DOI: 10.5281/zenodo.3668509
title: RheMAP: Non-linear warps between common rhesus macaque brain templates

description: <strong>General description.</strong> This dataset contains a set of non-linear registration warps between some of the most commonly used rhesus macaque brain templates (D99, INIA19, MNI macaque, NMTv1.2, NMTv1.3, NMTv2.0, Yerkes19). Non-linear registration warps were generated using ANTs. The code used to generate the warps and example code on how to use them to remap data between different standard spaces is available on GitHub as RheMAP (http://doi.org/10.5281/zenodo.3819979). The actual templates are not included in this dataset since redistribution is often not allowed. Links to there sources can be found in the documentation of RheMAP. <strong>Rationale. </strong>Group analysis of (f)MRI data is commonly performed in a standard template space to which individual data is registered. The choice and adoption of such a standard space is becoming especially relevant now that data sharing initiatives make it much more feasible to obtain larger sample sizes. For human fMRI, the MNI template provides a widely adopted standard space. For non-human fMRI, widely adopted standard templates are often lacking. In 2018, the PRIME-DE (PRIMatE Data Exchange) consortium launched a platform for the exchange of non-human primate MRI data. The initiative was expanded in 2020 with PRIME-RE (PRIMatE Resource Exchange) that aims to provide a portal to analysis approaches related to the non-human primate MRI. Since the generation of non-linear registrations between different brains is a timely and computationally heavy operation, we have created a set of non-linear registration warps that allow the direct remapping of (f)MRI data across different common template brains. Since the code for this approach is also provided, the set can easily be expanded to include additional template brains. <strong>Code. </strong>All code and extensive documentation is available on GitHub as RheMAP. The RheMAP repository is also archived by Zenodo under doi 10.5281/zenodo.3780711. <strong>Data structure. </strong>The data is provided as compressed directories. The <code>warps_linear.zip</code> file contains all the affine registrations, the <code>warps_nonlinear.zip</code> file contains all the nonlinear warps of the already linearly aligned volumes. The final full warps across templates are further divided in individual zip-files for warps from each template to all other, e.g. <code>warps_final_D99.zip</code> contains all warps between the D99 template and other templates. The zip-file <code>warped_templates_linear.zip</code> file contains the results of the affine registration, the <code>warped_templates_nonlinear.zip</code> folder contains the results of the nonlinear registration of the already linearly aligned volumes, and the <code>warped_templates_final.zip</code> file contains the results of all final template-to-template registrations (linear + non-linear). Finally, the <code>warped_templates_metatemplate.zip</code> file contains a meta-template which is the average of all coregistered templates in NMTv2.0-sym space. It is mostly there as an example of the nice coregistation of all templates. See the code on GitHub for more details. *NB Versions v1.0 and v1.1 of RheMAP contained both individual files and a single zip file with all the data. From v1.2, the dataset is substantially (it contains more templates and warps) and this duplication of the data is no longer sustainable. Unfortunately this means that if you want all the data, you now have to download multiple files and if you only want a single warp, you will still have to download a larger zip file first (or contact one of the authors and ask for a specific file). We apologize for the inconvenience, but Zenodo limits both the number of files and the total size of a dataset. We have tried to compress things in a way to optimize efficiency. <strong>Diagnostic images. </strong>A set of diagnostic images is included as <code>images.zip</code> for quality control and visual inspection of the results. These images are also provided as directory specific pdf files. <strong>Acknowledgements.</strong> This project was initiated at the Brainhack: Comparative MRI event in London (September 2019), following the PRIME-DE Global Collaboration Workshop. <strong>Citation. </strong>Sirmpilatze, N. and Klink, P.C. (2020). RheMAP: Non-linear warps between common rhesus macaque brain templates (Version 1.2)[Data set]. Zenodo. <strong>Future updates.</strong> Additional templates may be added to the set of warps in the future. Zenodo cannot do version control to easily facilitate that. We have therefor mirrored the RheMAP data-set on G-NODE where you can find the complete set of latest warps. Updates that have happened there: [2022-10-09] Added the ONPRC18 template (Weiss et al. Neuroimage)
description: v1.3 RheMAP now includes the NMTv2.0 templates as published (Jung et al. 2021 NeuroImage; https://doi.org/10.1016/j.neuroimage.2021.117997) v1.2 RheMAP now includes the NMTv2.0 templates (4 different templates) and provides warps across all combination 10 different template brains. v1.1 In v1.0 a version of the NMTv1.3 template was used that is different than the one available from the NMT GitHub repository. In v1.1 we used the available version and re-calculated the warps.