= Using the anatomy templates = ''Author: Francois Tadel'' <> == Changing the default anatomy == When you create a new protocol, the program makes a copy of the ICBM152 anatomy, processed with FreeSurfer 6, and sets it as the default for the protocol. It means that you will be able to use this template 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 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. == 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_2020, but without the white matter envelopes, in order to minimize the size of the standard Brainstorm distribution. * '''ICBM152_2020''': Nonlinear asym average of 152 subjects, FreeSurfer 7.1: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009|more information]] * '''ICBM152_2019''': Nonlinear asym average of 152 subjects, FreeSurfer 6: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009|more information]] * '''Colin27_2016''': Average of 27 scans of the same head, FreeSurfer 5.3: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27|more information]] * '''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)]].<
>It is the default FreeSurfer brain: please [[https://surfer.nmr.mgh.harvard.edu/registration.html|register here]] if you are using it.<
>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]]<
>(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]] <
>__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)]]. == 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. 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