Cannot find MEM in Compute Source [2018]

Bugs
1

Hi,

I'd like to use MEM for source loc of MEG data.
If I right click on the file, then --> compute source [2018], I can select MEM and it seems to work well;
If I try to call MEM from run --> sources --> compute sources [2018], I cannot find it. There does not seem to be the possibility to run MEM from here.

Any suggestion on how to solve this?

2

You have to use the process "Compute sources : BEST" instead.

3

Thank you Francois,

I don't seem to have this option. I can't find the "Compute source : BEST" anywhere.
The only possibility I have so far is to right click on the file and select MEM from there, but this is very inconvenient when you have hundreds of files to process.
I have updated brainstorm and MEM, but this does not seem to solve the issue.
Do you have any further recommendations?

Thanks again for your help

4

Hello Giovanni,
You should have it under the dipole scanning process in the Sources submenu.

Edouard

5

Thanks Edouard,

unfortunately I don't seem to have it there...
Any suggestions on how to have this process available?
Calling it from Matlab script is good as well, as long as I don't have to manually click for all the sources I have to compute.

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6

ok. that is weird.

Can you check that the brainentropy toolbox is loaded? Also, can you check that when you open Brainstorm you don't have a message saying "BST> Invalid plug-in function: "process_inverse_mem.m" ?

If you have that, can you check what is the output of "which process_inverse_mem" ? it should be .brainstorm/plugins/brainentropy/best-brainstorm-master/processes/process_inverse_mem.m

In case that helps, i ask brainstorm to generate the script that calls MEM process:

% Script generated by Brainstorm (31-Mar-2023)

% Input files
sFiles = {'... .mat'};

% Start a new report
bst_report('Start', sFiles);

% Process: Compute sources: BEst
sFiles = bst_process('CallProcess', 'process_inverse_mem', sFiles, [], ...
    'comment',     '', ...
    'mem',         struct(...
         'MEMpaneloptions', struct(...
               'InverseMethod', 'MEM', ...
               'automatic',     struct(...
                     'MEMexpert',   1, ...
                     'version',     '2.7.3', ...
                     'last_update', ''), ...
               'clustering',    struct(...
                     'neighborhood_order',   4, ...
                     'MSP_window',           10, ...
                     'clusters_type',        'static', ...
                     'MSP_scores_threshold', 0), ...
               'optional',      struct(...
                     'TimeSegment',     [-20, 30], ...
                     'groupAnalysis',   0, ...
                     'Baseline',        [], ...
                     'BaselineHistory', {{'within'}}, ...
                     'display',         0, ...
                     'BaselineSegment', [-20, 0]), ...
               'mandatory',     struct(...
                     'pipeline', 'cMEM'), ...
               'model',         struct(...
                     'active_mean_method', 2, ...
                     'alpha_method',       3, ...
                     'alpha_threshold',    0, ...
                     'initial_lambda',     1), ...
               'solver',        struct(...
                     'spatial_smoothing',  0.6, ...
                     'active_var_mult',    0.05, ...
                     'inactive_var_mult',  0, ...
                     'NoiseCov_method',    2, ...
                     'Optim_method',       'fminunc', ...
                     'parallel_matlab',    1, ...
                     'NoiseCov_recompute', 1))), ...
    'sensortypes', 'EEG');

% 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');
7

Thank you so much

  1. yes, brain entropy toolbox is loaded
  2. yes, you are right, I just noticed the message "BST> Invalid plug-in function: "process_inverse_mem.m"
  3. which process_inverse_mem gives me the following: '/Users/GPellegrino/.brainstorm/process/process_inverse_mem.m'

So I have deleted that old process (probably I kept it from the time I was in Montreal) and now it seems to be ok. Thanks a lot for your help

Giovanni

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