Difference: DocsSectionsRunningExperiments (1 vs. 10)

Revision 1014 Nov 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="WebHome"
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Running Experiments

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 Generate current PDF
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When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI). Data collected during the experiment will be saved in the output folder.
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When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI).
 

Startup of the BrainStream GUI

The BrainStream GUI can be opened from Matlab with the command start_brainstream. If the startup function is used without any input arguments, a popup window will appear containing a list of recently opened experiment files. You can select an experiment from this list or press cancel and select another experiment file via the GUI.

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start_brainstream(block_file [,path_fnc,bfiles_path,com_bfiles_path]) 
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block_file: filename of a block file (.blk) or experiment file (.exp or .bsp). Include (relative) path name or make sure it can be found on the Matlab path.
path_fnc (optional): function that handles setting Matlab path. In general, it is recommended to specify this function in the block file (see here? ) rather than via this input argument.
bfiles_path (optional): starting folder for browsing block files
com_bfiles_path (optional): starting folder for browsing common block files
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block_file: filename of a block file (.blk) or BrainStream Project file (.bsp or .exp). Include (relative) path name or make sure it can be found on the Matlab path.
path_fnc (optional): function that handles setting Matlab path. In general, it is recommended to specify this function in the block file (see here) rather than via this input argument.
bfiles_path (optional): starting folder for browsing block files
com_bfiles_path (optional): starting folder for browsing common block files
 

Using the BrainStream GUI

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  Figure 1: GUI before experiment specification
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You can load your experiment files by clicking on the 'Browse exp.def.files' button and selecting your experiment file (.exp or .bsp). All block files and common block files included in this experiment will be loaded. Alternatively, you can add block files and common block files manually (block files via 'Browse exp.def.files' and common block files via 'Browse common block files').
>
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You can load your experiment files by clicking on the 'Browse exp.def.files' button and selecting your experiment file (.bsp or .exp). All block files and common block files included in this experiment will be loaded. Alternatively, you can add block files and common block files manually (block files via 'Browse exp.def.files' and common block files via 'Browse common block files').
  Based on information in the (common) block files, other fields of the GUI will be filled in automatically:
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GUI_screenshot2.png
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GUI_screenshot2_numbered.png
  Figure 2: GUI after experiment specification
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All block files and common block files included in the experiment are listed in the top right part of the GUI. You can select one of the block files by clicking on it. The information in other fields of the GUI shows the settings specified in the currently selected block file.
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1. All block files and common block files included in the experiment are listed in the top right part of the GUI. You can select one of the block files by clicking on it. The information in other fields of the GUI shows the settings specified in the currently selected block file.
 
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In the Experiment section of the GUI, the datasource, the name of the block, the sample rate and the location of the experiment definition table are obtained from the block files. A subject's name must be entered manually.
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2. In the Experiment section of the GUI, the datasource, the name of the block, the sample rate and the location of the experiment definition table are obtained from the block files. A subject's name must be entered manually.
 
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Information in the Files section is also automatically obtained from the block files, but can be changed manually by clicking on the buttons on the right. The Out folder is the folder where the recorded data will be saved.
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3. Information in the Files section is also automatically obtained from the block files, but can be changed manually by clicking on the buttons on the right. The Out folder is the folder where the recorded data will be saved.
 
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The block settings of the selected block file are shown in the bottom part of the GUI, where the can be changed. Note that the changed settings will be used when the experiment is started. In this part of the GUI, you can also view Log info, which shows the Log file of the experiment, and Warning info, which shows a list of warning messages.
>
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4. The block settings of the selected block file are shown in the bottom part of the GUI, where the can be changed. Note that the changed settings will be used when the experiment is started. In this part of the GUI, you can also view Log info, which shows the Log file of the experiment, and Warning info, which shows a list of warning messages.
 
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You can start the experiment by clicking on the Start button at the bottom. You can end the experiment with either the Quit or Exit button. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here? .
>
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5. You can start the experiment by clicking on the Start button at the bottom. You can end the experiment with either the Quit or Exit button. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here.
 

Command window startup (no GUI)

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  start_brainstream_nogui(block_file [,subject,user_folders])
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block_file: filename of a block file (.blk). Include (relative) path name or make sure it can be found on the Matlab path. If addition (common) block files are required, specify a cell array of block files in order of relevance (settings of block files that appear earlier in this list will overwrite the same settings specified in subsequently listed block files).
subject (optional): name of the subject (default = 'test')
user_folders (optional): cell array with paths you need for the experiment. If you need several folders on your Matlab path, you can enter them as a cell array.
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block_file: filename of a block file (.blk). Include (relative) path name or make sure it can be found on the Matlab path. If more than one (common) block file is required, specify a cell array of block files in order of relevance (settings of block files that appear earlier in this list will overwrite the same settings specified in subsequently listed block files).
subject (optional): name of the subject (default = 'test')
user_folders (optional): cell array with paths you need for the experiment. If you need several folders on your Matlab path, you can enter them as a cell array.
 
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The following example shows you what to enter in the command window when you want to start BrainStream using already installed paths (see InstallationGuide): start_brainstream_nogui('bci_example1.blk','subject').
In the next example, we want to start BrainStream, but we also want to add the folders containing code for the cap montage and the artefact detection to the Matlab path: start_brainstream_nogui('bci_example1.blk','subject',{/Volumes/MyCode/CapMontage,/Volumes/MyCode/EpochArtifacts}).
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The following example shows the command for starting the block bci_example1 for a subject called 'subject'. In addition, folders containing code for cap montage and artefact detection are added to the Matlab path:
start_brainstream_nogui('bci_example1.blk','subject',{/Volumes/MyCode/CapMontage,/Volumes/MyCode/EpochArtifacts}).
  BrainStream can also be started without the GUI with the function
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Manually inserting markers during the experiment

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You have the option to manually insert markers while your experiment is running. This is primarily useful in design and test stages of your experiment, as it allows you to for example trigger or skip the execution of certain functions.
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You have the option to manually insert markers while your experiment is running. This can be useful in the design and test stages of your experiment, as it allows you to for example trigger or skip the execution of certain functions.
  During your experiment, a window will appear containing a list with the names of all markers that are used in your experiment:
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META TOPICMOVED by="MarjoleinVanDerWaal" date="1321264231" from="BrainStream.DocsSectionsRunningExperiments" to="BrainStreamDocs.DocsSectionsRunningExperiments"

Revision 914 Nov 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
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META TOPICPARENT name="WebHome"
 
<---Start1--->

Running Experiments

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Generate current PDF
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Generate current PDF
 

When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI). Data collected during the experiment will be saved in the output folder.

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META TOPICMOVED by="MarjoleinVanDerWaal" date="1321264231" from="BrainStream.DocsSectionsRunningExperiments" to="BrainStreamDocs.DocsSectionsRunningExperiments"

Revision 820 Oct 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
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Running Experiments

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  You can insert a marker simply by selecting it and clicking the 'Insert selected markers' button.
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Output folders

The output folder must be specified in the block file under topic Files and key OutFolder? .

The output folder contains:

subject folders: a separate folder is created for each new subject. The folder has the subject's name.

session folders: a separate folder is created for each session with the same subject. The folder's name is the date of the session (YYYYMMDD).

session folder ('brainstream'): contains the most recently saved version of user defined variables. This is the folder where BrainStream looks for variables when a 'load' statement is present in the Actions table.

runfolders: a separate runfolder is created for each block within the experiment. The name of the folder is the name of the block followed by _ and a number indicating how many times this block has been run. Each runfolder contains:

log file

brainstream folder: containing copies of the user defined variables that have been saved with a 'save' statement in the Actions table.

expdefs folder: contains copies of the experiment definition tables and blocksettings.

raw_bdf folder: contains the raw EEG data.

 
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Revision 710 Oct 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
<---Start1--->

Running Experiments

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Generate current PDF
 

When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI). Data collected during the experiment will be saved in the output folder.

Revision 630 Sep 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
<---Start1--->

Running Experiments

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  If no block or experiment file is specified during startup of the GUI, the GUI will be empty:
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GUI_screenshot1.png
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GUI_screenshot1.png
  Figure 1: GUI before experiment specification
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  Based on information in the (common) block files, other fields of the GUI will be filled in automatically:
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GUI_screenshot2.png
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GUI_screenshot2.png
  Figure 2: GUI after experiment specification
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  During your experiment, a window will appear containing a list with the names of all markers that are used in your experiment:
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InsertMarkers_screenshot.png
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InsertMarkers_screenshot.png
  Figure 3: Insert markers menu
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<-- 
  • Access control
    • Set DENYTOPICVIEW =
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Revision 528 Sep 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
<---Start1--->

Running Experiments

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  The block settings of the selected block file are shown in the bottom part of the GUI, where the can be changed. Note that the changed settings will be used when the experiment is started. In this part of the GUI, you can also view Log info, which shows the Log file of the experiment, and Warning info, which shows a list of warning messages.
Changed:
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You can start the experiment by clicking on the Start button at the bottom. You can end the experiment with either the Quit or Exit button. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here? ). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here? .
>
>
You can start the experiment by clicking on the Start button at the bottom. You can end the experiment with either the Quit or Exit button. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here? .
 

Command window startup (no GUI)

Revision 428 Sep 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
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<---Start1--->
 

Running Experiments

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  If no block or experiment file is specified during startup of the GUI, the GUI will be empty:
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GUI_screenshot1.png
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GUI_screenshot1.png
  Figure 1: GUI before experiment specification
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  Based on information in the (common) block files, other fields of the GUI will be filled in automatically:
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GUI_screenshot2.png
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GUI_screenshot2.png
  Figure 2: GUI after experiment specification
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  During your experiment, a window will appear containing a list with the names of all markers that are used in your experiment:
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InsertMarkers_screenshot.png
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InsertMarkers_screenshot.png
  Figure 3: Insert markers menu
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 raw_bdf folder: contains the raw EEG data.
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Revision 327 Sep 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"

Running Experiments

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When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI).
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When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI). Data collected during the experiment will be saved in the output folder.
 

Startup of the BrainStream GUI

The BrainStream GUI can be opened from Matlab with the command start_brainstream. If the startup function is used without any input arguments, a popup window will appear containing a list of recently opened experiment files. You can select an experiment from this list or press cancel and select another experiment file via the GUI.

Alternatively, the startup function can be used with one or more input arguments. The settings that can be specified by means of these input arguments can also be selected in the GUI after startup. The following input arguments have to be entered as type 'string'.

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start_brainstream(blockfile [,setmatlabpathfunction,blockfiles_startpath,commonblockfiles_startpath]) 
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start_brainstream(block_file [,path_fnc,bfiles_path,com_bfiles_path]) 
  block_file: filename of a block file (.blk) or experiment file (.exp or .bsp). Include (relative) path name or make sure it can be found on the Matlab path.
path_fnc (optional): function that handles setting Matlab path. In general, it is recommended to specify this function in the block file (see here? ) rather than via this input argument.
bfiles_path (optional): starting folder for browsing block files
com_bfiles_path (optional): starting folder for browsing common block files
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The BrainStream GUI

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Using the BrainStream GUI

  If no block or experiment file is specified during startup of the GUI, the GUI will be empty:
Line: 21 to 23
  Figure 1: GUI before experiment specification
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The first step is to load your experiment files. Click on the 'Browse exp.def.files' button and select your experiment file (.exp or .bsp). All block files and common block files included in this experiment will be loaded. Alternatively, you can add block files and common block files manually (block files via 'Browse exp.def.files' and common block files via 'Browse common block files').
>
>
You can load your experiment files by clicking on the 'Browse exp.def.files' button and selecting your experiment file (.exp or .bsp). All block files and common block files included in this experiment will be loaded. Alternatively, you can add block files and common block files manually (block files via 'Browse exp.def.files' and common block files via 'Browse common block files').
  Based on information in the (common) block files, other fields of the GUI will be filled in automatically:
Line: 37 to 39
  The block settings of the selected block file are shown in the bottom part of the GUI, where the can be changed. Note that the changed settings will be used when the experiment is started. In this part of the GUI, you can also view Log info, which shows the Log file of the experiment, and Warning info, which shows a list of warning messages.
Changed:
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You can start the experiment by clicking on the Start button at the bottom. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here? ). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here? .
>
>
You can start the experiment by clicking on the Start button at the bottom. You can end the experiment with either the Quit or Exit button. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here? ). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here? .

 

Command window startup (no GUI)

It is also possible to use BrainStream without the GUI. BrainStream can be started from the Matlab command window using the following function:

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  blocksettings.Files.OutFolder = '/Volumes/data/my_project/'; blocksettings.Experiment.Block = 'my_block';
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 The block settings RunMode.Subject and Files.Referencefolder are only required when BrainStream is started without the GUI. If the GUI is used, these settings are automatically included.
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Manually inserting markers

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Manually inserting markers during the experiment

  You have the option to manually insert markers while your experiment is running. This is primarily useful in design and test stages of your experiment, as it allows you to for example trigger or skip the execution of certain functions.
Line: 74 to 81
  You can insert a marker simply by selecting it and clicking the 'Insert selected markers' button.
Added:
>
>
 

Output folders

The output folder must be specified in the block file under topic Files and key OutFolder? .

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 session folders: a separate folder is created for each session with the same subject. The folder's name is the date of the session (YYYYMMDD).
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session folder ('brainstream'): contains the most recently saved version of user defined variables.
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session folder ('brainstream'): contains the most recently saved version of user defined variables. This is the folder where BrainStream looks for variables when a 'load' statement is present in the Actions table.
  runfolders: a separate runfolder is created for each block within the experiment. The name of the folder is the name of the block followed by _ and a number indicating how many times this block has been run. Each runfolder contains:

Revision 227 Sep 2011 - Main.MarjoleinVanDerWaal

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META TOPICPARENT name="BrainStreamDocs"
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Running Experiments

Starting BrainStream

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Running Experiments

 
Added:
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When you have created all the necessary files for your experiment, you can run your experiment via BrainStream's Grapical User Interface (GUI).

Startup of the BrainStream GUI

The BrainStream GUI can be opened from Matlab with the command start_brainstream. If the startup function is used without any input arguments, a popup window will appear containing a list of recently opened experiment files. You can select an experiment from this list or press cancel and select another experiment file via the GUI.

Alternatively, the startup function can be used with one or more input arguments. The settings that can be specified by means of these input arguments can also be selected in the GUI after startup. The following input arguments have to be entered as type 'string'.

start_brainstream(blockfile [,setmatlabpathfunction,blockfiles_startpath,commonblockfiles_startpath]) 

block_file: filename of a block file (.blk) or experiment file (.exp or .bsp). Include (relative) path name or make sure it can be found on the Matlab path.
path_fnc (optional): function that handles setting Matlab path. In general, it is recommended to specify this function in the block file (see here? ) rather than via this input argument.
bfiles_path (optional): starting folder for browsing block files
com_bfiles_path (optional): starting folder for browsing common block files

 

The BrainStream GUI

Added:
>
>
If no block or experiment file is specified during startup of the GUI, the GUI will be empty:

GUI_screenshot1.png

Figure 1: GUI before experiment specification

The first step is to load your experiment files. Click on the 'Browse exp.def.files' button and select your experiment file (.exp or .bsp). All block files and common block files included in this experiment will be loaded. Alternatively, you can add block files and common block files manually (block files via 'Browse exp.def.files' and common block files via 'Browse common block files').

Based on information in the (common) block files, other fields of the GUI will be filled in automatically:

GUI_screenshot2.png

Figure 2: GUI after experiment specification

All block files and common block files included in the experiment are listed in the top right part of the GUI. You can select one of the block files by clicking on it. The information in other fields of the GUI shows the settings specified in the currently selected block file.

In the Experiment section of the GUI, the datasource, the name of the block, the sample rate and the location of the experiment definition table are obtained from the block files. A subject's name must be entered manually.

Information in the Files section is also automatically obtained from the block files, but can be changed manually by clicking on the buttons on the right. The Out folder is the folder where the recorded data will be saved.

The block settings of the selected block file are shown in the bottom part of the GUI, where the can be changed. Note that the changed settings will be used when the experiment is started. In this part of the GUI, you can also view Log info, which shows the Log file of the experiment, and Warning info, which shows a list of warning messages.

You can start the experiment by clicking on the Start button at the bottom. Clicking the Quit button is equivalent to inserting the BS_QUIT marker and clicking the Exit button is equivalent to inserting the BS_EXIT marker (for more information about these markers, click here? ). In the bottom right corner of the GUI, you can specify the amount of output that is displayed on the screen during the experiment. You can also specify this amount in the block file under topic RunMode and key screenoutputlevel. For more information about the different levels of screen output, click here? .

Command window startup (no GUI)

It is also possible to use BrainStream without the GUI. BrainStream can be started from the Matlab command window using the following function:

start_brainstream_nogui(block_file [,subject,user_folders])

block_file: filename of a block file (.blk). Include (relative) path name or make sure it can be found on the Matlab path. If addition (common) block files are required, specify a cell array of block files in order of relevance (settings of block files that appear earlier in this list will overwrite the same settings specified in subsequently listed block files).
subject (optional): name of the subject (default = 'test')
user_folders (optional): cell array with paths you need for the experiment. If you need several folders on your Matlab path, you can enter them as a cell array.

The following example shows you what to enter in the command window when you want to start BrainStream using already installed paths (see InstallationGuide): start_brainstream_nogui('bci_example1.blk','subject').
In the next example, we want to start BrainStream, but we also want to add the folders containing code for the cap montage and the artefact detection to the Matlab path: start_brainstream_nogui('bci_example1.blk','subject',{/Volumes/MyCode/CapMontage,/Volumes/MyCode/EpochArtifacts}).

BrainStream can also be started without the GUI with the function

brainstream_block(blocksettings).

The argument 'blocksettings' needs to be available as a Matlab type structure variable. Topics from the block file become fields of this structure and keys become subfields of these fields. You can obtain the blocksettings in two ways:

  1. Translate an existing block file into the blocksettings structure using the function blocksettings = bs_get_blockvalue(blockfile), where blockfile is the name of your block file (.blk).
  2. Manually generate a blocksettings structure. The following example contains the minimally required items to start BrainStream without the GUI:
        blocksettings.DataSources.eeg = 'buffer://localhost:1972:my_device';
        blocksettings.RunMode.Subject = 'a_subjects_name';
        blocksettings.Files.ReferenceFolder = '/Volumes/exps/defs/my_project/';
        blocksettings.Files.ExperimentDefinitionFile = '/Volumes/exps/defs/my_project/my_block.edt';
        blocksettings.Files.OutFolder = '/Volumes/data/my_project/';
        blocksettings.Experiment.Block = 'my_block';    
     
The block settings RunMode.Subject and Files.Referencefolder are only required when BrainStream is started without the GUI. If the GUI is used, these settings are automatically included.

Manually inserting markers

You have the option to manually insert markers while your experiment is running. This is primarily useful in design and test stages of your experiment, as it allows you to for example trigger or skip the execution of certain functions.

During your experiment, a window will appear containing a list with the names of all markers that are used in your experiment:

InsertMarkers_screenshot.png

Figure 3: Insert markers menu

You can insert a marker simply by selecting it and clicking the 'Insert selected markers' button.

Output folders

The output folder must be specified in the block file under topic Files and key OutFolder? .

The output folder contains:

subject folders: a separate folder is created for each new subject. The folder has the subject's name.

session folders: a separate folder is created for each session with the same subject. The folder's name is the date of the session (YYYYMMDD).

session folder ('brainstream'): contains the most recently saved version of user defined variables.

runfolders: a separate runfolder is created for each block within the experiment. The name of the folder is the name of the block followed by _ and a number indicating how many times this block has been run. Each runfolder contains:

log file

brainstream folder: containing copies of the user defined variables that have been saved with a 'save' statement in the Actions table.

expdefs folder: contains copies of the experiment definition tables and blocksettings.

raw_bdf folder: contains the raw EEG data.

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META FILEATTACHMENT attachment="GUI_screenshot2.png" attr="" comment="Screenshot of the BS GUI" date="1317117256" name="GUI_screenshot2.png" path="GUI_screenshot2.png" size="166829" stream="GUI_screenshot2.png" tmpFilename="/var/tmp/CGItemp47645" user="MarjoleinVanDerWaal" version="1"
META FILEATTACHMENT attachment="InsertMarkers_screenshot.png" attr="" comment="Insert marker menu" date="1317122591" name="InsertMarkers_screenshot.png" path="InsertMarkers_screenshot.png" size="50727" stream="InsertMarkers_screenshot.png" tmpFilename="/var/tmp/CGItemp47556" user="MarjoleinVanDerWaal" version="1"

Revision 127 Sep 2011 - Main.MarjoleinVanDerWaal

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Running Experiments

Starting BrainStream

The BrainStream GUI

 
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