Select Resource Category
<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>
- AFNI afni_proc.py
- C-PAC
- MR Comparative Anatomy Toolbox (MrCat)
- NeuroElf
- NHP-BIDS
- NHP-pycortex
- Pypreclin
[tutorials](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_demos/main_toc.html) **Link** : [https://afni.nimh.nih.gov](https://afni.nimh.nih.gov/) **Language** : python, tcsh, C, AFNI **Publication** : [Cox (1996)](https://pubmed.ncbi.nlm.nih.gov/8812068/)
[Jung et al. (submitted)](https://www.biorxiv.org/content/10.1101/2020.08.05.237818v1) **Communication** : [AFNI message board](https://afni.nimh.nih.gov/afni/community/board/list.php?1) **Restrictions** : Please cite the above publications **Authors** : Steven Giavasis, Cameron Craddock, Michael Milham **Description** : The Configurable Pipeline for the Analysis of Connectomes (C-PAC) is a configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. It is designed and tested for use with human data (all ages), as well as with non-human primate and rodent data. **Documentation** : [http://fcp-indi.github.io/](http://fcp-indi.github.io/) **Link** : [Quick-Start](http://fcp-indi.github.io/docs/user/quick.html) **Language** : Python **Publication** : [Craddock et al. (2013)](https://www.frontiersin.org/10.3389/conf.fninf.2013.09.00042/event_abstract) **Communication** : [C-PAC Forum](https://groups.google.com/forum/#!forum/cpax_forum) **Restrictions** : None **Authors** : Rogier B. Mars, Lennart Verhagen, and the members and collaborators of the Cognitive Neuroecology Lab **Description** : A collection of tools for processing of multi-species neuroimaging data. **Documentation** : [Online doc](http://www.neuroecologylab.org) **Link** : [www.neuroecologylab.org](http://www.neuroecologylab.org) **Language** : shell, matlab **Publication** : [Mars et al. 2016](http://www.rbmars.dds.nl/pubs/Mars2016NBR.pdf), among others **Communication** : [www.neuroecologylab.org](http://www.neuroecologylab.org) **Restrictions** : None **Authors** : Jochen Weber **Description** : NeuroElf is a powerful Matlab-based toolbox for working with neuroimaging data. **Documentation** : [NeuroElf website](http://neuroelf.net/) **Link** : [http://neuroelf.net/](http://neuroelf.net/) **Language** : Matlab **Publication** : [http://neuroelf.net/](http://neuroelf.net/) **Communication** : [GitHub](https://github.com/neuroelf/neuroelf-matlab) **Restrictions** : See [license](http://neuroelf.net/wiki/doku.php?id=neuroelf_license) **Authors** : Chris Klink **Description** : This pipeline uses NiPype to organize and (pre)process NHP-MRI data in accordance with BIDS. It covers the entire pipeline from exporting the data from the scanner, via motion correction and warping, to running a GLM. **Documentation** : [GitHub WIKI](https://github.com/VisionandCognition/NHP-BIDS/wiki) **Link** : [GitHub link](https://github.com/VisionandCognition/NHP-BIDS/tree/public) **Language** : Python, Shell **Publication** : - **Communication** : [GitHub profile](https://github.com/pcklink) **Restrictions** : None **Authors** : Chris Klink **Description** : Import surfaces generated with [NHP-Freesurfer](pipelines_structural.md#NHP-Freesurfer) into a version of pycortex that is adapted for NHP use. This opens up the possibility of using pycortex to visualize fMRI results on the surface. **Documentation** : Available in Jupyter notebook on GitHub **Link** : [GitHub link](https://github.com/VisionandCognition/NHP-pycortex) **Language** : Jupyter notebooks with Python 3 **Publication** : - **Communication** : [GitHub profile](https://github.com/pcklink) **Restrictions** : None **Authors** : Jordy Tasserie, Antoine Grigis, Lynn Uhrig, Morgan Dupont, Alexis Amadon and Béchir Jarraya. **Description** : Pypreclin is a flexible and automatic tool for preprocessing of macaque fMRI data available for the growing community of primate fMRI. **Documentation** : [GitHub](https://github.com/neurospin/pypreclin) **Link** : The Python project can be found on [GitHub](https://github.com/neurospin/pypreclin), on the Python Package Index [PyPI](https://pypi.org/project/pypreclin/) for easy installation and upgrading, and also as a [Singularity container](biodev.cea.fr/pypreclin/pypreclin-ubuntu.simg).
**Language** : Python **Publication** : Tasserie J, Grigis A, Uhrig L, Dupont M, Amadon A, Jarraya B. Neuroimage. 2019 Nov 16:116353. doi: 10.1016/j.neuroimage.2019.116353. [Pubmed](https://www.ncbi.nlm.nih.gov/pubmed/31743789) - [Journal website](https://www.sciencedirect.com/science/article/pii/S1053811919309449?via%3Dihub)
**Communication** : [GitHub profile](https://github.com/AGrigis) **Restrictions** : Please cite the related publication <script type="text/javascript">(function(d, t, e, m){ // Async Rating-Widget initialization. window.RW_Async_Init = function(){ RW.init({ huid: "461543", uid: "08f35e7d11687ef3ae7b3e7c219b6114", source: "website", options: { "advanced": { "layout": { "lineHeight": "12px" }, "nero": { "showDislike": false }, "text": { "rateThis": "Like this resource" } }, "type": "nero", "style": "check", "isDummy": false, "showTooltip": false, } }); RW.render(); }; // Append Rating-Widget JavaScript library. var rw, s = d.getElementsByTagName(e)[0], id = "rw-js", l = d.location, ck = "Y" + t.getFullYear() + "M" + t.getMonth() + "D" + t.getDate(), p = l.protocol, f = ((l.search.indexOf("DBG=") > -1) ? "" : ".min"), a = ("https:" == p ? "secure." + m + "js/" : "js." + m); if (d.getElementById(id)) return; rw = d.createElement(e); rw.id = id; rw.async = true; rw.type = "text/javascript"; rw.src = p + "//" + a + "external" + f + ".js?ck=" + ck; s.parentNode.insertBefore(rw, s); }(document, new Date(), "script", "rating-widget.com/")); </script>