Hi
I am running analysis for MEG-data. I started the analysis a year ago and have only now returned to it. It seems that the Matlab-scripts that I have are no longer producing the same results as they did a year ago. I have problems with extracting values from scouts. I am using exactly the same scripts and data as in Spring 2023, but I no longer can get the same source information out. I only now tried to do "extract values" and I am using it for the same processed data as last year so the input files are exactly the same as previous.
For example, I want to extract values from 6 scouts (left and right for Fusiform, medial Orbitofrontal and lateral Orbitofrontal using Desikan-Killiany Atlas). I have done the source localization with minimum norm estimation using unconstrained orientation. For analysis I want to use the norm from the three orientations. I have below the screen shot of the Matlab script for extracting source values. I also tried it with the pipeline editor using the following steps:
( I tried to include screenshots but can't seem to get them to this text-editor)
I chose the following steps for pipeline-editor:
- Selecting the unconstrained source files that I have for 3 different stimulus conditions. Selected -- process sources -- run -extract -extract values:
- time-window: 400 ms - 600 ms
- Use scouts: (from Desikan-Killiany Atlas), clicked active the 6 scouts
- scout function: mean
- compute absolute values
- average time window
- concatenate time
Here is the same in script: (trying to get mean value for time window 400-600 ms for the 6 scouts)
% Script generated by Brainstorm (19-Apr-2024)
% Input files
sFiles = {...
'Subject21_2/average/results_dSPM-unscaled_MEG_GRAD_MEG_MAG_KERNEL_230303_1257.mat', ...
'Subject21_2/average/results_dSPM-unscaled_MEG_GRAD_MEG_MAG_KERNEL_230303_1300.mat', ...
'Subject21_2/average/results_dSPM-unscaled_MEG_GRAD_MEG_MAG_KERNEL_230303_1302.mat'};
% Start a new report
bst_report('Start', sFiles);
% Process: Extract values: [400ms,600ms] 6 scouts abs
sFiles = bst_process('CallProcess', 'process_extract_values', sFiles, [], ...
'timewindow', [0.4, 0.6], ...
'scoutsel', {'From volume: Desikan-Killiany', {'Fusiform L', 'Fusiform R', 'Lateral orbitofrontal L', 'Lateral orbitofrontal R', 'Medial orbitofrontal L', 'Medial orbitofrontal R'}}, ...
'scoutfunc', 1, ... % Mean
'isnorm', 1, ...
'avgtime', 1, ...
'dim', 2, ... % Concatenate time (dimension 2)
'Comment', '');
% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
% bst_report('Export', ReportFile, ExportDir);
% bst_report('Email', ReportFile, username, to, subject, isFullReport);
% Delete temporary files
% gui_brainstorm('EmptyTempFolder');
Previously with these selections (if I look at the results of extraction that was done last year): I did get one value for each 6 scouts and for each 3 stimuli. Show a 6 x 3 table. Now I get 18 x 3 table.
It seems that the selections don’t work similarly as previously. I only get values for the first selected scouts (Fusiform left and right) while all the other scouts are empty. Instead of one value for each scout I get 9 values for the first scout. They are labeled as: Fusiform_L1.1; Fusiform_L1.2, Fusiform L1.3, Fusiform 2.1, Fusiform L2.2, FusiformL2.3, Fusiform L3.1, Fusiform L3.2, Fusiform L3.3. After this it is the same for Fusiform_R. There is also column labeled time which has three rows: 1, 2, 3.
Could it be that it is extracting all the 3 orientations for each scout and somehow also presenting the results for the 3 stimuli multiple times?
How can I extract values for the selected scouts and time windows? How to set the selections so that I get norm of the orientations for each scout and also an average over a selected time window?
I have updated the Brainstorm, so it should be the latest version.
Thank you for your help!
-Elisa