Skip to content

Latest commit

 

History

History
116 lines (90 loc) · 8.77 KB

templates_and_atlases.md

File metadata and controls

116 lines (90 loc) · 8.77 KB
Raw
<style> .dropbtn {background-color: #1e6bb8; color: white; padding: 16px; font-size: 1rem; border: none; cursor: pointer; width: 30rem} .dropbtn:hover, .dropbtn:focus {background-color: #2980B9;} .dropdown {position: relative; display: inline-block;} .dropdown-content {display: none; position: absolute; background-color: #f1f1f1; min-width: 100%; overflow: auto; box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2); z-index: 1; text-align: center; font-size: 1rem;} .dropdown-content a { color: black; padding: 12px 16px; text-decoration: none; display: block;} .dropdown a:hover {background-color: #ddd;} .show {display: block;} .dropbtn + .dropbtn { margin-left: auto; } @media screen and (min-width: 64em) { .dropbtn { max-width: 64rem; width: 40rem; padding: 0.75rem 1rem; } } @media screen and (min-width: 42em) and (max-width: 64em) { .dropbtn { width: 30rem; padding: 0.6rem 0.9rem; font-size: 0.9rem; } } @media screen and (max-width: 42em) { .dropbtn { display: block; width: 20rem; padding: 0.75rem; font-size: 0.9rem; } .dropbtn + .dropbtn { margin-top: 1rem; margin-left: 0; } } </style> <script> function myFunction() {document.getElementById("myDropdown").classList.toggle("show");} window.onclick = function(event) { if (!event.target.matches('.dropbtn')) { var dropdowns = document.getElementsByClassName("dropdown-content"); var i; for (i = 0; i < dropdowns.length; i++) {var openDropdown = dropdowns[i]; if (openDropdown.classList.contains('show')) {openDropdown.classList.remove('show'); } } } } </script>

Templates & atlases

Jump to

Details

Template: A standard brain, typically used for registering multiple individuals into a common coordinate space. This space can be either volumetric (3D coordinates system), surface-based (mesh), or a combination of both.

Atlas: a percellation of the brain into areas, often provided in a specific template space. Atlases are typically used for defining regions-of-interest (ROIs) or for identifying the location of activation sites.

For human MRI, the MNI template serves as the community standard volumetric template. Its integration into most major software packages makes it easy for researchers to register their results to MNI space. This facilitates data-sharing, cross-study comparisons and metanalyses. Most human brain atlases are also provided in MNI space. For surface-based analysis the FsAverage (freesurfer average) template serves the same purpose.

When it comes to NHP neuroimaging though, there are two complications:

  1. The usage of multiple species creates the need for species-specific templates
  2. Even for the most commonly imaged species (macaques and marmosets), multiple templates are available, with no single one of them adopted as the go-to community standard.

Below, we provide a non-exhaustive list of existing templates and atlases. For a more detailed resource list of templates and atlases see this list for macaques or here for marmosets.


Macaque

Template Species Resolution (mm3) With atlas Volume format Surface format Links
NMT M. mulatta 0.25 Saleem Logothetis (D99-SL) NIFTI GIFTI reference download
D99 v1 M. mulatta 0.25 D99-SL NIFTI GIFTI reference download
D99 v2 M. mulatta 0.25 D99-SL NIFTI GIFTI reference download
INIA19 M. mulatta 0.50 Neuromaps NIFTI N/A reference download
MNI macaque M. fascicularis & M. mulatta 0.25 Paxinos MINC & NIFTI N/A reference download
Yerkes19 M. mulatta 0.50 F99 NIFTI & MGZ GIFTI & MGZ reference1 reference2 download1 download2
Japanese macaque atlas M. fuscata 0.50 N/A ANALYZE N/A reference download
112RM-SL M. mulatta 0.50 D99-SL & F99 NIFTI N/A reference
UNC-Emory developmental atlas M. mulatta 0.60 multiple NRRD N/A reference download

For a more detailed resource list of macaque templates and atlases see this list.

Warps between macaque templates

Transforming data (e.g. parcellations, statistical maps) between the various template spaces requires the registration of those templates to one another. The RheMAP package provides pre-calculated warps between a set of common rhesus macaque brain templates. These warps can be directly downloaded from Zenodo. Corresponding code is available on GitHub.

DOI


Marmoset

Template Species Resolution (mm3) With atlas Volume format Surface format Links
NIH C. jacchus 0.15 NIH (3 parcellations) NIFTI CARET reference download1 download2
RIKEN C. jacchus 0.2 N/A NIFTI N/A reference download
3D Paxinos et al. (2012) C. jacchus 0.04×0.5×0.04 Cortical areas of the Paxinos et al., (2012) NIFTI N/A reference
Nencki-Monash C. jacchus 0.05 Cortical areas of the Paxinos et al., (2012) NIFTI N/A reference

For a more detailed resource list of marmoset templates and atlases see this list.


Other species

Template Species Resolution (mm3) With atlas Volume format Surface format Links
Mouse Lemur atlas Microcebus murinus 0.091 YES NIFTI N/A reference download