Templates & atlases
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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:
- The usage of multiple species creates the need for species-specific templates
- 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.
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 |