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* Multiple screens: does not work in all the configurations<<BR>>Cause: Too many possible configuration possible (each version of Linux and Matlab handle this in a different way) <<BR>>Workaround: work only with your main screen | * "Java heap space" error in Matlab. <<BR>>__Workaround__: In the Matlab preferences, increase the Java Heap Space memory from 128Mb to 256Mb. * Brainstorm gets very slow after a while, you have to restart Matlab to make it work again. <<BR>>__Workaround__: Increase the Java Heap Space memory from 128Mb to 256Mb. * Automatic updates crash while downloading the new software version. <<BR>>__Workaround__: Increase the Java Heap Space memory from 128Mb to 256Mb. * Any error related with the function "fminsearch"<<BR>>__Cause__: You have a toolbox in your Matlab path, such as EEGLAB, that redefines the basic Matlab function "fminsearch".<<BR>>__Workaround__: From the Matlab preferences: Remove the folder containing this other fminsearch function from your static Matlab path, or remove entirely EEGLAB from your path. * Multiple screens: does not work in all the configurations<<BR>>__Cause__: Too many possible configuration possible (each version of Linux and Matlab handle this in a different way) <<BR>>__Workaround__: work only with your main screen |
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* Tree is not updated well and some nodes are missing<<BR>>Cause: Unpredictible order of execution of Java/Matlab operations<<BR>>Workaround: Press F5 to refresh * Colormap sliders for contrast / brightness do not work with versions of Matlab < 7.4<<BR>>Workaround: Manipulate the colormap by clicking on the colorbar and moving up/down (brightness) and left/right (contrast) |
* Tree is not updated well and some nodes are missing<<BR>>__Cause__: Unpredictible order of execution of Java/Matlab operations<<BR>>__Workaround__: Press F5 to refresh |
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* Tree menu: "File > XTerm" does not work with all the linux distributions * Tree menu: "Group conditions" does not update all the filename links (in results files, linkresults files, etc.) * Display time series t=[0,end] + Display time series t=[begin,end]: time bounds are not good for the second figure * Save figures as AVI movies: only available on Windows operating system |
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* Popup menus and "Open file" dialogmay generate the following error: <<BR>>The class "!BstFileSelector" is undefined. Perhaps Java is not running.<<BR>>Workaround: Restart Matlab. | * Popup menus and "Open file" dialog may generate the following error: <<BR>>The class "BstFileSelector" is undefined. Perhaps Java is not running.<<BR>>__Workaround__: Restart Matlab. |
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* Click on "Close all windows" button may freeze Matlab... Sorry... | * On some computers, the Matlab folder has to remain the brainstorm3 folder, if not it crashes with weird errors... |
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== Figures issues (recordings / results) == * Colormap menus do not work from the 3D figures with some versions of Matlab (eg. R2007a)<<BR>>Workaround: Use the Colormaps menu in the main Brainstorm window. |
== Figures and display == * Problems in the display of the figures or the colorbars, especially on 64bit machines or when working on a remote system (X-server, VirtualBox, Windows remote desktop connection...).<<BR>>__Cause__: This might be due to the many bugs of the OpenGL support of Matlab, that appear only with specific combinations of OS/Matlab version/video card.<<BR>>__Workaround__: Change the OpenGL rendering properties. In Brainstorm main window, select menu File > Edit preferences, and select "software" or "disable". All the 3D views will be very slow and there will be no transparency, but it may solve all the problems. * Mouse wheel operations (zoom, scroll, change channel gain) do not work on older Matlab versions<<BR>>__Cause__: Support for mouse wheel was introduced in Matlab 7.4 (R2007a), so there is no way to get the wheel events on previous versions.<<BR>>__Workaround__: Upgrade Matlab or run the compiled version of Brainstorm. * Colormap menus do not work from the 3D figures with some versions of Matlab (eg. R2007a)<<BR>>__Workaround__: Use the Colormaps menu in the main Brainstorm window. * Colormap sliders for contrast / brightness do not work with versions of Matlab < 7.4<<BR>>__Workaround__: Manipulate the colormap by clicking on the colorbar and moving up/down (brightness) and left/right (contrast) |
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* Modelized data / Residuals: no sensors selection available * "Save image" may capture a blank image on Linux |
* "Save image" may capture a blank image on Linux and MacOS (functions getscreen and getframe do not work properly on many systems) |
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* Tree menu "Project on default anatomy" : does not work for kernel / absolute values * Tree menu "Project on default anatomy" : does not work for kernels if there are some bad channels * Tree menu "Project on default anatomy" : cause Out of memory errors when processing FULL results (=> proceed by time blocks) * OS_MEG crashes Matlab when scalp in not very well aligned with sensors<<BR>>Workaround: register them well... * OS_MEG (overlapping spheres) fails when the scalp surface is not perfect (some garbage inside the head)<<BR>>Workaround: do your scalp extraction with FreeSurfer * Permutation tests do not work on "kernel only" results == Scientific issues == * Grand average computation does not weight the different subjects with the number of trials for each subject * New t-tests and old t-test do not give the same results, because the processing of bad channels is different: * Old tests: reject a channel when it is bad at least for one file * New tests: reject a channel only when it is bad in all the files |
* Importing surfaces for an MRI that was re-oriented manually: surfaces are not properly oriented.<<BR>>__Workaround__: Use an MRI that is already properly oriented (BrainVISA and FreeSurfer re-write the MRI in a good orientation before processing them). * OS_MEG (overlapping spheres) may crash when: * The scalp in not very well aligned with sensors<<BR>>__Workaround__: register them well... * The scalp surface is not very clean (some garbage inside the head)<<BR>>__Workaround__: do your scalp extraction with FreeSurfer |
Known bugs
Main window and database
"Java heap space" error in Matlab.
Workaround: In the Matlab preferences, increase the Java Heap Space memory from 128Mb to 256Mb.Brainstorm gets very slow after a while, you have to restart Matlab to make it work again.
Workaround: Increase the Java Heap Space memory from 128Mb to 256Mb.Automatic updates crash while downloading the new software version.
Workaround: Increase the Java Heap Space memory from 128Mb to 256Mb.Any error related with the function "fminsearch"
Cause: You have a toolbox in your Matlab path, such as EEGLAB, that redefines the basic Matlab function "fminsearch".
Workaround: From the Matlab preferences: Remove the folder containing this other fminsearch function from your static Matlab path, or remove entirely EEGLAB from your path.Multiple screens: does not work in all the configurations
Cause: Too many possible configuration possible (each version of Linux and Matlab handle this in a different way)
Workaround: work only with your main screenTree is not updated well and some nodes are missing
Cause: Unpredictible order of execution of Java/Matlab operations
Workaround: Press F5 to refresh- Some user preferences are not saved in compiled versions
- Popup menus and "Open file" dialog take a few seconds to appear on some XP systems. Unknown cause...
Popup menus and "Open file" dialog may generate the following error:
The class "BstFileSelector" is undefined. Perhaps Java is not running.
Workaround: Restart Matlab.Navigator: may not work if more than one condition/subject opened at the same time, and next file do not have the same time definition.
Only things that this prevents you to do is to review at the same time different raw files that were imported in small time blocks... So not a major issue...- On some computers, the Matlab folder has to remain the brainstorm3 folder, if not it crashes with weird errors...
Figures and display
Problems in the display of the figures or the colorbars, especially on 64bit machines or when working on a remote system (X-server, VirtualBox, Windows remote desktop connection...).
Cause: This might be due to the many bugs of the OpenGL support of Matlab, that appear only with specific combinations of OS/Matlab version/video card.
Workaround: Change the OpenGL rendering properties. In Brainstorm main window, select menu File > Edit preferences, and select "software" or "disable". All the 3D views will be very slow and there will be no transparency, but it may solve all the problems.Mouse wheel operations (zoom, scroll, change channel gain) do not work on older Matlab versions
Cause: Support for mouse wheel was introduced in Matlab 7.4 (R2007a), so there is no way to get the wheel events on previous versions.
Workaround: Upgrade Matlab or run the compiled version of Brainstorm.Colormap menus do not work from the 3D figures with some versions of Matlab (eg. R2007a)
Workaround: Use the Colormaps menu in the main Brainstorm window.Colormap sliders for contrast / brightness do not work with versions of Matlab < 7.4
Workaround: Manipulate the colormap by clicking on the colorbar and moving up/down (brightness) and left/right (contrast)- 2D/3D topography of modelized data (Fsynth) are always display with EEG colormap, even it is MEG
- "Save image" may capture a blank image on Linux and MacOS (functions getscreen and getframe do not work properly on many systems)
- "Save file" do not check if file already exists on Linux
Computation issues
Importing surfaces for an MRI that was re-oriented manually: surfaces are not properly oriented.
Workaround: Use an MRI that is already properly oriented (BrainVISA and FreeSurfer re-write the MRI in a good orientation before processing them).- OS_MEG (overlapping spheres) may crash when:
The scalp in not very well aligned with sensors
Workaround: register them well...The scalp surface is not very clean (some garbage inside the head)
Workaround: do your scalp extraction with FreeSurfer