= Tutorial 9: Select files and run processes =
''Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet''

The Brainstorm window includes a graphical batching    interface. With the two tabs Process1 and Process2 in the lower part of the window, you can easily select files from the database explorer and assemble a processing pipeline. Most of the operations available in the interface can also be executed this way, including everything we've been doing with Brainstorm so far.

On the other hand, some features are only available this way. It is the case for the frequency filters we will need for the pre-processing of our auditory recordings. This tutorial is a parenthesis to explain how to select files and run processes on them, the cleaning of the recordings will resume in the next tutorial.

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== Selecting files to process ==
The tab '''Process1''' contains a empty box in which you can drag and drop any number of files or folders from the database explorer. The easier way to understand how it works is to try it.

 * Try to drag and drop in Process1 all the nodes you currently have in your database explorer.
 * You will see that it accepts all the folders and all the recordings, but not the channel file.
 * When you add a new node, the interface evaluates the number of files of the selected type that each of them contain. The number in the brackets next to each node represents the number of  data   files that where found in of them.
 * On top of the box, a comment shows the total number of files that are currently selected. <<BR>><<BR>> {{attachment:process1_example.gif}}
 * The   buttons on the left side allow you to select what type of file you  want  to process: Recordings, sources, time-frequency, other. When you select another button, all the counts are updated to reflect the  number of files the selected type that are found for each node.
 * Right now, if you select another file type, it would show only "0" everywhere because there are no sources or time-frequency decompositions available in the database yet. <<BR>><<BR>> {{attachment:process1_sources.gif||height="159",width="464"}}

 * To remove files from the Process1 list:
  * Right-click on the list > '''Clear list'''

  * Select the nodes to remove (holding Shift or Ctrl key) and press the '''Delete''' key.

== Filter the files by name or comment ==
When  you have lots of files in a folder, like multiple source  reconstructions of time-frequency files for each trial, it is difficult  to grab just the ones you are interested in. After selecting your files in the Process1 box, you can refine the selection by entering something in the '''Filter search box''' at  the bottom-right of the Brainstorm window.

 * The example below shows how select the data file corresponding to the noise recordings: by typing "Noise" in the search box and selecting the option "Search file names". We cannot perform the search "by comment" because all the data files have the same comment "Link to raw file".<<BR>><<BR>> {{attachment:process1_search.gif||height="148",width="436"}}

 * Reminder: To see the file name corresponding to a node in the database, leave your mouse over it for a few seconds. You can do this both in the database explorer and the Process1 list.<<BR>><<BR>> {{attachment:process_filename.gif||height="148",width="490"}}

The options offered in the Filter menu are:

 * '''Search comments''':  Look for the string in the comments of the files, ie. what is displayed  in the database explorer to represent them (the .Comment field).
 * '''Search file names''': Look for the string in the full file names (including their relative path).
 * '''Select files''': Only the files that contain the string are selected.
 * '''Exclude files''': Only the files that DO NOT contain the string are selected.
 * '''Reset filters''': Removes the current file filters applied on Process1 and Process2.
 * '''Case insensitive''':  Note that the search is not sensitive to case.

== Running a process ==
 * Clear the file list and the search filters.
 * Select the Link to raw file for run AEF#02.
 * Click on the '''[Run]''' button at the bottom-left corner of the Process1 tab.
 * The '''Pipeline editor''' window appears, with which you can  create  an   analysis pipeline (ie. a list of process that are applied on  the    selected files one after the other). The first button in the  toolbar    shows the list of processed that are currently available. If  you click    on a menu, it's added to the list.
 * Some    menus appear in grey. This    means that they are not meant to  be applied to the type of data that  you   have in input, or at the end  of the current pipeline. <<BR>><<BR>>{{attachment:process1_addprocess.gif}}

[START FROM HERE]

 1. When you select a process, a list of options specific to this process is shown in the window.
  * To delete a process: Select it and press the ''Delete'' key, or the big cross in the toolbar.
  * With the "up arrow" and "down arrow" buttons in the toolbar, you can move up/down a process in the pipeline.
 1. Now add the following processes, and set their options:
  * '''Pre-process > Band-pass filter''': 2Hz - 30Hz
   * In    some processes, you can specify the type(s) of sensors on which you     want to apply the process. This way you can for instance apply  different    filters on the EEG and the MEG, if you have both in the  same files.
  * '''Extract > Extract time''': 40.00ms - 49.60ms, overwrite initial file
   * This will extract from each file a small time window around the main response peak.
   * Selecting    the overwrite option will replace the previous file (bandpass), with    the output of this process (bandpass+extract). This option is usually    unselected for the first process in the list, then selected    automatically.
  * '''Average > Average over time''': Overwrite initial file
   * Compute the average over this small time window.
  {{http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses?action=AttachFile&do=get&target=pipeline2.gif|pipeline2.gif|class="attachment"}}
 1. Save your pipeline: Click on the last button in the toolbar > Save > New... > Type "process_avg45".

== Creating a pipeline ==
=== Saving/exporting a pipeline ===
The last button in the the toolbar offers a list of menus to save, load and export the pipelines.

 . {{http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses?action=AttachFile&do=get&target=pipeline3.gif|pipeline3.gif|class="attachment"}}

 * '''Load''': List of processes that are saved in the user preferences
 * '''Load from file''': Import a pipeline from a pipeline_...mat file (previously saved with the menu "Save as Matlab matrix")
 * '''Save''': Save the pipeline in the user preferences, to be able to access it really fast after
 * '''Save as Matlab matrix''':    Exports the pipeline for a Matlab structure in a .mat file. Allows    different users to exchange their analysis pipelines (or a single user    between different computers).
 * '''Generate .m script''': This option generates a human-readable Matlab script that can be re-used for other purposes or modified.
 * '''Delete''': Remove a pipeline that is saved in the user preferences.
 * '''Reset options''':    Brainstorm saves automatically for each user the options of all the    processes. This menu removes all the saved options, and set them back  to   the default values.

Here is the Matlab script that is generated automatically for this pipeline.

 . {{http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses?action=AttachFile&do=get&target=script.gif|script.gif|class="attachment"}}
 .

Click    on Ok, in the pipeline window. After a few seconds, you will see  two    new files in the database, and the "Report  viewer" window.

== Process: Select files with tag ==
You can get  to the exact same result by adding the process  "File > Select files  with tag" before the process you want to execute, to keep only a subset  of the files that were placed in the Process1 list. It is less  convenient in interactive mode because you don't see immediately the  effect of your file filter, but it can be very useful when writing  scripts.

{{http://neuroimage.usc.edu/brainstorm/SelectFiles?action=AttachFile&do=get&target=selectFiles.gif|selectFiles.gif|class="attachment"}}

To  see the list of files that was selected by the process, you can open  the report viewer (File > Report viewer). This lists the input files  (all the files) and the final files (the selected files), with a summary  of how many files where selected on the top.

{{http://neuroimage.usc.edu/brainstorm/SelectFiles?action=AttachFile&do=get&target=selectReport.gif|selectReport.gif|class="attachment"}}

==== After ====
This process  is useless if it is not followed immediately by another process that  would do something with the selected files. An application can be the  deletion of some files, by adding the process "File > Delete files".

== How to control the output file names ==
If you are  running two processes with different parameters but that produce exactly  the same file names and file comments, you wouldn't be able to select  them with this process. But immediately after calling any process, you  can add the process "File > Add tag" to tag one specific set of  files, so that you can re-select them easily later.

Example:  you run twice the time-frequency decomposition with different options  on the same files, tag the files after calculating them with different  tags.

{{http://neuroimage.usc.edu/brainstorm/SelectFiles?action=AttachFile&do=get&target=addTag.gif|addTag.gif|class="attachment"}}

=== Report viewer ===
Each time   the pipeline editor is used to executed to run a list of processes, a   report is generated and saved in the user home folder   (/home/username/reports/). The report viewer shows as an HTML page some   of the information saved in this report structure: the date and  duration  of execution, the list of processes, the input and output  files. It  reports all the warning and errors that happen during the  execution.

The   report viewer does not necessarily appear automatically at the end of   the last process: it is shown only when more than one processes were   executed, or when any of the processes returned an error or a warning.

When   running processes manually from a script, the calls bst_report(Start,   Save, Open) explicitly indicate when the logging of the events should   start and stop.

You can add images to the reports for quality control using the process "File > Save snapshot".

{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutProcesses?action=AttachFile&do=get&target=report.gif|output.gif|class="attachment"}}

After you close the report window, you can re-open the last report with the main menu of the Brainstorm window: '''File > Report viewer'''.

With the buttons in the toolbar, you can go back to the previous reports saved from the same protocol.

PROCESSES AND PLUG-INS

The  available processes are  organized in a  plug-in structure. Any Matlab    script that is added to  the plug-in  folder   (brainstorm3/toolbox/process/functions/) and has  the right  format  will   be automatically detected and made available  in the GUI.  This   mechanism  makes the contribution from other  developers to  Brainstorm   very easy.

REPORT: OTHER TUTORIALS

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