Differences between revisions 1 and 9 (spanning 8 versions)

Import and process Neuromag raw recordings

This tutorial describes how to process raw Neuromag recordings. It is based on median nerve stimulation acquired at MGH in 2005 with a Neuromag Vectorview 306 system. The sample dataset contains the results for one subject for both arms.

This document shows what to do step by step, but does not really explain what is happening, the meaning of the different options or processes, the issues or bugs you can encounter, and does not provide an exhaustive description of the software features. Those topics are introduced in the basic tutorials based on CTF recordings; so make sure that you followed all those initial tutorials before going through this one.

The script file tutorial_mind_neuromag.m in the brainstorm3/toolbox/script folder performs exactly the same tasks automatically, without any user interaction. Please have a look at this file if you plan to write scripts to process recordings in .fif format.

Contents

Import and process Neuromag raw recordings

Download and installation

It is considered that you followed all the basic tutorials and that you already have a fully working copy of Brainstorm installed on your computer.
Go to the Download page of this website, and dowload the file "bst_sample_mind_neuromag.zip".
Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder). This is really important that you always keep your original data files in a separate folder: the program folder can be deleted when updating the software, and the contents of the database folder is supposed to be manipulated only by the program itself.
Start Brainstorm (Matlab scripts or stand-alone version)
In the protocols drop-down list, select the menu "Create new protocol".
Name it "TutorialNeuromag", and select all the options as illustrated: No default anatomy, Use inidividual anatomy, Use one channel file per condition.

Importing anatomy

Create the subject

Select the "Anatomy" exploration mode (first button in the toolbar above the database explorer).
Right-click on the protocol node and select "New subject".
You can leave the default name "Subject01" and the default options. Then click on Save.

Import the MRI

Right-click on the subject node, and select "Import MRI". Select the file: sample_mind_neuromag/anatomy/T1.mri
The orientation of the MRI is already ok, you just have to mark all the six fiducial points, as explained in the following wiki page: Coordinate systems. Click on save button when you're done.
If at some point you do not see the files you've just imported in the database explorer, you just need to refresh the display: by pressing F5, or using the menu File > Refresh tree display.

Import the surfaces

Right-click again on the subject node, and select "Import surfaces". Select the "FreeSurfer surfaces" file type, and select all the surface files at once, holding the SHIFT or CTRL buttons. Click on Open.
Answer "Yes" to the question "Align surfaces with MRI now?". You should see the following nodes in the database.
- "outer skin" = Head, used for surfaces/MRI registration
- "inner skull" = Internal surface of the skull, used for the computation of the "overlapping spheres" forward model
- "lh" = Left hemisphere
- "rh" = Right hemisphere
- "pial" = External cortical surface = grey matter/CSF interface (used for source estimation)
- "white" = External white matter surface = interface between the grey and the white matter (not used in this tutorial)
Downsample the two pial and the two white surfaces to 7,500 vertices each (right-click > Less vertices)
Merge the two downsampled hemispheres of the pial surface (select both lh.pial_7500 and rh.pial_7500 files, right-click > Merge surfaces). Rename the new surface in "cortex".
Do the same with the white matter. Call the result "white".
Delete all the intermediate lh and rh surfaces. Rename the head and the inner skull with shorter names. Display all the surfaces and play with the colors and transparency to check that everything what imported correctly. You should obtain something like this:

Importing MEG recordings

Select the "Functional data / sorted by subject" exploration mode (second button in the toolbar above the database explorer).
Right click on the subject, select Import MEG/EEG. Select the "Neuromag FIFF" file type, and open the only .fif file in the folder sample_mind_neuromag/data.
Select "Event channel" when asked about the events. This will read the "STI 014" channel in the raw fif file, which contains the information about the stimulation, and reconstruct the list of recorded in the file.
You can answer "Yes" when asked whether to save this list of events. This would create a .eve file in the same folder, that would be read instead of the stimulation channel during later access to the raw .fif file (much faster access to the events list).

-  ⇤ ← Revision 1 as of 2010-05-28 18:47:07 → 
  Size: 902
  Editor: cpe-76-168-90-100
  Comment:
+   ← Revision 9 as of 2010-05-28 20:52:20 → ⇥
  Size: 5603
  Editor: cpe-76-168-90-100
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-This tutorial describes how to process raw Neuromag recordings. It is based on median nerve stimulation acquired at MGH in 2005.
+This tutorial describes how to process raw Neuromag recordings. It is based on median nerve stimulation acquired at MGH in 2005 with a Neuromag Vectorview 306 system. The sample dataset contains the results for one subject for both arms.
 Line 4:
-This document shows only what to do step by step, but does not really explain what is happening, what is the meaning of the different options or processes, and does not provide an exhaustive description of the software features. Those topics are introduced in the basic tutorials based on CTF recordings; so make sure that you followed all those initial tutorials before going through this one.
+This document shows what to do step by step, but does not really explain what is happening, the meaning of the different options or processes, the issues or bugs you can encounter, and does not provide an exhaustive description of the software features. Those topics are introduced in the basic tutorials based on CTF recordings; so make sure that you followed all those initial tutorials before going through this one.
 Line 6:
-The script file '''tutorial_mind_neuromag.m''' in the brainstorm3/toolbox/script folder perform exactly the same task automatically, without any user interaction. Please have a look at this file if you plan to write scripts to process recordings in .fif format.
+The script file '''tutorial_mind_neuromag.m''' in the brainstorm3/toolbox/script folder performs exactly the same tasks automatically, without any user interaction. Please have a look at this file if you plan to write scripts to process recordings in .fif format.
 Line 11:
+ * It is considered that you followed all the basic tutorials and that you already have a fully working copy of Brainstorm installed on your computer.
 * Go to the [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] page of this website, and dowload the file "bst_sample_mind_neuromag.zip".
 * Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder). This is really important that you always keep your original data files in a separate folder: the program folder can be deleted when updating the software, and the contents of the database folder is supposed to be manipulated only by the program itself.
 * Start Brainstorm (Matlab scripts or stand-alone version)
 * In the protocols drop-down list, select the menu "Create new protocol".

 * Name it "!TutorialNeuromag", and select all the options as illustrated: No default anatomy, Use inidividual anatomy, Use one channel file per condition.<<BR>><<BR>> {{attachment:createProtocol.gif}}

== Importing anatomy ==
=== Create the subject ===
 * Select the "Anatomy" exploration mode (first button in the toolbar above the database explorer).
 * Right-click on the protocol node and select "New subject".<<BR>><<BR>> {{attachment:createSubjectMenu.gif}}
 * You can leave the default name "Subject01" and the default options. Then click on Save.<<BR>><<BR>> {{attachment:createSubject.gif}}

=== Import the MRI ===
 * Right-click on the subject node, and select "Import MRI". Select the file: sample_mind_neuromag/anatomy/T1.mri<<BR>><<BR>> {{attachment:mriImportMenu.gif}} {{attachment:mriFile.gif}}
 * The orientation of the MRI is already ok, you just have to mark all the six fiducial points, as explained in the following wiki page: [[CoordinateSystems|Coordinate systems]]. Click on save button when you're done.<<BR>><<BR>> {{attachment:fiducials.gif}}
 * If at some point you do not see the files you've just imported in the database explorer, you just need to refresh the display: by pressing F5, or using the menu File > Refresh tree display.

=== Import the surfaces ===
 * Right-click again on the subject node, and select "Import surfaces". Select the "FreeSurfer surfaces" file type, and select all the surface files at once, holding the SHIFT or CTRL buttons. Click on Open.<<BR>><<BR>> {{attachment:surfaceFiles.gif}}
 * Answer "Yes" to the question "Align surfaces with MRI now?". You should see the following nodes in the database.<<BR>><<BR>> {{attachment:surfListInit.gif}}
  * "outer skin" = Head, used for surfaces/MRI registration
  * "inner skull" = Internal surface of the skull, used for the computation of the "overlapping spheres" forward model
  * "lh" = Left hemisphere
  * "rh" = Right hemisphere
  * "pial" = External cortical surface = grey matter/CSF interface (used for source estimation)
  * "white" = External white matter surface = interface between the grey and the white matter (not used in this tutorial)
 * Downsample the two pial and the two white surfaces to 7,500 vertices each (right-click > Less vertices)
 * Merge the two downsampled hemispheres of the pial surface (select both lh.pial_7500 and rh.pial_7500 files, right-click > Merge surfaces). Rename the new surface in "cortex".
 * Do the same with the white matter. Call the result "white".
 * Delete all the intermediate lh and rh surfaces. Rename the head and the inner skull with shorter names. Display all the surfaces and play with the colors and transparency to check that everything what imported correctly. You should obtain something like this:<<BR>><<BR>> {{attachment:surfListFinal.gif}} {{attachment:surfTest.gif}}

== Importing MEG recordings ==
 * Select the "Functional data / sorted by subject" exploration mode (second button in the toolbar above  the database explorer).
 * Right click on the subject, select Import MEG/EEG. Select the "Neuromag FIFF" file type, and open the only .fif file in the folder sample_mind_neuromag/data.<<BR>><<BR>> {{attachment:megImportMenu.gif}} {{attachment:megImportFile.gif}}
 * Select "Event channel" when asked about the events. This will read the "STI 014" channel in the raw fif file, which contains the information about the stimulation, and reconstruct the list of recorded in the file.
 * You can answer "Yes" when asked whether to save this list of events. This would create a .eve file in the same folder, that would be read instead of the stimulation channel during later access to the raw .fif file (much faster access to the events list).
 *

Software

Users

Development