Functional analysis

Overview

Details

AFNI afni_proc.py

Authors : Rick Reynolds, Paul Taylor, Daniel Glen, Gang Chen, Bob Cox
Description : FMRI analysis pipeline tool in AFNI. This widely used, general purpose and flexible tool for creating a full, single subject FMRI processing stream can be used for macaque analyses. This program creates fully commented, single subject processing scripts for all FMRI study designs (task, resting state, naturalistic, etc.) and for either volumetric- or surface-based analyses. The typical goal is to create volumes of aligned response magnitudes (stimulus beta weights from a GLM) to use as input for a group analysis.
Documentation : documentation
tutorials
Link : https://afni.nimh.nih.gov
Language : python, tcsh, C, AFNI
Publication : Cox (1996)
Jung et al. (submitted)
Communication : AFNI message board
Restrictions : Please cite the above publications

C-PAC: The Configurable Pipeline for the Analysis of Connectomes

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/
Link : Quick-Start
Language : Python
Publication : Craddock et al. (2013)
Communication : C-PAC Forum
Restrictions : None

MR Comparative Anatomy Toolbox (MrCat)

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
Link : www.neuroecologylab.org
Language : shell, matlab
Publication : Mars et al. 2016, among others
Communication : www.neuroecologylab.org
Restrictions : None

NeuroElf

Authors : Jochen Weber
Description : NeuroElf is a powerful Matlab-based toolbox for working with neuroimaging data.
Documentation : NeuroElf website
Link : http://neuroelf.net/
Language : Matlab
Publication : http://neuroelf.net/
Communication : GitHub
Restrictions : See license

NHP-BIDS

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
Link : GitHub link
Language : Python, Shell
Publication : -
Communication : GitHub profile
Restrictions : None

NHP-pycortex

Authors : Chris Klink
Description : Import surfaces generated with 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
Language : Jupyter notebooks with Python 3
Publication : -
Communication : GitHub profile
Restrictions : None

Pypreclin

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
Link : The Python project can be found on GitHub, on the Python Package Index PyPI for easy installation and upgrading, and also as a Singularity container.
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 - Journal website
Communication : GitHub profile
Restrictions : Please cite the related publication