The preprocessing and analysis of nonhuman primate (NHP) magnetic resonance imaging (MRI) data presents some unique challenges. Over the years, many laboratories and researchers have created their own custom solutions to many of these problems. PRIME-RE aims to provide an overview of the main difficulties and curate a collection of solutions that currently exist within the broader NHP-MRI communnity for specific processing steps that are commonly performed on NHP MRI data. Since this is a cimmunity effort, we strongly encourage you to contribute your workflows and pipelines.
PRIME-RE is maintained by members of the PRIME-DE consortium.
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A wiki have been set up to share knowledge about NHP MRI acquisition and image processing. Anyone can share knowledge and experience (problems with solutions, fixes, tricks...).
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.
| 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 | 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 |
We used ANTs to compute transformation warps between the volumetric spaces of the first 5 macaque templates on the table above. See how macaque template warps were computed - Download jupyter notebook These warps can be used to transform images (parcellations, statistical maps etc.) between various template spaces. See how to use macaque template warps - Download jupyter notebook
| 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 |
| Template | Species | Resolution (mm3) | With atlas | Volume format | Surface format | Links |
|---|---|---|---|---|---|---|
| Mouse Lemur atlas | Microcebus murinus | 0.091 | YES | NIFTI | N/A | reference download |
| Name | Short description | Links |
|---|---|---|
| Surfaces and flatmaps | Jupyter notebook that ... | view - download |
| Macapype | Python package for anatomical preprosessing using Nipype. | github - details |
(description should be here) Chris' notebook html - Download Chris' notebook
Python package that provides pipelines for NHP anatomical preprocessing using Nipype. framagit repository
Nothing here. Need of contributions ! :)
| Name | Short description | Links |
|---|