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

Brainstorm orients most of its database organization and processing stream for handling anatomical information together with the MEG/EEG recordings. The introduction tutorials start with the import of the T1 MRI of the subject, and this anatomy seems mandatory everywhere. These choices were made because the primary focus of Brainstorm was to estimate brain sources from MEG/EEG, which ideally requires an accurate spatial modelling of the head.

If you don't have access to anatomical images of your subjects or if you are not interested in source reconstruction, Brainstorm will still require that you explicitly define an anatomy; in those case you would use an anatomy template. In the case of group analysis at the source level, you would also use a template on which you would project of the individual results.

Several templates are available, with a large preference for using the MNI ICBM152 package distributed with Brainstorm because it provides the highest level of compatibility between different features within Brainstorm and with other software environments. You might be interested in using another one if you are working with different age ranges, or if you need to obtain results in a specific space. This tutorial provides references to the various templates available in Brainstorm.

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== Scenarios ==
An anatomy template is a set of anatomical  files (MRI, surfaces, parcellations) representing a brain atlas. As the  reference anatomy, we recommend using the [[http://nist.mni.mcgill.ca/?p=904|ICBM125 2009c Nonlinear Asymmetric]], distributed by default with Brainstorm, but other options are described below. An anatomy template can be used for various purposes:

 * Replacing  the subject anatomy in the Brainstorm database when no individual scans  are available for the subject, or when their quality is too low to process them with FreeSurfer or CAT. Setting the anatomy of the subject is  necessary for 2D/3D topography display and source estimation.
 * Warping an anatomy template to match the digitized head shape of a subject. See tutorial: [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutWarping|Warping the anatomy templates]]
 * For group analysis at the source level: an intermediate step of projection on an anatomy template is necessary. See tutorial: [[https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects|Group analysis: Subjects coregistration]]

When using an anatomy template as a substitution for the subject anatomy, you have to be careful with the spatial distortions it creates. As the reference anatomy has a different shape and cortical folding from your subject, with sometimes important differences in head size, it is preferable to follow these guidelines:

 * If you have a head shape for the anatomy: Warp the anatomy.
 * Chose a template close to the age range of the subject, especially for younger populations.
 * '''EEG''': If you are not using default electrode positions distributed with the a Brainstorm template, align and project the electrodes on the template head (right-click on the channel file > MRI registration > Edit)
 * '''MEG''': Using an anatomy template with MEG recordings is less indicated than with EEG, because it is not possible to move the MEG sensors to follow the head shape. Use this option with caution, and make sure the template you use has a similar head size as your subject. If you use the ICBM152 template to estimate brain sources from MEG recordings of a 1yr-old baby, most of your source space would be outside of the actual head of the baby.

== Subject configuration ==
=== Using the default anatomy ===
When creating a new subject, select the option "'''Yes, use protocol's default anatomy'''". This causes the contents of the subject anatomy folder to be replaced with the text ''Default anatomy''. When a Brainstorm process or display function requests the default MRI or surfaces for this subject, the files from the ''Default anatomy'' are returned.

By default, all new protocols use as their default anatomy the simplified version of the ICBM152 MNI template distributed with Brainstorm (brainstorm3/defaults/anatomy/ICBM152). When creating the protocol, Brainstorm makes a copy of the ICBM152 anatomy, processed with FreeSurfer 6, and sets it as the default for the protocol. This template brain is used as a  substitute for the subjects without an individual MRI, or as the common  brain for group analysis.

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=== Modify the default 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.  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  these 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

=== Changing the default anatomy ===
Other sets of MRI+surfaces are available to replace the ICBM152/FreeSurfer 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.

 . {{attachment:changeDefault.gif}}

If you click on any of the download options, it downloads it into your templates folder, then the list of files in the (default anatomy) folder is replaced with the new template.

 . {{attachment:changeDefault2.gif||width="228",height="90"}} {{attachment:changeDefault3.gif||width="352",height="187"}}

If the automatic download doesn't work, you can download the templates manually from the [[http://neuroimage.usc.edu/bst/download.php|Download]] page and copy the .zip files directly in the folder $HOME/.brainstorm/templates. More instructions in the [[https://neuroimage.usc.edu/brainstorm/Installation#No_internet_access|Installation]] page.

== Group analysis ==
When performing a group analysis with multiple subjects for which you have the individual MRI scans, you need to project the sources estimated on each subject on a common template, as explained in this tutorial: [[Tutorials/CoregisterSubjects|Group analysis]].

For accurate registration between different brains (from a subject to a template or between subjects), you need to use a template that was generated using the '''same program''' as the one you used for running the segmentation of all the subjects of your studies.

You can use either '''BrainSuite''' or '''FreeSurfer/''''''CAT12''' for processing the MRIs or your subjects, but you need to use a template that matches this choice in order to use the accurate registration methods.

== FreeSurfer templates ==
Available options:

 * '''ICBM152''': Distributed directly with the Brainstorm package. Same  as ICBM152_2023b, but without the white matter and mid surfaces, in order to  minimize the size of the Brainstorm installation files.
 * '''ICBM152_2023b''': Same as ICBM152_2023 but with updated BEM surfaces computed from FieldTrip, and cortex surfaces slightly modified not to cause any problem with OpenMEEG.
 * '''ICBM152_2023''': ICBM 2009c Nonlinear Asymmetric, FreeSurfer 7.3.2, T1 only: [[https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/|more info]]
  * New volume atlases from [[https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Volume_parcellations|FreeSurfer]] (7.3.2): ASEG, DKT, Deskian-Killiany, Destrieux.
  * New volume atlases from [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12#Volume_parcellations|CAT12]] (r2170): AAL3, Anatomy3, Cobra, Hammers, JulichBrain, LPBA40, Neuromorphometrics, Thalamus
  * New tissue classification from SimNIBS4/CHARM: Tissues
  * New surface atlases: Brainnetome, HCP-MMP1, PALS-B12, Schaefer, OASIS
  * New features: Contralateral registration
 * '''ICBM152_2022''': Same as ICBM152_2023, but without the volume parcellations from CAT12.
  * The template was generated with this package (scripts+data): [[http://neuroimage.usc.edu/bst/getupdate.php?d=ICBM152_2022_src.zip|ICBM152_2022_src.zip]]
 * '''ICBM152_2019''': ICBM 2009c Nonlinear Asymmetric, FreeSurfer 6: [[https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/|more info]]
 * '''Colin27_2016''': Average of 27 scans of the same head, FreeSurfer 5.3: [[https://nist.mni.mcgill.ca/colin-27-average-brain-2008/|more info]]

 * '''FsAverage_2020''': Average of 40 subjects using a spherical averaging [[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

 * '''Oreilly infant templates''': 13 anatomical models for subjects between zero and 24 months of age ([[https://www.biorxiv.org/content/10.1101/2020.06.20.162131v1|O'Reilly et al. 2020]])

They all include the following information:

 * T1 MRI volume
 * Cortex/white surface: high-resolution  (~300.000 vertices) and low-resolution (15.000 vertices)
 * Head layers: scalp, outer skull, inner skull
 * FreeSurfer spherical registration of each hemisphere, for subject co-registration.
 * FreeSurfer surface-based atlases: [[https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation|Desikan-Killiany]], [[https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation|Destrieux]], [[http://ftp.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps|Brodmann]], [[http://www.mindboggle.info/data.html|Mindboggle]]<<BR>>(plus Yeo2011 and PALS for FSAverage only)
 * ASEG sub-cortical atlas.

For more information on the interactions between FreeSurfer and Brainstorm: [[Tutorials/LabelFreeSurfer|read this tutorial]].

== BrainSuite templates ==
Available options:

 * '''Colin27_BrainSuite_2016''': Average of 27 scans, processed with BrainSuite 15b: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27|more information]]
 * '''ICBM152_BrainSuite_2016''': Non-linear average of 152 subjects, BrainSuite 15b: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009|more information]]
 * '''BCI-DNI_BrainSuite_2020''': Single subject atlas from USC, BrainSuite 15c: [[http://brainsuite.org/svreg_atlas_description/|more information]]
 * '''USCBrain''''''_BrainSuite_2020''': Anatomical and functional hybrid atlas from USC, BrainSuite 17a: [[http://brainsuite.org/uscbrain-description/|more]]

<<BR>>__Warning__: If you are using '''BrainSuiteAtlas1''' for BrainSuite processing, then you should use '''Colin27_BrainSuite_2016 '''or '''ICBM152_BrainSuite_2016''' as the default anatomy.''' '''If you are using the '''BCI-DNI_brain_atlas''', then you should use '''BCI-DNI_BrainSuite_2016 '''as the template in BrainStorm.

They all include the following information:

 * T1 MRI volume
 * Cortex/white surfaces: high-resolution  (~300.000 vertices) and low-resolution (15.000 vertices)
 * Head layers: scalp, outer skull, inner skull
 * BrainSuite square registration of each hemisphere, for subject co-registration.
 * BrainSuite surface-based atlas: SVReg

For more information on the interactions between BrainSuite and Brainstorm: [[Tutorials/SegBrainSuite|read this tutorial]].

== BrainVISA templates ==
Note that the BrainVISA-based templates '''do not allow any accurate registration''' procedure.

 * '''Kabdebon_7w''': 7-week infant brain with the anatomical atlas from [[http://www.sciencedirect.com/science/article/pii/S105381191400411X|(Kabdebon et al. 2014)]].

== MNI parcellations ==
It is possible to import anatomical parcellations of the brain defined in MNI space into any subject anatomy for which the [[https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MNI_coordinates|MNI normalization]] (linear or non-linear) was computed, or into any MNI anatomy template. Each parcellation is a volume of integers where each value represents an anatomical label, and registered to an MNI space. For a subject anatomy which [[https://neuroimage.usc.edu/brainstorm/CoordinateSystems#MNI_coordinates|MNI normalization]] was computed, the MNI parcellation in the subject space is obtained by '''reslicing''' the MNI parcellation into the subject space. This can be done for subjects with either linear or non-linear MNI normalization. The anatomical regions defined in these files can be used as [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases|volume scouts]], for reference in the [[https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#Subcortical_regions:_Volume|MRI viewer]], or for [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|labelling SEEG contacts]].

Right-click on the anatomy folder > '''Add MNI parcellation'''. There are some MNI parcellations available for download directly from the Brainstorm interface:

 * AAL: [[https://www.gin.cnrs.fr/en/tools/aal/|Website]]
 * AICHA: [[https://www.gin.cnrs.fr/en/tools/aicha|Website]]
 * Brainnetome: Two quite versions are available, one coming from the [[http://atlas.brainnetome.org/|Brainnetome website]], and one found in the [[https://www.lead-dbs.org/download/|Lead-DBS]] distribution.
 * Brodmann: Brodmann areas, distributed as part of the [[https://people.cas.sc.edu/rorden/mricro/lesion.html#brod|MRIcron software]].
 * Hammers: [[http://brain-development.org/brain-atlases/adult-brain-atlases/|Website]]
 * Julich-Brain v2.5: [[https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6|Website]]
 * Neuromorphometrics: [[http://www.neuromorphometrics.com/?page_id=310|Website]]
 * Schaefer2018: [[https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal|Website]]

You can find detailed descriptions of these MNI parcellations, and link to many other atlases here:

 * [[https://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/cortical-atlas-parcellations-mni-space/|Lead-DBS Cortical Atlases]]
 * [[https://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/atlases/|Lead-DBS Subcortical Atlases]]
 * [[https://en.wikibooks.org/wiki/SPM/Atlases|Wikibook SPM/Atlas]]

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