= Using the anatomy templates =
''Author: Francois Tadel''

<<TableOfContents(2,2)>>

== Possible uses ==
 * There is always a copy of the Colin27 anatomy in every protocol you create
 * It can be used as a replacement for the subject's anatomy if you don't have the MRI scan
 * It is used for group studies: the individual source maps are first projected on a standard brain

== Changing the default anatomy ==
ADD IMAGES FOR ALL THE MODELS + DETAILS OF WHAT IS AVAILABLE

When you create a new protocol, the program makes a copy of the Colin27 anatomy and sets it as the default for the protocol. It means that you will be able to use the Colin27 brain as a substitute for the subjects without an individual MRI, or as the common brain for group analysis.

Other sets of MRI+surfaces are available to replace the Colin27 anatomy. Right-click on ''(Default anatomy)'' > Use template. If a package is not currently available on your system, it will be downloaded from the Brainstorm website and saved in $HOME/.brainstorm/templates. The available options are:

 * '''Colin27''': Average of 27 scans of the same head, processed with FreeSurfer 5.3: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27|more information]]
 * '''Colin27_2012''': Previous version of the default anatomy distributed with Brainstorm
 * '''ICBM152''': Non-linear average of 152 subjects, processed with FreeSurfer 5.3: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009|more information]]
 * '''FSAverage''': Average of 40 subjects using a spherical averaging described in [[http://nmr.mgh.harvard.edu/~fischl/reprints/morphing_human_brain_mapping_reprint.pdf|(Fischl et al. 1999)]].<<BR>>It is the default FreeSurfer brain: please [[https://surfer.nmr.mgh.harvard.edu/registration.html|register here]] if you are using it.<<BR>>More images: http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#FSAverage_template
 * '''Infant7w''': 7-week infant brain with the antomical atlas presented in [[http://www.sciencedirect.com/science/article/pii/S105381191400411X|(Kabdebon et al. 2014)]].

They all include the following information:

 * T1 MRI volume
 * Cortex surface: high-resolution  (~300.000 vertices) and low-resolution (15.000 vertices)
 * Head surface: based on the head used for FSAverage in the MNE software
 * FreeSurfer spherical registration of each hemisphere, with which we can co-register the individual brains processed with FreeSurfer with the selected default anatomy
 * FreeSurfer surface-based atlases: Desikan-Killiany, Destrieux, Brodman, Mindboggle<<BR>>(plus Yeo2011 and PALS for FSAverage only)

The atlases will be discussed in the following tutorials. For more information on the interactions between FreeSurfer and Brainstorm: [[Tutorials/LabelFreeSurfer|read this tutorial]].

{{attachment:changeDefault.gif|changeDefault1.gif}}

If you click on any of the download options, it downloads it into your $HOME/.brainstorm/templates folder:

{{attachment:changeDefault2.gif}}

Then the list of files in the (default anatomy) folder is replaced with the new template.

{{attachment:changeDefault3.gif}}

== Modify the default MRI fiducials ==
The fiducial   points (Nasion, LPA, RPA) used in your recordings might not be the  same  as the ones used in the anatomy templates in Brainstorm (Colin27,  ICBM152, FSAverage). By  default, the LPA/RPA points are defined at the  junction between the  tragus and the helix, as represented with the red  dot in the [[http://neuroimage.usc.edu/brainstorm/CoordinateSystems|Coordinates systems page]].

If  you want to use an anatomy template but you are using a different  convention when digitizing the position of  those points, you have to  modify the default positions of the template with the MRI Viewer.

 * Go to the anatomy view
 * In (default anatomy), right-click on the MRI > Edit MRI
 * Modify the position of the fiducial points to match your own convention
 * Click on [Save], it will update the surfaces to match the new coordinate system