113 | MATLAB | 17,903 | 528 | function res = vl_simplenn(net, x, dzdy, res, varargin)
%VL_SIMPLENN Evaluate a SimpleNN network.
% RES = VL_SIMPLENN(NET, X) evaluates the convnet NET on data X.
% RES = VL_SIMPLENN(NET, X, DZDY) evaluates the convnent NET and its
% derivative on data X and output derivative DZDY (foward+bacwkard pass).
% RES... |
1e423f272dd87b7a176ccc8254e201130d0989fba2d1462439f6cc922d036547 | MATLAB | 17,905 | 354 | function out = NL_PersistentHomology(y, tau, m, maxDim, maxN)
% NL_PersistentHomology Topological data analysis of a time-delay embedding.
%
% Time-delay embeds the time series (Takens' theorem) and computes the
% persistent homology of the resulting point cloud under a Vietoris-Rips
% filtration, via the ripser tool... |
1c7f3512e6972a2e3233091c6fa0e78f19ab35f3edb68cc80a4a0dfeec395a13 | MATLAB | 17,919 | 370 | % STD_ERSP - Compute ERSP and/or ITC transforms for ICA components
% or data channels of a dataset. Save results into Matlab
% float files.
%
% Function description:
% The function computes the mean ERSP or ITC for the selected
% dataset ICA components or data cha... |
f3111e4751db9bd836545d65d086779cf12f1a34ad1c7cb0222fbbc93ffbc004 | MATLAB | 17,920 | 495 | %% MakeAFMmap_RectangularGrid_measuresetnumber.m 17/07/2019 Julia Becker
% This script allows the user to tailor a rectangular AFM measurement grid.
% Based on three landmark points for which the stage coordinates are known,
% this script establishes conversion variables between the stage and the
% overview im... |
f314dda423f2c7fb679a71d13aa2aa4248d24c43ff74d4a88441427eec7323f4 | MATLAB | 17,948 | 478 | %% Aplha-power analysis
clear
ft_defaults
% set params
selsensors = 'occ';
% select files
folder = 'Q:/MEG_data/';
filelist = dir(fullfile(folder, '**', 'tfr_all3.mat'));
filelistHiLo = filelist([1 5 3 8 9 13 12 16 17 20 21 24 25 29 27 34 32 36 37 40]); %HIGH-LOW condition
filelistLoHi = filelist([7 2 6 4 11 ... |
aadca8437d2bcaf2f5bd412e93d201a5950744d5d5a078a2d6734b8d7fcb4a36 | MATLAB | 17,972 | 498 | function [results, center, Cn, PNR, save_avi] = greedyROI_endoscope(Y, K, options,debug_on, save_avi)
%% a greedy method for detecting ROIs and initializing CNMF. in each iteration,
% it searches the one with large (peak-median)/noise level and large local
% correlation. It's the same with greedyROI_corr.m, but with so... |
696ff3210ca26a44b306f9387f1352ca8310eb5c2cffd8d74738b41de8788f28 | MATLAB | 17,990 | 434 | % REJSTATEPOCH - reject bad eeg trials based a statistical measure. Can
% be applied either to the raw eeg data or the ICA
% component activity. This is an interactive function.
%
% Usage:
% >> [ Irej, Irejdetails, n, threshold, thresholdg] = ...
% rejstatepoc... |
cc25aeec0f5737d824a1800dd9b31b587a13369a24944dd39e1af86944809095 | MATLAB | 17,990 | 329 | function [post nlZ dnlZ] = infEP(hyp, mean, cov, lik, x, y, opt)
% Expectation Propagation approximation to the posterior Gaussian Process.
%
% The (sequential) EP algorithm performs a number of sweeps over the data in
% random order, for better performance when cases are ordered according to the
% targets. During a s... |
f9834a52bfcdbdd09a275ee732a9662a161e4695fa216166df5b1d7485240506 | MATLAB | 18,014 | 534 | function [ mri_all ] = nmri_mri_segment( cfg, params )
% [ mri_all ] = nmri_mri_segment( cfg, params )
% will segment (SPM12, new segement) MRI scans for
% use in Fieldtrip (e.g. for headmodeling). Data should be passed in a
% cfg-struct
%
% cfg.t1 = path to T1 image or Fieltrip mri struct (needed)
% .flair ... |
17395c3e4aec6a8d823c0f10cf74611fc41c50b147ba4ca72f69c04f1e2e65fa | MATLAB | 18,019 | 351 | %% get_AHEAD_atlas_labels(input,mask,output_dir,algorParam)
%
% Usage:
%
% Input
% --------------
% input : structure that contains input nifti file names
% mask : structure that contains mask nifti file names
% output_dir : directiry where the output files will be stored
% algorParam : algorithm... |
19a093fc726b4e6fac91db698cc4b617dda6f5fa1ef3af1a15a71048cd44f515 | MATLAB | 18,031 | 484 | function [err,FigHndls] = DispIVSurf (NodeList,FaceSetList,UsedNodeSet,ITvect,FigHandle,DispOpt)
%
% [err,FigHndls] = DispIVSurf (NodeList,FaceSetList,UsedNodeSet,ITvect,FigHandle,[DispOpt])
%
% NodeList is a Nx3 matrix containing the node index and the
% XYZ coordinates of each of the N nodes that form the surface mo... |
6d7cea81b2f7590211a13396b3a90a03f3a02a14a520adb9b565f653b40232ff | MATLAB | 18,040 | 522 | % TIMTOPO - plot all channels of a data epoch on the same axis
% and map its scalp map(s) at selected latencies.
% Usage:
% >> timtopo(data, chan_locs);
% >> timtopo(data, chan_locs, 'key', 'val', ...);
% Inputs:
% data = (channels,frames) single-epoch data matrix
% chan_locs = channel locat... |
f1422fe42e02d4537445a59f96911360fee2758fea5d020787d64297140ad21c | MATLAB | 18,043 | 511 | function [Out] = icaDim(Origdata, DEMDT, VN, Iterate, NDist)
%
% ICADIM(Origdata, DEMDT, VN, Iterate, NDist)
%
% Estimates the number of ica components that are not due to random noise,
% and makes a standard deviation map of the random noise estimate
%
% DEMDT: 1 to detrend, 0 to only demean, -1 to do nothing, >1 to... |
b68c20278dbc92253b15f96c3ffee1256316100840006cfd0c6dcf421e1fd414 | MATLAB | 18,051 | 362 | %% jobTwix_MEGA_LCModel_Example.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, option... |
cd618862313709eb759a7866b6d65ab9cdb39c9d24984d8e4c96c22475ef8e55 | MATLAB | 18,072 | 417 | % STD_CHECKSET - check STUDY set consistency
%
% Usage: >> [STUDY, ALLEEG] = std_checkset(STUDY, ALLEEG);
%
% Input:
% STUDY - EEGLAB STUDY set
% ALLEEG - vector of EEG datasets included in the STUDY structure
%
% Output:
% STUDY - a new STUDY set containing some or all of the datasets in ALLEEG,
% ... |
d21ceeb47bed79ebf304da5faceb4115b540d3fdf53711a6fdb61db69f1affd8 | MATLAB | 18,077 | 430 | % PAC_CONT - compute phase-amplitude coupling (power of first input
% correlation with phase of second). There is no graphical output
% to this function.
%
% Usage:
% >> pac_cont(x,y,srate);
% >> [pac timesout pvals] = pac_cont(x,y,srate,'key1', 'val1', 'key2', val2' ...);
%
% Inputs:
% x =... |
0a086a3aa89096c1866ddfb40f3c17e482fd81771a82b95069ec9b3661d4fc41 | MATLAB | 18,078 | 445 | % POP_PROP - plot the properties of a channel or of an independent
% component.
% Usage:
% >> pop_prop( EEG); % pops up a query window
% >> pop_prop( EEG, typecomp); % pops up a query window
% >> pop_prop( EEG, typecomp, chanorcomp, winhandle,spectopo_options);
%
% Inputs:
% EEG ... |
c2b7270ccc1fe4dcd67c91459cac27adab44836e60108be19263ea7548e336a9 | MATLAB | 18,130 | 401 | classdef clusteringGUI < handle
properties
currentCluster = 1
page = 1
thumbnail_size = [50 100]
clustAssign
clusters
rejected
ClusteringData
minfreq
maxfreq
fig
image_axes = gobjects()
handle_image = gobjects()
... |
0d25d4c25e44bd0eb781948fc2a6d8e453ef867f16a5f3758762f06d160ea586 | MATLAB | 18,136 | 549 | % io_loadspec_niimrs.m
% Georg Oeltzschner, Johns Hopkins University 2021
%
% USAGE:
% out = io_loadspec_niimrs(filename);
%
% DESCRIPTION:
% Reads in MRS data stored according to the NIfTI MRS format.
% See the specification under
% https://docs.google.com/document/d/1tC4ugzGUPLoqHRGrWvOcGCuCh_Dogx_uu0cxKub0EsM/edit
%... |
311657a53df4d775d919871b6f9db97581b56b8d03fdb1ddca2859cc449c116f | MATLAB | 18,173 | 424 | function [n_best P_best V C]=fast_oopsi(F,V,P)
% this function solves the following optimization problem:
% (*) n_best = argmax_{n >= 0} P(n | F)
% which is a MAP estimate for the most likely spike train given the
% fluorescence signal. given the model:
%
% <latex>
% \begin{align}
% C_t &= \gamma*C_{t-1} + n_t, \qquad... |
0be7a6bea585f5b7f5d2d0c179e7782adccc7b404d3db5248eb6b923aee8e27f | MATLAB | 18,174 | 333 | function outbytes = cifti_write_xml(cifti, keep_metadata)
if ~(nargin > 1 && keep_metadata)
prov = cifti_metadata_get(cifti.metadata, 'Provenance');
cifti.metadata = struct('key', 'Provenance', 'value', 'cifti_write_xml.m v2.2.3');
if ~isempty(prov)
cifti.metadata = cifti_metadat... |
ec5c7deef705132c6f9de73dbab4b6c19fd96a2e46dc80b243b2e09bd57e7592 | MATLAB | 18,184 | 444 | % EEG_INTERP - interpolate data channels
%
% Usage: EEGOUT = eeg_interp(EEG, badchans, method, t_range);
%
% Inputs:
% EEG - EEGLAB dataset
% badchans - [integer array] indices of channels to interpolate.
% For instance, these channels might be bad.
% [chanlocs structure] cha... |
f57d7a149bf0efb2f6087cdae1488ef9d696f215d1f2776181a6400fd2a30da0 | MATLAB | 18,200 | 484 | clearvars;
close('all');
clc
dropboxpath = '/Volumes/Seagate Backup Plus Drive/';
studypath = [dropboxpath 'SWITCH_EEG2'];
addpath([studypath '/scripts'])
fs = filesep;
datapath = sprintf('%s%sdata',studypath,fs);
fieldtrippath = sprintf('/Users/paulmk/Documents/MATLAB/toolboxes/fieldtrip-20180830/');
%f... |
ad6329d4fdf2229899553795fea3880efa9d9dcf4e5cf295bf2fa09eb2781097 | MATLAB | 18,225 | 537 | function plotFigureS2_divNorm10trial(behaviorPath)
% Process and plot data for figure S2. Plots divisive normalization model
% predictions for a trial integration window of 10. Plots conditional wait
% times for 20ul trials for experts, inference model, and 10 trial divisive
% normalization model. Plot sigmoid fit hi... |
e9742539759a2bbc5bd752e5f2565ba07507c8418dcae8768dafe1b482eab8fe | MATLAB | 18,230 | 515 | function akZoom_PR(handles, mButtons_ZoomPanReset)
% allows direct zooming and panning with the mouse in 2D plots.
%
% Default mouse button functions (can be customized, see below):
% Scroll wheel: zoom in/out
% Left Mouse Button: select an ROI to zoom in
% Middle Mouse Button: pan view
% Right Mouse ... |
95b887f22e3cd6d1e42274d42fb7bc13dd6b654ac5b142c976f3ecbdaf8936da | MATLAB | 18,236 | 368 | function spectralTrials(params, resp, triggers)
% given cell array resp{sess} of 2D data: [samples, ch] computes the STFT
% normalizes spectra to baseline time to compensate for the 1/f decay
% for each class & channel extracts + plots mean of trials
% the trials are cutted from triggers{1}.sampleSessLabel
% further, ... |
80eed79d7c03e774cabc21c0089d0010a7e57178b89aafd0b9dc4e3cb102ebec | MATLAB | 18,244 | 405 | % STD_PLOTTF - plot ERSP/ITC images a component
% or channel cluster in a STUDY. Also allows plotting scalp
% maps.
% Usage:
% >> std_plottf( times, freqs, data, 'key', 'val', ...)
% Inputs:
% times - [vector] latencies in ms of the data points.
% freqs - [vector] frequencies in Hz ... |
97ad3fa1a85a5cf4d8f67edb1b98bbd81bbae571872e4467e809e4efbd8cfa43 | MATLAB | 18,252 | 430 | function coactAnalysesReactPipeline(rootDir,sessionName,varargin)
load(fullfile(rootDir,sessionName,[sessionName '.basicMetaData.mat']))
reAnalyses=false;
for idx=1:length(varargin)/2
varName=varargin{2*idx-1};
varVal=varargin{2*idx};
switch lower(varName)
case lower('reAnalyses')
... |
7cf97538317248bf8dc2904e86d8c57a2546908d8044ecafbadaa9ddc5337037 | MATLAB | 18,264 | 461 | % POP_RESAMPLE - resample dataset (pop up window).
%
% Usage:
% >> [OUTEEG] = pop_resample( INEEG ); % pop up interactive window
% >> [OUTEEG] = pop_resample( INEEG, freq);
% >> [OUTEEG] = pop_resample( INEEG, freq, fc, df);
%
% Graphical interface:
% The edit box entitled "New sampling rate" contains the frequ... |
32c78197ae33f3a25a0768887f4591fb6abe9b2eca655601f0de95dcc1a5cc99 | MATLAB | 18,344 | 581 | function [BestFit_mf, BestFit_mb,...
BestFit_mb_lambda] = Figure3(datadir, codedir)
%Figure3 - Computational modeling reveals distinct value computations for
% wait time and trial initiation
% datadir = directory of dataset
% codedir = director of code
%% Set up paths
s = pathsep;
pathStr = [s, path, s];
onPa... |
149d3d3499795efeec78a09bdca6f887bea0ae592dcb73f465c3e93d1674c79a | MATLAB | 18,354 | 289 | % POP_IMPORTDATA - import data from a Matlab variable or disk file by calling
% IMPORTDATA.
% Usage:
% >> EEGOUT = POP_IMPORTDATA; % pop-up a data entry window
% >> EEGOUT = pop_importdata( 'key', val,...); % no pop-up window
%
% Graphic interface (refer to a previous version of the GUI):
% "D... |
b4e6386882cc311b86623451c00a15cbc896280a0d94984f92fc5495c7bb8142 | MATLAB | 18,370 | 365 | %% jobSDAT.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imag... |
ede411bcef2625b759cb0c11e2d527a9dd07326af25e7a18baf7e1fc964b7fde | MATLAB | 18,422 | 419 | function [map,num,typ] = brewermap(N,scheme)
% The complete selection of ColorBrewer colorschemes (RGB colormaps).
%
% (c) 2015 Stephen Cobeldick
%
% ### Function ###
%
% Returns any RGB colormap from the ColorBrewer colorschemes, especially
% intended for mapping and plots with attractive, distinguishable colors.
%
% ... |
60d8155befd627967f807efc7c7fa6a30534fa2988bd45c20bf682b56a646211 | MATLAB | 18,434 | 483 | function TS_SimSearch(varargin)
% TS_SimSearch Nearest neighbors of a given time series from an hctsa analysis.
%
% Nearest neighbors can provide a local context for a particular time series or
% operation.
%
%---(OPTIONAL) INPUTS:
% targetID, the ID of the target time series or operation
% tsOrOps, 'ts' (for time ser... |
741da0b8ecfb36d4ca68b0cfb7ee4e81e4831ef178f46aba27bf543f8ee3a5e1 | MATLAB | 18,440 | 519 | function [Out1, Out2, Out3] = fastica(mixedsig, varargin)
%FASTICA - Fast Independent Component Analysis
%
% FastICA for Matlab 7.x and 6.x
% Version 2.5, October 19 2005
% Copyright (c) Hugo Gävert, Jarmo Hurri, Jaakko Särelä, and Aapo Hyvärinen.
%
% FASTICA(mixedsig) estimates the independent components from given
% ... |
fc2c7085f74fd56f7621cbf6adde8e9c84182a0746e18438da8d7bf93aaf4f26 | MATLAB | 18,449 | 63 | function map = twilight(N)
% Perceptually uniform cyclic colormap from MatPlotLib.
%
% Copyright (c) 2015 Bastian Bechtold
% Copyright (c) 2017-2020 Stephen Cobeldick
%
%%% Syntax:
% map = twilight
% map = twilight(N)
%
% Colormap designed by Bastian Bechtold.
%
% Cyclic colormaps are designed for plotting data that ... |
2c8e3ddccb732afbc000a94d636734fdad7ef3a61b942c7158fb03a85b736794 | MATLAB | 18,547 | 539 | function glm_nsdsynthetic(ppdir,ppdirname,designfile,hrfbasisfile,tr,glmdirname,hrfmanifoldfile)
% notes:
% - inherit from glm_nsd.m
% - went through and did minimum necessary changes to get it to work.
% the code will eventually have to be modularized and generalized!
glmdir = regexprep(ppdir,'ppdata',glmdirn... |
5d8049bf89ab181a87f6f734792ed989d3135a1d493fa286fa7751f506502fdf | MATLAB | 18,552 | 548 | % function rippleDetection7(lfpFile,chList,[options])
% detect ripples from .lfp file, use ripple band power and sharp waves
%
% lfpFile: path of .lfp file
% chList: cell containing ch lists on each shank
%
% options (name and default values)
% param.nChTot=basicMetaData.nCh;
% param.nSample=basicMetaData... |
e125a03a53e5176c19a1999e4a8d3ad14479778e53e02d89facec46f71cf8f1d | MATLAB | 18,584 | 357 | %% jobSDAT.m
% This function describes an Osprey job defined in a MATLAB script.
%
% A valid Osprey job contains four distinct classes of items:
% 1. basic information on the MRS sequence used
% 2. several settings for data handling and modeling
% 3. a list of MRS (and, optionally, structural imag... |
88bb493fec79ad6bc2ad1fef507d3f5e4971aa991bdda19fa7bde794dfa89fa0 | MATLAB | 18,596 | 424 | function [n_best P_best V C]=fast_oopsi(F,V,P)
% this function solves the following optimization problem:
% (*) n_best = argmax_{n >= 0} P(n | F)
% which is a MAP estimate for the most likely spike train given the
% fluorescence signal. given the model:
%
% <latex>
% \begin{align}
% C_t &= \gamma*C_{t-1} + n_t... |
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