rcassani
/ call_mini_epi_m.m
Created
February 5, 2026 19:26
Brainstorm: Example on using Brainstorm from Python
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| % This Matlab script calls the "mini_epi.m" which is a Brainstorm pipeline | |
| % Call is done unsing Matlab | |
| % | |
| % See also the equivalent Python script: "call_mini_epi_m.py" | |
| % | |
| % More details about "mini_epi.m" in the comments of that function | |
| % Full paths | |
| Brainstorm3Dir = '/home/rcassani/Desktop/brainstorm3'; | |
| TutorialDir = '/home/rcassani/Desktop'; |
rcassani
/ figure_popup_test.m
Last active
February 6, 2026 16:52
Matlab Java JPopupMenu remains open in R2023b and newer when using New Desktop
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| % Create figure with mouse up callback | |
| fig = figure('WindowButtonUpFcn', @FigureMouseUpCallback); | |
| % Create popup menu on click place on right click | |
| function FigureMouseUpCallback(hFig, ev) | |
| import java.awt.MouseInfo.getPointerInfo | |
| import javax.swing.JPopupMenu | |
| import javax.swing.JMenuItem | |
| if strcmpi(get(hFig, 'SelectionType'), 'alt') |
rcassani
/ save_bst_cnx_coh.m
Created
January 6, 2026 02:33
Save coherence spectra as .csv file. If time defined, one csv file per time sample
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| % 1. Load the contents of the coherence `.mat` file | |
| TfMat = in_bst_timefreq('Subject01/Simulation/timefreq_connectn_cohere_260105_1544.mat'); | |
| % 2. Get the coherence spectra for each pair of signals: [nSignalA*nSignalB, nTime, nFreq] | |
| R_3d = process_compress_sym('Expand', TfMat.TF, length(TfMat.RowNames)); | |
| [~, nTime, nFreq] = size(R_3d); | |
| % Handle the case of one time sample | |
| if nTime == 1 && length(TfMat.Time) == 2 | |
| TfMat.Time = mean(TfMat.Time); | |
| end |
rcassani
/ add_locs_cytoview24_for_bst.m
Created
August 11, 2025 18:48
Brainstorm: Add locations to electrodes in Axion CYTOVIEW MEA 24
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| % Script to add locations to electrodes in Axion CYTOVIEW MEA 24 for Brainstorm | |
| % | |
| % Simone Doad, 2025 | |
| % Raymundo Cassani, 2025 | |
| % | |
| % MEA channel names are composed of 4 characters that give the location information: | |
| % 1st char: WellRow = 1st index in 4D array, 'A', 'B',... = 1, 2,... | |
| % 2nd char: WellColumn = 2nd index in 4D array, '1', '2',... = 1, 2,... | |
| % 3rd char: ElectrodeColumn = 3rd index in 4D array, '1', '2',... = 1, 2,... | |
| % 4th char: ElectrodeRow = 4th index in 4D array, '1', '2',... = 1, 2,... |
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| % Brainstorm script | |
| % Cast a TimeFrequency file to a Data recording | |
| % TimeFreq file MUST have size [nChannels, nSamples, nFreqs] with nFreqs = 1 | |
| % This size can be obtained: | |
| % - From a TimeFreq file with the process Extract > Extract values | |
| % - Computing the TimeFreq file for only one frequency band | |
| % Input TimeFreq file | |
| timeFreqFile = 'Subject01/S01_AEF_20131218_01_600Hz_notch/timefreq_psd_231117_1140.mat'; |
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| % ICA variance explained | |
| %% Signals | |
| % Sound | |
| load chirp.mat | |
| nSamples = length(y); | |
| y = y'; | |
| % Create 10 signals | |
| y_noise = 0.4 * randn([9, nSamples]); | |
| F = [y; y_noise + repmat(y, 9, 1)]; |
rcassani
/ aggregate_volume_parcellations.m
Last active
July 7, 2025 15:46
Brainstorm, aggregate volume values per anatomical parcellation
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| % Brainstorm script to obtain the mean value for a Volume (PET or Neuromap) | |
| % for each of the parcellations in an anatomical parcellation (e.g. Desikan-Killiany) | |
| %% PARAMETERS | |
| % FileName for the Volume to use (Subject/VolFile) | |
| volFileName = 'sub-MTL0002/subjectimage_sub-MTL0002_ses-01_trc-18Fflortaucipir_pet_spm_reslice_volpet.mat'; | |
| % Anatomical parcellation | |
| volAtlasName = 'Desikan-Killiany'; | |
| %% COMPUTATION |
rcassani
/ fooof_parameters_brainstorm.m
Created
March 27, 2025 14:26
Understanding FOOOF parameters in Brainstorm
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| %% Understanding FOOOF parameters in Brainstorm, using one channel as example | |
| % This is based on the files from the FOOOF tutorial | |
| % https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof | |
| % | |
| % Raymundo Cassani, 2025 | |
| %% FIND PSD AND FOOOF FILES | |
| % Process: Select timefreq files in: Subject01/@rawS01_AEF_20131218_01_600Hz_notch | |
| sFiles = bst_process('CallProcess', 'process_select_files_timefreq', [], [], ... | |
| 'subjectname', 'Subject01', ... |
rcassani
/ example_sqlite_coalesce_bst_db.m
Created
March 21, 2025 16:42
SQLite COALESCE in Brainstorm DB
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| %% SQLite queries to Brainstorm database can be faster by using JOIN on tables | |
| % The existence of Raw and NoRaw Subjects complicates the JOIN as for | |
| % NoRaw subjects it is needed to copy some fields from the DefaultAnatomy | |
| % and this is done with the function COALESCE | |
| % However, using COALESCE, we must write down all the fields, as '*' is not supported | |
| % | |
| % See examples below | |
| %% Non-raw Subject | |
| % Keep only SQLite fields |
rcassani
/ project_eeg_sensors_on_scalp.m
Created
November 14, 2024 20:56
Brainstorm: Project EEG sensors on scalp for registered EEG caps and default anatomies
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| % Script for Brainstorm | |
| % For the provided anatomies ('testAnatomies'), find their already registered EEG caps | |
| % and adjust the location of the EEG sensor if request (isReplaceLocs) and if | |
| % one or more EEG sensors were moved more than ('distThreshold') millimeters | |
| % | |
| % Raymundo Cassani, 2024 | |
| %% ===== PARAMETERS ===== | |
| testAnatomies = {'Colin27_2016', 'ICBM152_2023b'}; | |
| isReplaceLocs = 1; |
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