sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8669a6c93da0fcb11ef94e3131534db410b86935486ff56bc5562c9d9d3d2d6f | MATLAB | 3,176 | 151 | %% Load this function in Cell Mode and read the code for example usage
clear
%Fit a noisy measurement with a spline
x = (0:.5:10)';
y = sin(x*pi*.41-.9)+randn(size(x))*.2;
%Triple knots at the end
knots = [0,0,0,0:10,10,10,10];
%Least squares fit for the weights of a spline
s = fastBSpline.lsqspline(knots,3,x,y);
clf... |
ff607c35d6ece50a0bbc0b43f5eb151f80425d55ecef637362b7350c192621b0 | MATLAB | 3,183 | 83 | classdef selectRoisGui < handle
properties
% The GUI is associated with an acq2p object, and specifically one
% slice in that object:
acq = Acquisition2P.empty;
slice = 1;
% Structure for all handles:
h = struct('fig', [], 'ax', [], 'img', [], 'ui', [], 'time... |
9e6662ae7497a8a4b7e357b94010cd6f09bc38d0076580dca678857c03f6fd83 | MATLAB | 3,200 | 58 | %% Variable declaration
%%%%%%%%%%%%%%% FOV and PATTERN parameters %%%%%%%%%%%%%%%
Grid.pxsize = 10; % Pixel size in nm (scalar)
Grid.pxnum = 1280; % Pixel count on axis (integer)
Pattern.shape = {"microtubules","microtubules"}; %"mithocondria","mithocondria" "microtubules","microtubules" Pattern shape: ci... |
9773858d2fc1282e4ed95bd1a41aed56900fb00cfbf33fc7bf239ce633079703 | MATLAB | 3,206 | 108 | function playMov(mov)
% playMov(mov) displays a H-by-W-by-nFrames array as a movie, similar to
% ImageJ. Clicking any spot in the image jumps to the frame at which the
% clicked point is brightest.
%
% To do:
% - Implement play button
% - align activity trace to slider.
mov = downsampleWithAvg(mov, 10);
% Display fi... |
cb34ff35a5f871680c57e82af78e4863ef2f9196628a816e085721f775f67453 | MATLAB | 3,274 | 58 | %% Variable declaration
%%%%%%%%%%%%%%% FOV and PATTERN parameters %%%%%%%%%%%%%%%
Grid.pxsize = 10; % Pixel size in nm (scalar)
Grid.pxnum = 1280; % Pixel count on axis (integer)
Pattern.num = 50;
Pattern.shape = {"DNAorigami"}; %"mithocondria","mithocondria" "microtubules","microtubules" Pattern shape: ci... |
4e0da1e9022a35f5c596cc5bc66fe144c6b150e52b7f977a66a76a2929975bc2 | MATLAB | 3,291 | 91 | %% csf mobility all subjects
%% purpose
% 1) plot average of ADC as it moves from 0
% 2) plot average of FA as it moves from 0
% 3) violinplot of ADC average as steps
% 4) violintplot of FA average as steps
% 5) statistical comparison
clear;
% Define project parameters
project_directory = '/exports/gorter-hpc/users... |
99830b548e02b643dcb8b895ecae0397dd92d5fa0f95b204820d3075c9c98517 | MATLAB | 3,331 | 95 | %% csf mobility all subjects
%% purpose
% 1) plot average of ADC as it moves from 0 for different cross sectionals
% 2) bar plots for ratings
% 3) statistical comparison
clear;
% Define project parameters
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
fig = 'donut02... |
fd0fde9ccbefda19a0a6ee439bf47ad1d120853f2e3663f4ea562bf1ac61c12c | MATLAB | 3,337 | 80 | function plotNeuropilTraces(sel, bodyInd, neuropilInd, isIndInNhCoords)
if ~exist('isIndInNhCoords','var') || isempty(isIndInNhCoords)
isIndInNhCoords = true;
end
%Load cell body and neuropil fluorescence
mov = sel.movMap.Data.mov;
if isIndInNhCoords %if currently in neighborhood coord
movIndBody = sel.nh2mov... |
674897c9e468eda3c8ba450bba95fad405c2bb05f905a9dcf10b056742139b6b | MATLAB | 3,417 | 63 | %% function, third party function from sofi-tool
function photons=brightness(Ion,Ton,Toff,Tbl,frames)
%Simulate the intensity trace of an emitter (photons per frame).
%
%Inputs:
% Ion maximum signal per emitter per frame [photons]
% Ton average duration of the on-state [frames]
% Toff average du... |
613c27e255484c4668472bc7ee9543b800e1d00ef524212c26640d0faa2def27 | MATLAB | 3,454 | 99 | function calcPxCovBin(obj, movNums, radiusPxCov, temporalBin, sliceNum, channelNum, writeDir)
% calcPxCov(obj, movNums, radiusPxCov, temporalBin, sliceNum, channelNum,
% writeDir) Function to calculate all pixel-pixel covariances within a
% square neighborhood around each pixel. Size of the neighborhood is
% radiusPxCo... |
1497ed319420b2bc7f1438cf6949f1e8b579c23f93213c08c8cc5286a8d72319 | MATLAB | 3,475 | 107 | %% calculating eigenpairs (λ1e1, λ2e2, λ2e2) (will give all principal diffusivity and orientation)
% nina fultz nov 27th, 2025
clear
close all
GENERALDIR = 'R:\- Gorter\CSF_STREAM\Data\';
newFolder = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\';
physioFolder = '\Cardiac\T2prep';
subject = dir... |
eedc39ff74db124ebb59acfb881f8b0d348073b5907a4eb0cc34217dcedafa1a | MATLAB | 3,609 | 98 |
function plotDonutBarPlots(filename, col_right, col_left, categories)
%%
% Read the Excel file
data = readtable(filename, 'FileType', 'spreadsheet'); % Reads .xlsx file
% Initialize counts for each category
category_counts = zeros(1, length(categories));
% Store category data for statistical te... |
e872c39ffda90d24cfb16cb6d72b564dadb9dd8878fc22e37e91edb4cc9299f2 | MATLAB | 3,630 | 106 | function [traces, rawF, roi, traceNeuropil] = ...
extractROIsBinWithEdgeSubtraction(obj,roiGroups,sliceNum,channelNum)
% Function for extracting ROIs from movies using grouping assigned by
% selectROIs. This function uses a memorymapped binary file of the entire
% movie, as output by indexMovie. See extractROIsTIFF... |
9c39ea336c4286d269333cd35a2b2c2f56b6878edc46ca5807a307bc1b537a25 | MATLAB | 3,722 | 122 | %% CAMERA CALIBRATION
% This script evaluates the offset and gain maps of a digital camera
% according to the procedure reported in [1]. Other useful information for
% an accurate gain calibration can be found in [2].
%
% Please, be aware that some sCMOS cameras have two gain regimes (low and
% high intensity), i... |
8a30f24b6ec6dd19af81f6a3eb544ae706d222ea79cf4cac780cfb93aef12a71 | MATLAB | 3,802 | 88 | function newDir(obj,destDir,doCor,doInd,doCov,doNMF)
%Copies an acquisition and the associated motion corrected files from
%the original location to a new one, and creates a new acquisition
%object associated with the new location.
%
%newDir(obj,destDir,doCor,doInd,doCov)
%destDir is the directory to which files will b... |
d87786828139cf7974a0c33030dc521a93fa2f793275e68849a8318bf6016ccd | MATLAB | 3,804 | 102 | function t1s_to_niftis(subjPath);
% goal: convert adc and fa maps to niftis
% register t2 maps to the b0
%% Paths
regDir = fullfile(subjPath, 'reg');
anatFolder = fullfile(subjPath, 'anat'); % anat folder path
% Target file path
echo1File = fullfile(regDir, '*_properOrientation.nii');
% Check if the ... |
02d6ea7b2d883ce0fb5cf78a3fd0a765399dcd521ffbe1f24a228741d30cf8f3 | MATLAB | 3,805 | 115 | %% WRITEXMLREC Write a Philips XMLREC image file pair
%
% [SUCCESS] = WRITEXMLREC(FILENAME,DATA,INFO)
%
% FILENAME is a string containing a file prefix or name of the XML header
% file or REC data file, e.g. SURVEY_1 or SURVEY_1.XML or SURVEY_1.REC
%
% DATA is an N-dimensional array holding the image d... |
d50ad6982bff4fe704aaf14c86056e080918d4f10de8658923c43285e1504d3a | MATLAB | 3,828 | 103 | function T2maps_to_niftis(subjPath);
% goal: convert adc and fa maps to niftis
% register t2 maps to the b0
%% Paths
t2maps_path = fullfile(subjPath, 't2_maps');
regDir = fullfile(subjPath, 'reg');
fa = fullfile(subjPath, 'fa');
adc = fullfile(subjPath, 'adc');
anatFolder = ful... |
1baf4a3421835521a18d19ff5f3cf2a9c3d4d997d6da82403b0c4ced95bc243d | MATLAB | 3,831 | 99 | function adcValues = plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size)
%% Load Subject Data
subject_code = subject_list(1).name;
subjPath = fullfile(project_directory, project_name, subject_code);
ROIs_dir = fullfile(subjPath, 'ROIs');
reoriented_dir = fullf... |
68bed0d6c821b367def3c387721c57e5a5799e8bf6cd2a29e8e99bb58375f71b | MATLAB | 3,864 | 119 | function plottingADCandFAacrossPhasesAllSubjectsACA(physio, signal, physio_bin, roi_pvsas, ...
nPhases, phasesLoaded, roiName, subject_code);
cardiac = phasesLoaded;
%% Extract mean ADC or FA over phases for each ROI
if strcmp(signal, 'FA')
ymax = 1; ymin = 0;
else
ymax = 0.055; ymin = 0;
end... |
313e5f86c1251e0abadaf74cc8068096bb9047dc62b90b1cb2ebe5eea886a2e3 | MATLAB | 3,884 | 109 | % The light version of the SWI matlab tool, without GUI.
% script SWI_Duyn_ParRec
% to do SWI and unwrapping retrospectively on PARREC data
% default is kernel = 92 and SWI = 4
% please contact Emiel in case of problems
clc;
clearvars;
%% data info
% nrFiles = 1;
source_location = "R:\Emiel\PRIDE\pride_duyn\... |
5946a972987d1f9599672a9bb471e555cf9f23c5bfda48cf511e2c71e22d56a2 | MATLAB | 3,960 | 140 | function [Id,dpx,dpy, B] = doLucasKanade(T,I,dpx,dpy)
% Parts of the Lucas Kanade motion correction code were obtained from
% https://xcorr.net/2014/08/02/non-rigid-deformation-for-calcium-imaging-frame-alignment/
% and/or are originally based on the method published in:
% Greenberg, David S., and Jason N.D. Kerr. “A... |
2975bf0c0579d8ee163568e2664497b35b5bf948a3b72b11f4b12ce5883787cd | MATLAB | 3,997 | 133 | function plottingADCandFAacrossPhases(physio, signal, physio_bin, roi_pvsas, ...
roi_sas, nPhases, phasesLoaded)
cardiac = phasesLoaded;
%% Extract mean ADC over phases for each ROI
extract_roi_means = @(data, roi) cellfun(@(d) mean(d.data(roi)), data);
card_pvsas = extract_roi_means(cardiac, roi_pvsas);... |
2ba064454116eecd5f78cd5058275292aa6ae63d131a796dfabccc719b2b6937 | MATLAB | 4,032 | 111 | function acq = mjlmInitialization(acqId, rawFileLocation, acqName)
% acq = mjlmInitialization(acqId, rawFileLocation, acqName)
%
% acqId (formerly fileId) is some fragment of the file name of the current
% acquisition that is unique to the current acquisition.
%
% rawFileLocation is where the tiff files are located. Th... |
a1bfeb7f8297c2229d7196f78a76937e2a64e31e5f17531f9fc977a25f6069a3 | MATLAB | 4,121 | 95 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Help file for acq2pJobProcessor class.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% INTRODUCTION:
%
% acq2pJobProcessor (aka ajp) is a tool for automatic processing (motion
% correction, binary movie file and... |
25752f59435636e77a2ba889547f78d992c7dbea9004a55b7ddd728463fceada | MATLAB | 4,155 | 117 | %%% Peak Sorted Heatmaps: Spikes & Vm with SEM Shading
%%% Aanchal Bhatia
clear all; close all; clc;
load('D:\Recordings\Figures\paperLists\controlCells.mat')
% --- CONFIGURATION ---
SHIFT_BINS = 45;
SMOOTH_WIN = 5;
spkSort = []; spkPlot = [];
vmPlot = [];
cellCounter = 0;
for i = 1:length(control... |
c47a148ecd012439f5ef62e4c8a02ecbd21f39bf97de7104ccf16badc23fcfde | MATLAB | 4,235 | 130 | %% plotting Concentric Circles lydianes way
% csf donut protocol for CAA patients
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% goals:
clear
clc
%%
% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane'
scripts = fullfile(proj... |
330049ed9d4994d9160ee9225a3d3c63db7a74461ebab2627081c450d062a7ac | MATLAB | 4,266 | 111 | function calcPxCov(obj, movNums, radiusPxCov, temporalBin, sliceNum, channelNum, writeDir)
% calcPxCov(obj, movNums, radiusPxCov, temporalBin, sliceNum, channelNum,
% writeDir) Function to calculate all pixel-pixel covariances within a
% square neighborhood around each pixel. Size of the neighborhood is
% radiusPxCov p... |
56cc303aee8e175712e89031ef06ac934eff2de40ca2002514485f3796f4a1af | MATLAB | 4,271 | 120 | function plotDonutInvidualSubjects(project_directory, project_name, subject_list, roi_patterns, voxel_size);
roi_data = struct();
for roi_name = roi_patterns
roi_data.(roi_name{1}).ADC = {}; % Cell array for variable-length ADC data
roi_data.(roi_name{1}).FA = {}; % Cell array for variable-length FA data
en... |
ccf87cf83756d114250b603f4366edf00f89617382a3c5662889fd65cf324a83 | MATLAB | 4,285 | 123 | function updateOverviewDisplay(sel, redrawAllRois)
%Helper function that updates the reference image with current ROI labels
if ~exist('redrawAllRois', 'var') || isempty(redrawAllRois)
redrawAllRois = true;
end
% % Redraw image if slider is used:
% if isfield(sel.h.ui,'sliderBlack') % Slider is not implemented in... |
be717ef8ccb6afd46d6818e6264f26780f3958c613ef071da3eb041fa541be1b | MATLAB | 4,335 | 118 | % Clear everything to ensure an empty environment before running
clear all
close all
clc
% Load the Calcium Model's data
load('Sim_TS_Less_Tunnelling.mat')
%% Specify the mesh points to track the calcium concentration in the model
% The tracking points can be changed by referring to the generated mesh in
% the Geom_... |
62a6842f2229b288d1b9384a241b5ad04af49e902f4e5f6a6f87f9cccbfb8415 | MATLAB | 4,359 | 107 | clear;
GENERALDIR = 'R:\- Gorter\CSF_STREAM\Data\';
newFolder = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\';
physioFolder = '\Cardiac\T2prep';
physio = 'cardiac';
threshold = 75;
allSubjects = dir([GENERALDIR '*20201014_Reconstruction']);
for s = 1:numel(allSubjects)
subject = allS... |
166587219e7706f70ec7f42c4d9630d048197baa9100ceb53d0d64ff655f283f | MATLAB | 4,406 | 99 | %% This is an example script for creating a training set for RESURF (or any other AI method)
% In this script, user defines the range of different input parameters
% Settings/BaseSettings_MISRGRU.m includes other default parameters (basesettings_path)
% Inputs:
% seed: seed for the random generator
% mainpath: fol... |
16e21260aa55287ce2aaae19ce88230d7fd42bc80f81f11626f1c3dbc70b1f9c | MATLAB | 4,434 | 117 | function [gt_convolved] = gtGen_v2(emitter_dist, GroundT, Param, savepath, folname, plotfig, useGPU)
% Function that convolves the emitter distribution and apply the necessary
% down/upscaling to create ground truth noise free data
% downsamples the fine-grid to match the image in camera plane and
% upsamples to match... |
90c5145c5bf59c4a1419dfa7201f4d0478824b5782bc810501f23a2754e2c4e0 | MATLAB | 4,466 | 141 | function t2star_venogram(project_directory, project_name, subject_code);
%t2star_venogram
% Define the switch block for subject-specific operations
switch subject_code
case 'csfdonut01'
subject_code = '';
common_prefix = 'T2star_3D_0.6_lowPNS';
case 'test'
... |
8992216521e21944d15c824691a582baeb659d947e72753c6284c415f12e15e0 | MATLAB | 4,480 | 115 | function [gt_convolved] = gtGen_v4(emitter_dist, GroundT, Param, savepath, folname, plotfig, useGPU)
% Function that convolves the emitter distribution and apply the necessary
% downscales the fine-grid to create ground truth by matching the FWHM and
% pixel size of the GT
% creates a GT folder including tiff files wi... |
e9d1e69bb1374138dfe0528e95076954101073b582537dda181ca5ccec865801 | MATLAB | 4,503 | 101 | %% This is an example script for creating a training set for RESURF (or any other AI method)
% In this script, user defines the range of different input parameters
% Settings/BaseSettings_MISRGRU.m includes other default parameters (basesettings_path)
% Inputs:
% seed: seed for the random generator
% mainpath: fol... |
d2bd8c524b25cdebda8d58cd4357a94a2df35f8f389e3f1f74dc5fa45258f72c | MATLAB | 4,631 | 302 |
%%
%model normal learning
%plot auditory vs. spatial weight
load model_chem_control.mat
rmsd_all=[];
for qq=10
load mod2lp_control_result
parm_results2=parm_results;
parm_results2(:,2:4)=parm_results2(:,2:4)/10e7;
qq=parm_results(qq,1);
param=parm_results(qq,2:5);
... |
d68ac94136a4d92de84efb4e6c51592e9fedf8bf3184841ef75e5eab5b15b959 | MATLAB | 4,640 | 110 | function calcSeedCovBin(obj,radiusPxCov,seedBin,temporalBin,sliceNum,channelNum,writeDir)
%Function to calculate sparse pixel-pixel covariances at an array of seed
%points distributed throughout an image.
%
% calcSeedCov(obj,movNums,radiusPxCov,seedBin,temporalBin,sliceNum,channelNum,writeDir)
%
% radiusPxCov - radius... |
5d70a260df874688ac6e2323dc4053b24a906822b2a340162be6a2eff4d733e5 | MATLAB | 4,670 | 144 | function plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size)
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile(project_directory, project_name, subject_code);
ROIs_dir = fullfile(subjPath, 'ROIs');
reoriented_dir = f... |
63e990bfe0fd02f65a47cf9f5e9bc2ff3c02f349adfaf03caaf22fbc020a7c3c | MATLAB | 4,773 | 157 | function plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size)
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile(project_directory, project_name, subject_code);
ROIs_dir = fullfile(subjPath, 'ROIs');
reoriented_dir = f... |
f794db81d593151b03ddfb32b54543ba2f2c0cb7a6ba617aab7b5964a1dcd9ae | MATLAB | 4,793 | 126 | % Clear everything to ensure an empty environment before running
clear all
close all
clc
% Load the Calcium Model's data
load('Sim_TS_Tunnelling.mat')
%% Specify the mesh points to track the calcium concentration in the model
% The tracking points can be changed by referring to the generated mesh in
% the Geom_Mesh ... |
06c1c7dd4ac2e4e20d81fcc1600996b0e9ea1ad2123d3f6826c32a8ef5910750 | MATLAB | 4,799 | 126 | % Clear everything to ensure an empty environment before running
clear all
close all
clc
% Load the Calcium Model's data
load('Sim_TS_No_Tunnelling.mat')
%% Specify the mesh points to track the calcium concentration in the model
% The tracking points can be changed by referring to the generated mesh in
% the Geom_Me... |
b8b61961a7a2fd25be918fe7cdeb6c24898928523c3def64ad2619fa2222ad16 | MATLAB | 4,815 | 247 |
%%
%Evaluate Model A--use cum all perf -independent 2 loops, with random noise
%plot fit performance
load mod2lp_control_result
parm_results2=parm_results;
parm_results2(:,2:4)=parm_results2(:,2:4)/10e7;
rmsd_all=[];
for qq=1:size(parm_results,1)
qq=parm_results(qq,1);
param=parm_results(qq,2:... |
1d83f4aecf534c2b2ee88f5096ddaac8f444f646b6940b0b99bbed3675455f88 | MATLAB | 4,864 | 103 | function fcMagnitude = computeNetworkMagnitude(fc_square, net_ids, subjects, task_type, align_type, curr_parc)
% computeNetworkMagnitude Per-subject FC "strength" (magnitude) for each network combination.
%
% RECONSTRUCTED FILE — the original was missing from the release. Please
% review against your archived outp... |
94336b52bf6fa61a282e6ae35a24617184b106e92a476c9f467bcfa1ea175a94 | MATLAB | 4,867 | 149 | function [trialData, trl] = ft_GenTrialData(dsname, varargin)
% ft_GenTrialData
% Trial definition + preprocessing for MEG data recorded on CTF systems (.ds).
% Uses FieldTrip to define trials based on an event label,
% then applies optional baseline correction, line-noise DFT filtering, and
% band-pass filtering.
%
% ... |
7ab4b99283ba50e5e300be81bc1b427c46120d9b9068869b8d0431f4409485e6 | MATLAB | 4,876 | 126 | function plotDonutMeans(project_directory, project_name, subject_list, roi_patterns, voxel_size);
roi_data = struct();
for roi_name = roi_patterns
roi_data.(roi_name{1}).ADC = {}; % Cell array for variable-length ADC data
roi_data.(roi_name{1}).FA = {}; % Cell array for variable-length FA data
end
num_rois =... |
a41dfae78766ab9121a3bfc931a09d03620e15a8a0d1fb768bd53d938e46eb8b | MATLAB | 4,876 | 140 | function [cleanedData, artLog] = ft_CleanTrials(data, varargin)
% ft_CleanTrials
% Deterministic, batch-friendly trial rejection for MEG/EEG raw data.
% Rejects trials based on:
% 1) absolute amplitude (max |x|)
% 2) robust z-score (max |(x-median)/MAD|)
% 3) temporal gradient (max |diff(x)|)
% 4) presence of N... |
1f5b342f6bf8d2d7b0d996fe9cf92dffc0c3772fbec24206a479030da19542bf | MATLAB | 4,935 | 140 | function [cleanedData, artLog] = ft_CleanTrials(data, varargin)
% ft_CleanTrials
% Deterministic, batch-friendly trial rejection for MEG/EEG raw data.
% Rejects trials based on:
% 1) absolute amplitude (max |x|)
% 2) robust z-score (max |(x-median)/MAD|)
% 3) temporal gradient (max |diff(x)|)
% 4) presence of N... |
62efd01c3b22f37269dddfc656889e3575d731be5183c799cba5cc3b981828a2 | MATLAB | 4,935 | 148 | function cbMouseclick(sel, objClick, ~, row, col)
%Allows selecting a seed location around which to perform clustering
%and select ROIs
persistent initialClusterNum
% Ignore if right click
if ~strcmp(get(objClick, 'SelectionType'), 'normal') %if right click
return
end
% Get current click location
if nargin < 4
... |
ab7d3b0cfacc4eacce96330557ec855859f1effc8f34798897be802f83551de6 | MATLAB | 4,943 | 149 | function plotADCandB0Valuesv5(project_directory, project_name, subject_list, roi_patterns, voxel_size)
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile(project_directory, project_name, subject_code);
ROIs_dir = fullfile(subjPath, 'ROIs');
reoriented_dir =... |
c7ff3d2a1120102e643590224fa215e436cece9884247c645dc9393f330725db | MATLAB | 4,958 | 117 | function [isc_herit, isc_herit_perm,isc_herit_jack] = runISCHeritability(curr_parc, base_dir, kinship, Subjects,alignType,dataType,isc_mz_id,isc_dz_id,isc_nz_id,scan_id,covari_motion,num_perm,fam_ids)
% --- USER CONFIGURATION (edit these for your own system) ---
desktop_dir = '/path/to/desktop'; % originally /Users/d... |
55f2699a7c1b44bd974a87074c581003ec07f7d1c73fb073a4213e2319af3d52 | MATLAB | 4,973 | 163 | function am2PInit(obj,movPath)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
if nargin < 2 || isempty(movPath... |
4cdd5112e96777ea74359e54e1fb6feb310b2ebb37b868e005f3d61553676b98 | MATLAB | 4,999 | 140 | function [blink_clean, Param] = ...
blinkPSF(Grid, Cam, Fluo, Optic, Params, plotfig, saveParam)
% Function that adds blinking to existing emitter locations and convolves
% with GT PSF
%
% Inputs:
% Grid struct
% pxsize scalar, size of pixels [nm]
% pxnum integer, amount of pixels on... |
37ac751230797c1ed9b284b1094fe58e4a245c8472afc5b56a76888849e6d961 | MATLAB | 5,065 | 157 | %% Running the rating analysis and plotting figures
%#ok<*HIST>
% Loading the clean and concatenated data
load("Data\Ratings.mat")
meana = mean(startlingness_all, 'omitnan'); % average startlingness rating for each sound
meane = mean(valence_all, 'omitnan'); % average valence rating for each sound
meanr = mean... |
5c6f46c38b5b75dea8f0278d34331ad87fc9949c8c71b31c9f65819148695dd9 | MATLAB | 5,091 | 121 | % Clear everything to ensure an empty environment before running
clear all
close all
clc
% Load the Calcium Model's data
load('Sim_TS_Tunnelling.mat')
% Specify the simulation time step used
plot_time = zeros(num_t+1,1);
plot_time(1) = 0;
plot_time(2:num_t+1) = time;
% Write the video destination and file name for ... |
62614de6358d018708cd3da126288588b9219ffc391293f1d13e51656096472b | MATLAB | 5,148 | 145 | function createAcquisitionObjects(folder,forceOverwrite)
%createAcquisitionObjects.m Looks through folder and creates acquisition
%objects to be processed
%
%INPUTS
%folder - folder to look through
%
%ASM 11/14
if nargin < 2 || isempty(forceOverwrite)
forceOverwrite = false;
end
if nargin < 1 || isempty(folder)
... |
404758469f9f9a7774cb2394252c66cc316be926633775b4d0eca0fc412a1cea | MATLAB | 5,150 | 151 | function indexMovie(obj, nSlice, nChannel, writeDir)
%Function for creating a single large binary file containing an entire
%movie for a given slice/channel, allowing rapid, indexed access to pixel
%values. Needed to view ROI traces online within selectROIs GUI.
%
%indexMovie(obj,nSlice,nChannel,writeDir)
%
%writeDir i... |
33b574a5422d7c144222270d13eab84243b03b044cdfd9716f0c336b593161f2 | MATLAB | 5,154 | 144 | % csf donut protocol for CAA patients
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% goals:
% output: in your CCDir you are going to get a nifti called: 'vesseltoCheck_ALL.nii'
% you will have to manually change that vessel mask, and then also split it
% into M1, M2, and ACA sections.
% name these files: '... |
83e1a875c6c41644ac334fbd158d1eaa1e66b894e698bb564b078059871e7dde | MATLAB | 5,236 | 152 | function adc_and_fa_masking_reorientating(subjPath, subject_code, ADC_map_avg, FA_map_avg);
% goal: convert adc and fa maps to niftis, create frangi filter on inverted
% image
% register t2 maps to the b0
%% Paths
regDir = fullfile(subjPath, 'reg');
fa = fullfile(subjPath, 'fa');
adc =... |
309241dac6b5773e6c0909f4e6e14ec83fad9a16aa0346f87a5f3175ab7b6e9b | MATLAB | 5,267 | 129 | function cbKeypress(sel, ~, evt)
%Allows interactive selection / manipulation of ROIs. Possibly keypresses:
% 'tab' - Cycles through selection of each cluster in seed region as current ROI.
% 'f' - loads fluorescence trace for currently selected ROI, can be iteratively called to display multiple traces within single se... |
e121b30f732068ee867a82832a3bd1199adb7b62c79bc021c92a57322e3eaece | MATLAB | 5,337 | 157 | function plottingADCandFAacrossPhasesAllSubjects(physio, signal, physio_bin, roi_pvsas, ...
roi_sas, nPhases, phasesLoaded, roiName, subject_code);
cardiac = phasesLoaded;
%% Extract mean ADC or FA over phases for each ROI
if strcmp(signal, 'FA')
ymax = 1; ymin = 0;
else
ymax = 0.055; ymin = 0;... |
a76c9076759ca65eab8d33c8a85d83064d755e3ed79cbf3cd6aca4732f5f7fb3 | MATLAB | 5,453 | 155 | function [ADC_map_avg, FA_map_avg] = ADCandFAmaps_to_niftis(subjPath, subject_code);
% goal: convert adc and fa maps to niftis
% register t2 maps to the b0
%% Paths
regDir = fullfile(subjPath, 'reg');
fa = fullfile(subjPath, 'fa');
adc = fullfile(subjPath, 'adc');
anatFolder = ful... |
763bad367c55e1278ea0581fc1a684de76054d5dea309dadf11de9d7e5f1fa3d | MATLAB | 5,525 | 145 | function motionCorrect(obj,writeDir,movieOrder,motionCorrectionFunction,namingFunction)
%Wrapper function managing motion correction of an acquisition object
%
%motionCorrect(obj,writeDir,motionCorrectionFunction,namingFunction)
%
%writeDir is an optional argument specifying location to write motion
% corrected data ... |
ecc2b6ad7579aaa49af7a31b8db135a8759442344d574aa7bba7e8fead8d10f4 | MATLAB | 5,556 | 194 | % csf donut protocol for CAA patients
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% output: mask of vasculature tree
clear
clc
%%
% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane'
scripts = fullfile(project_directory, '... |
2f1c55f1b4c5bd5f0cc1ff37aec77589f872f6c4a91584f59a60e4051e20123c | MATLAB | 5,659 | 263 | %%
%Simulate multiple CNO effect levels
load mod2lp_control_result
load model_chem_control.mat
parm_results2=parm_results;
parm_results2(:,2:4)=parm_results2(:,2:4)/10e7;
% figure;
% hold on;
figure
hold on;
for cnoeffect=[0.75 0.5 0.25];
% cnoeffect=0.56;
perfday=zeros(39,5,2);
for qq=1:size(p... |
7997edc71876ac6327ef1cff56df98320f8c7deb16a6d498c549d54c1ea9d8cf | MATLAB | 5,712 | 170 | function [trialData, trl] = ft_GenTrialData(dsname, varargin)
% ft_GenTrialData
% Trial definition + preprocessing for MEG data recorded on CTF systems (.ds).
% Uses FieldTrip to define trials based on an event label (e.g., EMG2/EMG3),
% then applies optional baseline correction, line-noise DFT filtering, and
% band-pa... |
1d1a95d57b9adecad6f26b5d37a6d57eb70844f8723ef9864a26dc30791989ba | MATLAB | 5,828 | 216 | function [upperEnv,lowerEnv] = envelope(x, n, method)
%ENVELOPE Envelope detector.
% [YUPPER,YLOWER] = ENVELOPE(X) returns the upper and lower envelopes of
% the input sequence, X, using the magnitude of its analytic signal.
%
% The function initially removes the mean of X and restores it after
% computing t... |
3f85b2565c5047a0082b5c5b3e6d162e752ab53c8cfb68ee5ca0acaa2c4dfda9 | MATLAB | 5,851 | 397 | function [img info] = metaImageRead(info, varargin)
%METAIMAGEREAD Read an image in MetaImage format
%
% IMG = metaImageRead(INFO)
% Read the image IMG from data given in structure INFO. INFO is typically
% returned by the metaImageInfo function.
%
% IMG = metaImageRead(FILENAME)
% Rea... |
5d293c4d0c9320e1174e4ed22f531992e2d78fbf8cb932a505ef31b52bd36b73 | MATLAB | 5,869 | 191 | function plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size, adc_map);
%%
% Inputs:
% project_directory
% project_name
% subject_list
% roi_patterns
% voxel_size
% adc_map
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile... |
23f5e3fa789ae24673ba31b4ffee68f54aac2788c287ba6c3a42b3f72451f871 | MATLAB | 5,963 | 141 | %% This is function to simulate multiple experiments with a same underlying pattern and blinking
% Only the noise and background level will change. The image sequence with
% the highest SNR will include 1000 frames to reconstruct common SOFI target and the rest will have 20 frames
% It will save the videos in 'Noisy' ... |
0ee72928e34301327f201b09883f255e84bb29ed17e38bc0d37fe5cb506b0bd2 | MATLAB | 6,024 | 192 |
clear; clc;
%% plot to show csf mobility ring around vessel and then SAS - M1 and M2
% Define paths
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scripts');
addpath(genpath(fullfile(scripts, 'Violinplot-Matlab-master')));
addpat... |
3fcf930c18f4dda37dfcb97e45c449e2c5de27d12f5de42380a7f1d9289006b3 | MATLAB | 6,091 | 164 | function plotDonutFAMeansB0Meanplotted(project_directory, project_name, subject_list, roi_patterns, voxel_size);
roi_data = struct();
for roi_name = roi_patterns
roi_data.(roi_name{1}).ADC = {}; % Cell array for variable-length ADC data
roi_data.(roi_name{1}).B0 = {}; % Cell array for variable-length FA data
... |
52243ff68a199e5ceaaf2912adbfd5fe3736e1e3c1cb479111ee8dc718135488 | MATLAB | 6,101 | 164 | function plotDonutMeansB0Meanplotted(project_directory, project_name, subject_list, roi_patterns, voxel_size);
roi_data = struct();
for roi_name = roi_patterns
roi_data.(roi_name{1}).ADC = {}; % Cell array for variable-length ADC data
roi_data.(roi_name{1}).B0 = {}; % Cell array for variable-length FA data
en... |
033c2901e2c0b571026a5fe8a5a44020ad39dbb800b6201bf999a37f51976a5c | MATLAB | 6,116 | 128 | classdef Acquisition2P < handle
%Class definition file for Acquisition2P class
%Includes constructer methods, and functions for reading raw (readRaw) or
%corrected (readCor) tiff's associated with acquisition
%
%obj = Acquisition2P;
%obj = Acquisition2P('acqName');
%Acquisition2P('acqName',@... |
17d05e083c1b9bdafa29bbdbfa595e3338dcd1d7d48e07df86e251c892a593f7 | MATLAB | 6,124 | 131 | function [gt_convolved] = gtGen_movie(emitter_dist, GroundT, Param, savepath, folname, plotfig, useGPU)
% Function that convolves the emitter distribution and apply the necessary
% down/upscaling to create ground truth noise free data
% downsamples the fine-grid to match the image in camera plane and
% upsamples to ma... |
a26eac50dbf9eee7617d8d8b5148a18fc3390394e03efcc6260b486208ea995f | MATLAB | 6,141 | 217 | function getBaseline_ransac_demo(sel)
% Load cell body and neuropil fluorescence
mov = sel.movMap.Data.mov;
fBodyRaw = mean(mov(:, sel.acq.mat2binInd(sel.nh2movInd(sel.disp.indBody))), 2)';
fNpRaw = mean(mov(:, sel.acq.mat2binInd(sel.nh2movInd(sel.disp.indNeuropil))), 2)';
f = fBodyRaw - fNpRaw*sel.disp.neuropilCoef(2... |
e83c9a3198713cbc61a0c75b62b73fae4c295677c13eb711a2172f1fe2ca6e38 | MATLAB | 6,160 | 204 | function plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size, adc_map);
%%
% Inputs:
% project_directory
% project_name
% subject_list
% roi_patterns
% voxel_size
% adc_map
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile... |
4067c907c9d5bc9633613ff50809f16e6872c5f20cf5c0c8bcf6bf84d03e916d | MATLAB | 6,164 | 203 | clear; clc;
%% plot to show csf mobility ring around vessel and then SAS - M1 and M2
% Define paths
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scripts');
addpath(genpath(fullfile(scripts, 'Violinplot-Matlab-master')));
addpath... |
58587767483dc2d8d5d2098857906e59a61128bf211ab511808c7558aab862da | MATLAB | 6,224 | 165 | function plotDonutMeansB0plotted(project_directory, project_name, subject_list, roi_patterns, voxel_size);
roi_data = struct();
for roi_name = roi_patterns
roi_data.(roi_name{1}).ADC = {}; % Cell array for variable-length ADC data
roi_data.(roi_name{1}).B0 = {}; % Cell array for variable-length FA data
end
n... |
5f95ca07bead821e8e30a77ec639e0022099269ead0e8bb0b231dfa4f4523666 | MATLAB | 6,261 | 173 | function modifyAdapterFromCSV(adapterFile, csvFile)
% MODIFYADAPTERFROMCSV - Modify adapter parameters using a CSV file
%
% Usage:
% modifyAdapterFromCSV('myProjectNameAdapter.m', 'adapter_params.csv')
%
% CSV Format:
% Parameter,Value,Type,Description
% sigma,0.7,numeric,A... |
5d14d20c891e71672dc1544de219263358551d109f5f6bd0e8762998e4ddd914 | MATLAB | 6,267 | 191 | % From the paper of DBlink, a microtubules generator that is based on the
% physical model of the paper: Shariff A, Murphy RF, Rohde GK.
% A generative model of microtubule distributions, and indirect
% estimation of its parameters from fluorescence microscopy images.
% Cytometry A. 2010; 77(5): 457 - 66.
%
% TU Del... |
a5753f83fd5e5f9bb793cf123066a5fc5aace42ebdf4c79f3eae49f1d56d8d65 | MATLAB | 6,291 | 174 | %% MAIN PROTOCOL FOR ECOMODEL CONSTRUCTION AND ANALYSIS
% This function performs a complete pipeline for constructing and analyzing
% an enzyme-constrained metabolic model (ecModel) using GECKO.
%
% Parameters (all optional via name-value pairs):
% project_name: Name of the project directory (string)
% input_folde... |
c79ce7a32d2a64e198e55118eb97a9d22ec0488302fc8baabf3c2a7cc6dc2e44 | MATLAB | 6,344 | 162 | %% Mesh Generation for the No Tunnelling Calcium Model with 2 Subdomains (Cytoplasm and ER)
% This is the code that generates the mesh of the Calcium Model (with
% interior boundary). This mesh generation code follows MATLAB's
% PDE Modeler User Guide.
% Clear everything to ensure an empty environment before running
... |
f40c2c6aac3d09e990c4dc502362c7a560e0716a14b4daf1b36cf6c962e912b5 | MATLAB | 6,383 | 131 | function [ADC,FA,VectorF,DifT,Y]=DTI(DTIdata,parameters)
% This function will perform DTI calculations on a certain
% DTI dataset.
%
% [ADC,FA,VectorF,DifT]=DTI(DTIdata,parameters)
%
% DTIdata: A struct containing DTIdata(i).VoxelData, DTIdata(i).Gradient
% and DTIdata(i).Bvalue of all the DTI dataset... |
6454768f5d56010b90d2822ae7d5ce48cdc9d0d923129830f90c20bf8365017f | MATLAB | 6,409 | 183 | % csf donut protocol for CAA patients
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% goals:
clear
clc
%%
% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane'
scripts = fullfile(project_directory, 'scripts', project_name);
%... |
5632476bd2a5be90fe3deae73a01d05de4ad1baf552c6e391c0d6e6ee5b96338 | MATLAB | 6,424 | 201 | function processCurrentAcq(ajp)
% Performs all processing of currently loaded acquisition.
%create cleanup obj
cleanupObj = onCleanup(@() moveBackToUnproc(ajp));
if ajp.debug
ajp.log('Skipping all processing because debug mode is on.');
return
end
% Ensure that default dir exists:
if ~exist(ajp.currentAcq.de... |
5157ffd7e12ffaa3561d4dc9bffcd1986b44135916532283ce9c8c2405b677e1 | MATLAB | 6,591 | 155 | %% plotting Concentric Circles lydianes way
% csf donut protocol for CAA patients
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% goals:
clear
clc
%%
% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project... |
a3908054e3af3a59b546118d656d3abb9abce65b6b5cbb76eedbef36f1b73c4b | MATLAB | 6,629 | 134 | function [VectorF1,VectorF2,VectorF3]=DTI_eigenpairs(DTIdata,parameters)
% This function will perform DTI calculations on a certain
% DTI dataset.
% it is going to extract lambda 1, 2, and 3
%
% [ADC,FA,VectorF,DifT]=DTI(DTIdata,parameters)
%
% DTIdata: A struct containing DTIdata(i).VoxelData, DTIdata(i).Grad... |
ab2bda012166a70319fc3b91a19a8273cc94deb0a9319f9c86240d6688ee5856 | MATLAB | 6,663 | 166 | %% Mesh Generation for the Calcium Tunnelling Model with 2 Subdomains (Cytoplasm and ER)
% This is the code that generates the mesh of the Calcium Model (with
% interior boundary). This mesh generation code follows MATLAB's
% PDE Modeler User Guide.
% Clear everything to ensure an empty environment before running
cle... |
2619a6d2c9fe9c395f52ee05fe050101b8aea2466aa0307669eb12c7cc97d0a3 | MATLAB | 6,687 | 155 | %% Script 2: Unification Analysis and Significance Group Bar Charts
clear all;
close all;
% --- 1. Load Clean Table Data ---
dataPath = 'PredictPlateaus\PlateauPrediction.mat';
if exist(dataPath, 'file')
load(dataPath, 'glmTable');
analysisTable = glmTable;
else
error('Run Script 1 first to creat... |
bb8bbf404ff267b4f463905fecbd10ecca621c9c698bcd072e0a51f5594ec1a4 | MATLAB | 6,764 | 221 | % csf donut protocol for t2 and csf mobility mapping
% nina fultz december 2024
% n.e.fultz@lumc.nl
clear
clc
%% goals:
%%
% defining paths
project_directory = '/exports/gorter-hpc/users/ninafultz/'
project_name = 'csfdonuts_lydiane'
subject_code = '20191029_Rec'
scripts = fullfile(project_dire... |
fea2e1d0d51ed1bb33acabe579f485ae490950e84480c3ed7c6e112af8ace296 | MATLAB | 6,790 | 173 | clear
close all
clc
GENERALDIR = '/exports/gorter-hpc/users/ninafultz/csf_donut/';
allSubjects = dir('/exports/gorter-hpc/users/ninafultz/csf_donut/csf*');
workingFolder = '/csf_donut/';
savingdir = '/reoriented/';
anatScanLoc = '/anat/';
anatScanLabel = '3dT1_0.9mm.nii';
templateLocation = '/exports/gorter-hpc/users/... |
1ad5d7caf9f28ead7308019918aeab5bbac0fd978e3f4409eba2ff86b21960ef | MATLAB | 6,830 | 191 | function [all_counts, short_counts, long_counts, all_plateau_times, short_plateau_times, long_plateau_times, dwell_times] = processEventsAroundAnchorDistance(...
anchor_starts, distance, reset, event_starts, event_durations, bin_size_m, ...
short_thresh_samples, speed, speed_threshold)
% Initialize parameters... |
76fd45ed9c786f5a0784194cfacdab1eb83331e17f80b08915de3d520c62fb51 | MATLAB | 6,964 | 157 | clear all
close all
FolderNameSt=uigetdir('','Y:\pressure_EMG_optogenetic');
FolderOffset=2;
listing1=dir(FolderNameSt);
if isempty(FolderNameSt)
return
end
n=1;
nn=1;
gap=2;
for folder_cnt=1:length(listing1)-FolderOffset
if listing1(folder_cnt+FolderOffset,1).isdir
FileName_0=list... |
30610d861c8fb2dfca3655f0cfbd88b2d1f4dff0caeb56a68113201c210d9b59 | MATLAB | 7,047 | 198 | name={'1'};
cc_peak_mouse=[];cc_all=[];cc_all_rand=[];
for mouseNum=1:size(name,2)
data1 = xlsread([name{mouseNum} '.xlsx'],1);
% data2 = xlsread('data1.xlsx',2);
%%%
testdata1=cell(1,size(data1,2));
for i=1:size(data1,2)
ind=~isnan(data1(:,i));
testdata1{i}=data1(ind,i);
... |
314cb210acf7f9264633fa62ff83ce1d8254f9c606d5c9cc390561c5b050b12b | MATLAB | 7,083 | 172 | %% Mesh Generation for the Less Tunnelling Calcium Model with 2 Subdomains (Cytoplasm and ER)
% This is the code that generates the mesh of the Calcium Model (with
% interior boundary). This mesh generation code follows MATLAB's
% PDE Modeler User Guide.
% Clear everything to ensure an empty environment before running... |
70ddb34f0e8fe292dcc7143da7a81de245c5b5c33ba6a48acbc9eecb58931de3 | MATLAB | 7,170 | 288 | function metaImageWrite(img, fileName, varargin)
%METAIMAGEWRITE Write header and data files of an image in MetaImage format
%
% metaImageWrite(IMG, FILENAME);
% IMG is a matlab array, and FILENAME is the generic name (without
% extension) of the metaimage file.
% The functions tries to determine which... |
59e395d866e5469e36653cdc006a3c693e29b72beb4a2b3184a229ad51bfd934 | MATLAB | 7,218 | 201 | function run_all_steps(varargin)
% run_all_steps
% Minimal runner for the MEG ROI-connectivity pipeline (FieldTrip-based).
% Runs (per subject): preprocessing/trials -> ROI time series -> wPLI+PSI
% Then (group): group means and optional CBPT.
%
% IMPORTANT
% - Keep only ONE FieldTrip on the MATLAB path (no addpath(gen... |
43b2ca522a1b1408743f49cb1ca5b85cd4674ae0845c6ff924449da4c24fa45a | MATLAB | 7,251 | 193 | %% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scripts', project_name);
%% params
binWidth = 0.45;
addpath(genpath(fullfile(scripts, 'csfdonuts_lydiane')));
addpath(genpath(fullfile(scri... |
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