Rap-music

[koffe]

Sylvain

I'll post the RAP-MUSIC errors and pictures here. I have updated with the full version.

this is in the message window:
http://homes.esat.kuleuven.be/~kdesmedt/pics/Image1.jpg

this is my screen when crash occurs:
http://homes.esat.kuleuven.be/~kdesmedt/pics/Image2.jpg

I did add the eegdata folder to the path (then channel.mat is found...). Other errors occur:

Co: 0.9998
Regularized: 0.9998
Filters a and b: 0.990 0.002 0.000 ; 0.990

qh_findbest: all neighbors of facet 59 are flipped or upper Delaunay.
Please report this error to qhull_bug@geom.umn.edu with the input and all of the output.

ERRONEOUS FACET:


While executing: | qhull d Qt Qbb Qc

Options selected for Qhull 2002.1 2002/8/20:
delaunay Qtriangulate Qbbound-last Qcoplanar-keep _pre-merge
_zero-centrum Pgood Qinterior-keep _max-width 3.5 Error-roundoff 4.8e-015
_one-merge 3.4e-014 Visible-distance 9.6e-015 U-coplanar-distance 9.6e-015
Width-outside 1.9e-014 _wide-facet 5.8e-014

Last point added to hull was p420.
Last merge was #5.



At error exit:



precision problems (corrected unless 'Q0' or an error)

5
coplanar horizon facets for new vertices

22
coplanar points during partitioning

---------
I can always try working with the raw files (channel loc, data..) or mat files you loaded and do exactly the same here...are you working with a warped phantom?

greets
koffe

[koffe]

Sylvain

Have been trying and trying.
Added some files in the path. Renamed some files.
Also on another computer with Matlab2006a instead of Matlab7....

This is the result, this seems to be correct and resembling your screenshot!

http://homes.esat.kuleuven.be/~kdesmedt/pics/bron1.JPG

It is a pity I cannot see this on my own computer, I still get the enormous big error of the erronous facet 59.............so strange.

greetings
koffe

[Sylvain]

This path problem should be fixed by properly declaring where your data is from the DataManager.

Make sure for example that files like test_ctfopt_esat_data.mat are in a subfolder of the path specified as the MEG/EEG data folder in your data manager.

For this, please type at the Matlab prompt after you have lauched BrainStorm

Users = get_user_directory;

You should get something like:

Users =
Comment: 'Koffe'
STUDIES: 'D:\Data\Studies\Koffe'
SUBJECTS: 'D:\Data\Subjects\koffe'
FILELIST: [1x1 struct]
CurrentData: [1x1 struct]

Just make sure that yuour data and channel and brainstormstudy files are all in the same (sub)folder of the STUDIES path.

Cheers,

[koffe]

Hi Sylvain

The directories seem to be okay.

Have installed MATLAB7,R14, SP3 (higher version than only the matlab7 I had before).

a) Which version of Matlab do you use to launch brainstorm?

b) RAPMUSIC works (thanks to your fixes!) . Same picture as posted before. When checking the interactive button as you suggested, I get a beautiful 3D head with the dipoles indicated at the right places. In doing this I also get 2 empty windows:
- MRI tool (beneath the window appears 'subject unknown' as you can see in the picture below)
- Source visualisation tool
(see picture beneath)
http://homes.esat.kuleuven.be/~kdesmedt/pics/untitled3.JPG

The matlab command window ends with:
...
...
Subcorr gui Comments:
Co: 0.9994
Regularized: 0.9994
Filters a and b: 0.990 0.000 0.000 ; 0.990
ans =
Probe value = 5.916540e-005
Undefined function or variable 'Comment'.
Attempt to reference field of non-structure array.
ans =
Probe value = 5.916540e-005

I suppose something should be automatically loaded in the MRI-tool window and Source visualisation tool?
-When loading the subjectimage.mat file myself in the MRI-tool with the button 'Load BST format' I get the next error:
Undefined function or variable 'Comment'.
-when loading the the test_ctfopt_esat_results_2040.mat file myself in the Source visualisation tool window I get the next error:
Undefined function or variable 'Comment'.
Attempt to reference field of non-structure array.

Can you help me?

c) In the above left there is the picture of the results file: original, modeled, residuals data (%). During the execution of rapmusic, different graphs of these are created, each time a source is found. But I do not find these graphs anywhere? Can I plot them myself out of the _results. mat file? How can I do this? (I found the variable 'Fsynth', but this seems to be the original data)

d) I also tried to replot with the Data Viewer- Data viewin section, whether original, modeled or residuals data, it keeps the same signal that is plotted? Any help?

Thanks
Koffe

[Sylvain]

Hi Koffe,

does this problem persist ? if yes we'll try to figure this out.

[koffe]

Dear Sylvain

Well, problem c) and d) are fixed! problem b) remains...
By the way: does a feature exist calculating source confidence regions in brainstorm?

thank you,
Koffe

[Sylvain]

Hi Koffe,

regarding the MRI file: is it a volume you have imported yourself or does it come with the BST package (ie the Phantom or MNI template files)? Could you please send it by mail if it's not too big ?

As for confidence intervals, we have technical solutions using the bootstrap approach which can easily be implemented in Matlab.

see Darvas F, Rautiainen M, Pantazis D, Baillet S, Benali H, Mosher JC, Garnero L, Leahy RM. 'Investigations of dipole localization accuracy in MEG using the bootstrap.' Neuroimage. 2005 Apr 1;25(2):355-68.

they're not in BST yet because you need to go back to invidiual data trials to generate surrogate data. This is something we're planning to release but we first need to rebuild some of the BST database to use individual trials (we're working on it).

Cheers

[koffe]

Hi

First I wanna thank you for the very good reference about the bootstrap!

The MRI file is the phantom.bst subjectimage.mat file... But I suppose this is not an important problem any more. The most important is that the rap-music algorithm works perfectly now. So if your time's a bit tight now, it is not a problem not investigating this error.

My post about the batch processing in the open discussion forum is more important for me. The command whereby the user chooses another database in the data manager list (with all gui windows opened, just after typing startup at prompt) is very helpfull I suppose..? (it is a lot of data) I wanna control the database brainstorm opens when it starts up. I found some variable UserDb but I do not know where it is stored on the system and how it is used to indicate the startup database...?
Is there an analogue to get_user_database, f.e. something like set_user_datbase ? Or is there another solution?

thank you
koffe

[Sylvain]

Have a look at the first lines in bstscript_forward_inverse_basic.mat:

% 2) Where is your data ? Create a database entry
% a) Anatomy (i.e. so-called SUBJECTS folder)
UserDB = getpref('BrainStorm','UserDataBase');
UserDB(end+1).STUDIES = 'C:\Users\Data\Studies\Claire'; % EDIT
% b) Functional (e.g. MEG/EEG, so-called STUDIES folder)
UserDB(end).SUBJECTS = 'C:\Users\Data\Subjects\claire'; % EDIT
UserDB(end).Comment = 'from script call'; % Name of a new database entry EDIT
UserDB(end).FILELIST = '';


% Store this information in Matlab's preferences
setpref('BrainStorm','UserDataBase',UserDB);
setpref('BrainStorm','iUserDataBase',length(UserDB ));

this is how you define and set the database to BrainStorm.