= Full analysis with one script =
This tutorial explains how to use the Brainstorm scripting interface to run a full analysis, from the raw recordings to the source reconstruction. It is based on a median  nerve stimulation experiment recorded at the  Montreal Neurological Institute in 2011 with a CTF MEG 275 system. The  sample dataset contains 6 minutes of recordings at 1200Hz for one  subject and includes 100 stimulations of each arm.

The tutorial follows the analysis steps detailed in the three advanced tutorials in the category [[Tutorials|Processing continuous recordings]]. You should read them before reading this tutorial, to have the explanations that go with the analysis steps.

<<TableOfContents(2,2)>>

== Creating the analysis pipeline ==
Select the menu File > Create new protocol. Name it "'''!TutorialScript'''" and select the options:

 * "'''No, use individual anatomy'''",
 * "'''Yes, use one channel file per subject'''".

To start building your analysis pipeline, just click on the "'''Run'''" button in the Process1 tab. Then add all the processes listed below.

==== Import anatomy > Import FreeSurfer folder ====
 * Subject name: Subject01
 * Folder to import: Select the folder sample_raw/Anatomy
 * Number of vertices (cortex): 15000
 * Fiducials: Copy what is indicated below. This is a reason it is usually easier to do this step in interactive mode, and then run only the script starting from the next step.
 * Input: None;  Output: None

{{attachment:procImportFs.gif}}

==== Import recordings > Create link to raw file ====
Input: None;  Output: Raw file

{{attachment:procLinkRaw.gif|procImportFs.gif}}

==== Pre-process > Sinusoid removal (notch) ====
Input: Raw file ;  Output: Raw file

{{attachment:procSin.gif|procImportFs.gif}}

==== Artifacts > Detect eye blinks ====
Input: Raw file ;  Output: Raw file

{{attachment:procDetectEog.gif|procImportFs.gif}}

==== Artifacts > Compute SSP: eye blinks ====
Input: Raw file ;  Output: Raw file

{{attachment:procSspEog.gif|procImportFs.gif}}