MRI SCS was not defined after RAP-MUSIC analysis

[JLH]

Dear brainstorm expert,
I download the latest version of brainstorm and use the montreal subjectimage, tesselation file to input my eeg data. After import data and image, I can see the channel on scalp also data display. I also can do the source image analysis. However, when I perform the RAP-MUSIC analysis, I got error message:
MRI SCS was not defined or subjectimage file is from another version of brainstorm.
It is very strange.
Also. I find the Bug reports page can not post new issue, so I wirte the mail directly.
thanks replay
JLH

----

Sorry, I forget to attach error message on matlab windows

Starting BrainStorm, watch for messages in Message Window . . .
BrainStorm Version:
BrainStorm Toolbox Version 2.0 (Alpha) 8-Jun-2004
If you cannot see BrainStorm windows, try typing bst_layout('full') at the command prompt
to reset window locations to their default full screen.
Subcorr gui Comments:
Co: 0.9889 0.9179
Regularized: 0.9867
Filters a and b: 0.990 0.988 0.856 ; 0.990 0.990
Subcorr gui Comments:
Co: 0.9742
Regularized: 0.9742
Filters a and b: 0.990 0.984 0.931 ; 0.990
Error using ==> load
Unable to read file c:\bst\Custom\Subject: file or directory does not exist.
Warning: One or more output arguments not assigned during call to 'scs2mri'.
> In C:\BST\Toolbox\bst_mriviewer.m (LoadSourceMap_Callback) at line 1101
In C:\BST\Toolbox\bst_mriviewer.m at line 242
In C:\BST\Toolbox\rapmusic_gui.m at line 1059
In C:\BST\Toolbox\rap_music_parameters.m (pushbutton_execute_Callback) at line 426
In C:\BST\Toolbox\rap_music_parameters.m at line 162
Warning: One or more output arguments not assigned during call to 'scs2mri'.

[snip]...

Warning: Unrecognized OpenGL version, defaulting to 1.0.

[Sylvain]

Dear JLH,

You get an error crash here because RAP-MUSIC result visualization needs an MRI file with subject coordinate system (SCS) defined to ensure co-registration between anatomy and MEG/EEG source localization.

If you're running the demo data, please follow the steps described in
http://neuroimage.usc.edu/brainstorm/TutorialImportMRIData.html which will help you define the SCS for this MR. Follow some similar steps if you're importing your own MR data.

Once this is done, you should be able to see the sources gently floating in the head volume :wink:

Please let me know how things are progressing.

Cheers !

[John Mosher]

Dear brainstorm expert,
Also. I find the Bug reports page can not post new issue, so I wirte the mail directly.
thanks replay
JLH


I believe what you found was that you could not post a new issue unless you first registered as a Forum user? We just changed the Forum on Tuesday to require Forum registration in order to post, and I see that you are our latest registered user.

Viewing of the posts here can be done by the world without registration.

[JLH]

Dear Brainstormer,
thanks replay. now I did not receive MRI SCS problem. I also find little problem.
1. in Data manager, edit subject windows. the save as button seem nor work. If I check the *.brainstormsubject.mat file, the Anatomy is [] when I use save as, but can work in save button
2. in RAP-MUSIC analysis, when I use the Demodata and latest version of brainstorm, I got error message:

Starting BrainStorm, watch for messages in Message Window . . .
BrainStorm Version:
BrainStorm Toolbox Version 2.0 (Alpha) 10-Jun-2004
If you cannot see BrainStorm windows, try typing bst_layout('full') at the command prompt
to reset window locations to their default full screen.
??? Index exceeds matrix dimensions.

Error in ==> c:\bst\toolbox\parametric_estimation.m (load_gui)
On line 452 ==> Data.Time = Data.Time(timeNdx);

Error in ==> c:\bst\toolbox\parametric_estimation.m
On line 233 ==> load_gui(fig,[],handles,[]); % load the current datamanager trial

Error in ==> c:\bst\toolbox\dataplot_cb.m
On line 2679 ==> figP = parametric_estimation;

Error in ==> c:\bst\toolbox\dataplot_cb.m
On line 652 ==> dataplot_cb('CallDataSelector')

??? Error while evaluating uicontrol Callback.

3. when I use myself EEG for RAP-MUSIC analysis, if the rank set above 6 or 7, I can see the source typography but I can not see any source number on MRI window.
thanks replay

[Sylvain]

Dear JLH,

thanks again for pointing useful bugs or software limitations.


1. in Data manager, edit subject windows. the save as button seem nor work. If I check the *.brainstormsubject.mat file, the Anatomy is [] when I use save as, but can work in save button

-> Will fix it in next version posting.

2. in RAP-MUSIC analysis, when I use the Demodata and latest version of brainstorm, I got error message:

-> known bug: you maybe have changed the time window of analysis before running RAP ? Will fix it in upcoming posting.


3> now you can see the source topography but can't see any source number on MRI window: does it mean no source can be spotted in any of the 3 orthogonal views of the MRI ? Can you see the source timeseries in a separate window ?

[JLH]

Dear Sylvain and brainstorm expert,
thanks replay.
1. for the RAP-MUSIC analysis, if I set the time range in data viewer equal to the parametric estimation data selector, I can run the program but it seem worng result, the rank always the same result even the data change. It seem Decpmoose can not work fine.

2. if the rank set high ( maybe about 10), I can chech the result and it is the same rank number of source but it can not plot on MR. here is the matlab windows showed:

BrainStorm Version:
BrainStorm Toolbox Version 2.0 (Alpha) 10-Jun-2004
If you cannot see BrainStorm windows, try typing bst_layout('full') at the command prompt
to reset window locations to their default full screen.
Error using ==> set
Bad value for axes property: 'XLim'
Values must be increasing and non-NaN.
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 1.000 0.997 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 1.000 0.999 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.995 0.986 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 1.000 0.999 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.999 0.999 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.999 0.986 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.999 0.889 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 1.000 0.999 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 0.9999
Filters a and b: 1.000 0.991 0.937 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.998 0.873 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 1.000 0.999 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.980 0.770 ; 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 1.000 0.991 ; 1.000 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.995 0.694 ; 1.000 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 0.8960
Filters a and b: 1.000 0.999 0.007 ; 1.000 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.998 0.985 ; 1.000 1.000 1.000
Subcorr gui Comments:
Co: 1.0000 1.0000
Regularized: 1.0000
Filters a and b: 1.000 0.996 ; 1.000 1.000
Subcorr gui Comments:
Co: 1.0000
Regularized: 1.0000
Filters a and b: 1.000 ; 1.000
Warning: Unrecognized OpenGL version, defaulting to 1.0.
> In c:\bst\toolbox\bst_mriviewer.m (LoadSourceMap_Callback) at line 1109
In c:\bst\toolbox\bst_mriviewer.m at line 242
In c:\bst\toolbox\rapmusic_gui.m at line 1060
In c:\bst\toolbox\rap_music_parameters.m (pushbutton_execute_Callback) at line 426
In c:\bst\toolbox\rap_music_parameters.m at line 162
Index exceeds matrix dimensions.
Warning: Unrecognized OpenGL version, defaulting to 1.0.
>>

3> now you can see the source topography but can't see any source number on MRI window: does it mean no source can be spotted in any of the 3 orthogonal views of the MRI ? Can you see the source timeseries in a separate window ?
A: no, only one timeseries curve show. but if I set the rank number lower than 6 or 7, I can see 4 or 5 time series curve corresponding with source typography and source location point in MR


thanks replay

[Sylvain]

Dear JLH,

I'll be looking at the problems you're encountering shortly but in the meantime, to make sure this is not an openGL issue, please type

feature('UseGenericOpenGL',1)

after you have typed 'startup' to start BrainStorm.

More soon then - Sylvain.

[JLH]

Dear Sylvain,
thank quick replay.
after I try it (type feature('UseGenericOpenGL',1) on matlab after startup),
the result is the same. Also I noticed that time point in each source typography is set to 1000 ms ? even I change different time range or data set.
thanks for replay

[John Mosher]

Please also see Forum topic:

Warning: Unrecognized OpenGL version http://neuroimage.usc.edu/brainstormforum/viewtopic.php?t=13

which may address the OpenGL warnings JLH is seeing.