Hi
trying to get the startup tutorial to work, I don’t see the MRI viewer; it’s been suggested i check to be sure my brainstorm folder has read/write/execute permission, possibly using chmod -R 777. However, I am very new to programming so I don’t know how to do this. I’m using a mac with OSX 10.5.8. Could someone advise me?
thanks
james
Hi James,
you need to open a X terminal under MacOS and type the command:
chmod -R 777 <your brainstorm folder>
hope this helps
HI Sylvain
Thanks for the direct to XTerminal. Now that I’ve done that, how to re-initiate the TutorialFirstSteps process? I reload Brainstorm at the command prompt, and the window appears. The first time round the paths for anatomy and datasets loaded automatically. not sure what to put in now to reload the TutorialFirstSteps protocol and continue…
sorry to be so totally ignorant!
james
I suggest you quit Matlab and restart BrainStorm and follow the tutorial right from the beginning.
HI Sylvain
sorry but this still doesn’t work; quit Matlab, restarted and restarted Brainstorm. The TutorialFirstSteps (anatomy) and MNI Colin27 are still loaded from before, though frame says ‘no data loaded’.
Window at the bottom has welcome message, and was sitting with "loading protocol #1: “TutorialFirstSteps”… Tried to Create New Protocol with TutorialFirstSteps, tells me it’s already loaded. Tried to reload
Error in db_updateLinkResults.m
Line 70: Attempt to reference field of non-structure array
Call stack:
>db_updateLinkResults.m at 70
>db_updateLingResults.m at 43
>db_loadStudiesDb.m at 151
>db_reloadDatabase.m at 42
>bst_safeCall.m at 31
>gui_creatMainWindow.m>(h,ev)bst_safeCall@db_reloadDatabase) at 80.
I then tried to remove TutorialFirstSteps and reload as per instructions. That worked, but still no Viewer. So then I dragged Brainstorm into the trash, re-unzipped the file, and restarted; no luck, same problem, and now, in addition, now Colin27 no longer appears as an option for the default anatomy.
Sorry, but I"m still stuck.
cheers
james
Hi James,
I don’t know what happened but you should start from scratch.
-
Open Matlab, go to brainstorm3 directory and type “brainstorm reset” in your command window.
-
Close Matlab
-
Delete all your brainstorm3 folders
-
Start everything from the very beginning: read carefully all the information in the “Download”, “Installation” and then “Tutorials” sections on the website.
-
If you’re still not managing to make it work, you might be doing something wrong, or there is really a bug somewhere:
5.a) Bug: to check, try installing brainstorm on an other operating system (ie. Windows) on a recent Matlab version (>R2006a)
5.b) You’re doing something wrong: Try to ask for some help from your co-workers / classmates / teachers who are a little more experienced with Matlab. At that point I cannot do anything else for you.
Good luck
Francois
PS: By “delete all your brainstorm3 folders”, I mean:
- the program folder (brainstorm3)
- the database folder (brainstorm_db)
- the tutorial data folder (TutorialCTF)
Dear Francois
Thanks for your suggestions and for taking time to look at this; I’m sure this must be tedious for you to deal with such a basic problem! I tried what you suggested, twice in fact, and being very very careful to exactly follow the instructions. Both times I got a hanging window called “Import template” saying “Parsing subject directory : @default_subject”, with no GUI window. The short welcome script looked normal, but the Matlab script indicated some problems. I’ll try to find someone here who can assist; mostly people seem to know PC systems, not Macs. In case you see something from the following that would solve it, I thought I’d send you the scripts. Cheers, James
Welcome to Brainstorm!
Brainstorm directory: /Users/jameshartzell/Documents/brainstorm3
Brainstorm version: Brainstorm 3.0 100414 14-Apr-2010
Loading protocol #1: “TutorialFirstSteps”…
Subjects database loaded.
Studies database loaded.
The Matlab prompt script ran as follows:
>> cd brainstorm3
>> brainstorm
BST> Starting Brainstorm:
BST> =================================
BST> Version: 3.0.100414 (14-Apr-2010)
BST> Checking internet connectivity… ok
BST> Starting OpenGL engine…
BST> Compiling main interface files…
BST> Emptying temporary directory…
BST> Compile MEX files:
BST> Compiling: pseudotvalue… /Applications/MATLAB_R2009b.app/bin/mex: line 1107: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 1086: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 997: gcc-4.0: command not found
mex: compile of ' "/Users/jameshartzell/Documents/brainstorm3/toolbox/stat/private/pseudotvalue.c"' failed.
failed
BST>
BST> *************************************************************************************************
BST> ** WARNING: Cannot compile MEX files in directory: toolbox/stat/private
BST> **
BST> ** CAUSE : MEX-compiler error.
BST> ** CONSEQUENCE: Some secondary features will not be accessible (mostly permutation statistics).
BST> ** HOW TO FIX : 1) Run “mex -setup” and check that you have a C compiler available.
BST> ** Select “lcc” if possible, or “gcc”, else try the different options.
BST> ** 2) If you have no other choice than “[0] None”, no compiler is detected by Matlab.
BST> ** You can choose to install one by yourself, or to ignore the compiled features.
BST> ** 3) Check the versions compatibility between your system
BST> ** compiler and the Matlab MEX-compiler.
BST> ** 4) If you cannot fix the problem, in order not to have this message each time you
BST> ** start brainstorm, you can edit the file brainstorm3/toolbox/core/bst_startup.m:
BST> ** => Comment line “mex(cFile);” (around line 208)
BST> ** (To comment a line, add a “%” at the beginning of the line).
BST> *************************************************************************************************
BST>
BST> Compiling: tvalue… /Applications/MATLAB_R2009b.app/bin/mex: line 1107: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 1086: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 997: gcc-4.0: command not found
mex: compile of ' "/Users/jameshartzell/Documents/brainstorm3/toolbox/stat/private/tvalue.c"' failed.
failed
BST> Compiling: tvalue_paired… /Applications/MATLAB_R2009b.app/bin/mex: line 1107: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 1086: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 997: gcc-4.0: command not found
mex: compile of ' "/Users/jameshartzell/Documents/brainstorm3/toolbox/stat/private/tvalue_paired.c"' failed.
failed
BST> Compiling: vertconn_max… /Applications/MATLAB_R2009b.app/bin/mex: line 1107: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 1086: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 997: gcc-4.0: command not found
mex: compile of ' "/Users/jameshartzell/Documents/brainstorm3/toolbox/stat/private/vertconn_max.c"' failed.
failed
BST> Compiling: vertconn_min… /Applications/MATLAB_R2009b.app/bin/mex: line 1107: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 1086: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 997: gcc-4.0: command not found
mex: compile of ' "/Users/jameshartzell/Documents/brainstorm3/toolbox/stat/private/vertconn_min.c"' failed.
failed
BST> Compiling: nearest_points… /Applications/MATLAB_R2009b.app/bin/mex: line 1107: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 1086: gcc-4.0: command not found
/Applications/MATLAB_R2009b.app/bin/mex: line 997: gcc-4.0: command not found
mex: compile of ' "/Users/jameshartzell/Documents/brainstorm3/toolbox/math/private/nearest_points.c"' failed.
failed
BST> Initializing GUI…
BST> Loading configuration file…
BST> License accepted.
BST> Done.
BST> =================================
??? Java exception occurred:
java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at
java.util.Vector.elementAt(Vector.java:432)
at
javax.swing.tree.DefaultMutableTreeNode.getChildAt(DefaultMutableTreeNode.java:230)
at
sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at
java.lang.reflect.Method.invoke(Method.java:592)
at
com.mathworks.jmi.AWTUtilities$Invoker$3.runWithOutput(AWTUtilities.java:492)
at
com.mathworks.jmi.AWTUtilities$Invoker$2.watchedRun(AWTUtilities.java:446)
at
com.mathworks.jmi.AWTUtilities$WatchedRunnable.run(AWTUtilities.java:409)
at
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at
java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
at
java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
Error in ==> awtinvoke at 127
result =
com.mathworks.jmi.AWTUtilities.invokeAndWait(obj,
meth, arglist);
Error in ==> tree_updateNode at 46
nodeRoot = awtinvoke(nodeRootTmp,
‘getChildAt(I)’, 0);
Error in ==> db_reloadSubjects at 88
tree_updateNode(‘Subject’, iSubjects);
Error in ==> db_setTemplate at 74
db_reloadSubjects(iSubject);
Error in ==>
gui_editProtocol>updateProtocolModificiations at 200
db_setTemplate( 0,
char(sTemplate.getFileName()) );
??? Error while evaluating javax.swing.JButton ActionPerformedCallback
>>
Hi James,
Did you manage to make it work ?
If not, try this beta version: http://neuroimage.usc.edu/~tadel/bst_src_100514.zip
What is your Matlab version ? Brainstorm needs 7.1 at least to work properly.
Can you type “ver” in your Matlab command-line window and copy-paste the output here?
Francois
Ciao Francois
Thanks for your message and for the beta version. (My Matlab version is 7.9.0). I downloaded the beta version and tried to run it just now. A friend suggested I try installing Xcode so I’d have a C++ compiler; I did that, so now the compiler failure notices disappear, but I still can’t run Brainstorm on the Mac (it works fine on PCs, but I don’t have a PC unfortunately…). I’ll check again with my friends here, but this is the error message I get (it also leaves the Brainstorm floating box–the one with the logos–onscreen):
Cheers, James
BST> Starting Brainstorm:
BST> =================================
BST> Version: 3.0.100518 (18-May-2010)
BST> Checking internet connectivity… ok
BST> Starting OpenGL engine…
BST> Compiling main interface files…
BST> Emptying temporary directory…
BST> Initializing GUI…
BST> Loading configuration file…
Warning: Cannot create node for study #-3.
Error: Reference to non-existent field ‘Timefreq’.
> In tree_createNodeStudy at 289
In tree_createNodeStudiesDB at 81
In tree_updateModel at 47
In db_setCurrentProtocol at 62
In bst_startup at 536
In brainstorm at 79
??? Subscripted assignment between dissimilar structures.
Error in ==> bst_getContext at 304
argout1(iTargetAnalysis) = repmat(ProtocolStudies.AnalysisStudy,
size(iTargetAnalysis));
Error in ==> bst_getContext at 593
[argout1, argout2] = bst_getContext(‘Study’, iAnalStudyInter);
Error in ==> tree_createNodeStudiesDB at 91
[sAnalysisStudy, iAnalysisStudy] = bst_getContext(‘AnalysisInterStudy’);
Error in ==> tree_updateModel at 47
bstDefaultNode = tree_createNodeStudiesDB(nodeRoot, ‘subject’);
Error in ==> db_setCurrentProtocol at 62
tree_updateModel();
Error in ==> bst_startup at 536
db_setCurrentProtocol(iProtocol);
Error in ==> brainstorm at 79
bst_startup(brainstormHomeDir);
Ciao Francois
somehow the error messages have now disappeared, but we can’t get the right click function to work–normally one just uses the right apple command button when using an apple keyboard with a pc program. nothing we’ve tried shows a right click function. any suggestions?
thanks
james
found right click, by using right side of the ‘mighty’ mouse