Tutorial: Add cMEM estimates in tutorials

[Edouard2laire]

Hello,

As we will be merging multifunkim/best-brainstorm#13 soon, this PR update the script corresponding to cMEM of the two following tutorials:

• Add cMEM estimate to tutorial_epilepsy.m and add it to tutorial page:
  https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy

• Create tutorial_BEst.m which reproduces the steps in the updated Brain Entropy tutorial page:
  https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst
  This script the Introduction protocol computed with tutorial_introduction

[rcassani]

When trying to run the pipeline, running:

sAvgSrcMEM = bst_process('CallProcess', 'process_inverse_mem', sFilesAvg, [], ...

gives the error:

Line 16: fminusub
Objective function is undefined at initial point. Fminunc cannot continue.
_______________________________________________
Call stack: 
>fminusub.m at 16 
>fminunc.m at 488 
>be_minimize_free_energy.m at 56 
>be_solve_mem.m at 56 
>be_launch_mem.m>MEM_mainLoop at 185 
>be_launch_mem.m at 79 
>be_cmem_solver.m at 182 
>be_main_call.m at 157 
>be_main.m at 60 
>process_inverse.m>Compute at 696 
>process_inverse.m at 24 
>process_inverse_mem.m>Run at 139 
>process_inverse_mem.m at 24 
>bst_process.m>Run at 236 
>bst_process.m>CallProcess at 2316
>bst_process.m at 38

How can i update the MEM figure from the tutorial ? i would like to change it to

Firs,t login in the in the Brainstorm website, button at upper right corner.
(If you do not have an account, please send me an email, so I can give you the necessary info details on creating one)

After login, on the tutorial page to edit, go to the top navigatin bar, then Menu > Attachments.
Then update the tutorial, use this use this syntax:

{{attachment:sim_ar_spectra_metrics.png||width="100%"}}
More info on working with images on Moinmoin here: http://moinmo.in/HelpOnImages

[Edouard2laire]

When trying to run the pipeline, running:

sAvgSrcMEM = bst_process('CallProcess', 'process_inverse_mem', sFilesAvg, [], ...

gives the error:

Line 16: fminusub
Objective function is undefined at initial point. Fminunc cannot continue.
_______________________________________________
Call stack: 
>fminusub.m at 16 
>fminunc.m at 488 
>be_minimize_free_energy.m at 56 
>be_solve_mem.m at 56 
>be_launch_mem.m>MEM_mainLoop at 185 
>be_launch_mem.m at 79 
>be_cmem_solver.m at 182 
>be_main_call.m at 157 
>be_main.m at 60 
>process_inverse.m>Compute at 696 
>process_inverse.m at 24 
>process_inverse_mem.m>Run at 139 
>process_inverse_mem.m at 24 
>bst_process.m>Run at 236 
>bst_process.m>CallProcess at 2316
>bst_process.m at 38

Did you download the new MEM version https://github.com/Edouard2laire/best-brainstorm/archive/refs/heads/wMEM.zip?

this error is due to the fact that the script is having an error with the forward model

So for some vertex, G is 0 for all the sensors and it cause issue with MEM. I made the new version of MEM more robust to that multifunkim/best-brainstorm@9fe8740 but I guess we should also fix the forward model from the script :)

How can i update the MEM figure from the tutorial ? i would like to change it to

Firs,t login in the in the Brainstorm website, button at upper right corner. (If you do not have an account, please send me an email, so I can give you the necessary info details on creating one)

After login, on the tutorial page to edit, go to the top navigatin bar, then Menu > Attachments. Then update the tutorial, use this use this syntax:

{{attachment:sim_ar_spectra_metrics.png||width="100%"}} More info on working with images on Moinmoin here: http://moinmo.in/HelpOnImages

Thx. :)

[Edouard2laire]

also @rcassani, what do you think of the idea to move MEM just after sLoreta ? i think it make more sense to do all the Source analysis: Surface at the same time instead of sLoreta, then volume then back to surface with MEM

[rcassani]

I tried with the master branch on https://github.com/Edouard2laire/best-brainstorm which is the one used in Brainstorm when installing and updating the brainentropy plugin

About the order, I think we can move MEM after sLORETA. With its own section with the [Advance] label.

[Edouard2laire]

About the order, I think we can move MEM after sLORETA. With its own section with the [Advance] label.

ok. if I may, the tutorial editor is probably the worst editor i had to use to write text so far. Like, i think it can really remove the will to live to even the most joyous person...

Page took 20 minutes to save and is now full of conflict without even the slightest possibility to go back in time, that pasting doesn't work (what text editor doesn't support ctrl+c, ctrl+v???), or that the editor chooses randomly to put half of the page in bold without possibility to remove it if you select the link at the same time as text... or the attachment system!

[rcassani]

Indeed, writing in MoinMoin is a real pain, apologies for all the suffering.
Few pointers:

• Admin users can revert pages (let me know if you need to do so)
• The slowness things is not on MoinMoin side, but today's issue with the server
• It helps to edit the text without their fancy editor, but using the "Show Raw Text" editor

[Edouard2laire]

Hi @rcassani

it seems that the change in the BEM surface fcce1d7 to fix the warning about dipole outside the skull is making quite a difference in the inverse problem solution; including for sLoreta:

Do you know if that is correct ?

[Edouard2laire]

Indeed, writing in MoinMoin is a real pain, apologies for all the suffering. Few pointers:

• Admin users can revert pages (let me know if you need to do so)
• The slowness things is not on MoinMoin side, but today's issue with the server
• It helps to edit the text without their fancy editor, but using the "Show Raw Text" editor

Indeed, the raw text editor is much better ! :)

[Edouard2laire]

multifunkim/best-brainstorm#13 is now merged. The PR is now ready to be reviewed :)

[rcassani]

@Edouard2laire, to avoid duplication of code, and potential problems in maintenance.
I think for the tutorial_BEst.m we can use the same approach as in the brain fingerprint tutorial script, where it starts with an already processed Protocol.

• https://neuroimage.usc.edu/brainstorm/Tutorials/BrainFingerprint

• brainstorm3/toolbox/script/tutorial_brain_fingerprint.m

  Lines 63 to 68 in 6c646d2

  	%% ===== VERIFY REQUIRED PROTOCOL =====
  	% Check Protocol that it exists
  	iProtocolOmega = bst_get('Protocol', ProtocolNameOmega);
  	if isempty(iProtocolOmega)
  	error(['Unknown protocol: ' ProtocolNameOmega]);
  	end

So tutorial_BEst.m will look for the the 'TutorialIntroduction' and do the steps starting with L411:

%% ===== TUTORIAL #20: HEAD MODEL ====================================================
%  ===================================================================================

EDIT: Solved at 100d51f

[Edouard2laire]

Done :)

it's ready to review