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http://afni.nimh.nih.gov/afni/

Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.

Proper citation: Analysis of Functional NeuroImages (RRID:SCR_005927) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nyu_trt/

EPI-images of 25 participants gathered during rest as well as anonymized anatomical images of the same participants. The resting-state fMRI images were collected on several occasions: # the first resting-state scan in a scan session # 5-11 months after the first resting-state scan # about 30 (< 45) minutes after 2. Each scan occasion is released as a new version release of the resource. ---Caution: Participants here are part of the NewYork_a contribution to the 1000 Functional Connectomes Project. DO NOT combine datasets.

Proper citation: NYU CSC TestRetest (RRID:SCR_005975) Copy   

•   Source: SciCrunch Registry

http://martinos.org/mne/

Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.

Proper citation: MNE software (RRID:SCR_005972) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/art

ART ''''acpcdetect'''' program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans. ART ''''brainwash'''' program for automatic multi-atlas skull-stripping of 3D structural MRI scans. ART ''''3dwarper'''' program of non-linear inter-subject registration of 3D structural MRI scans. Software (art2) for linear rigid-body intra-subject inter-modality (MRI-PET) image registration. Data resource: The ART projects makes available corpus callosum segmentations of 316 normal subjects from the OASIS cross-sectional database. ART ''''yuki'''' program for fast, robust, and fully automatic segmentation of the corpus callosum on 3D structural MRI scans.

Proper citation: Automatic Registration Toolbox (RRID:SCR_005993) Copy   

•   Source: SciCrunch Registry

https://analyzedirect.com/

Software toolkit for the visualization, segmentation, registration and analysis of multidimensional biomedical imaging data. With Analyze, both anatomic structure and associated function can be studied and fused together for synergistic display and measurement of important structure-to-function relationships.

Proper citation: Analyze Software System (RRID:SCR_005988) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/arctic

An end-to-end application allowing individual regional analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line. * Operating System: MacOS, Linux * Programming Language: C++ * Supported Data Format: ANALYZE, Nrrd, Other Format * build requires: Insight Toolkit

Proper citation: ARCTIC (RRID:SCR_005989) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/toads-cruise/

A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: TOADS-CRUISE Brain Segmentation Tools (RRID:SCR_005977) Copy   

•   Source: SciCrunch Registry

http://mousetracker.jbfreeman.net

A free, user-friendly software package that allows researchers to record and analyze hand movements traveling toward potential responses on the screen (via the x, y coordinates of the computer mouse). By looking at the dynamics of how participants' hand movements settle into a response alternative--and how they may be partially pulled toward other alternatives--researchers glean valuable information about real-time cognitive processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. MouseTracker has impressive temporal resolution, comparable to eye-tracking and event-related brain potential (ERP) measures. Experiments can incorporate images, letter strings, sounds, and videos. Once recorded, mouse trajectories can be visualized, averaged, and explored, and measures of attraction/curvature, complexity, velocity, and acceleration can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, cognitive science, and beyond.

Proper citation: MouseTracker (RRID:SCR_005979) Copy   

•   Source: SciCrunch Registry

http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/asl_spm8/

Quick ASL Wrapper for preprocessing arterial spin labeled (ASL) Data and computing blood flow measurements using UPenn ASL toolbox.

Proper citation: ASL spm8 (RRID:SCR_008873) Copy   

•   Source: SciCrunch Registry

https://www.humanconnectome.org/software/connectome-workbench

Software brain visualization, analysis and discovery tool for fMRI and dMRI brain imaging data, including functional and structural connectivity data generated by the Human Connectome Project. Used to map brain imaging data. Allows for visualization of outputs from HCP pipelines from single subject, or average data from group of subjects and register that data onto standard brain atlas.

Proper citation: Connectome Workbench (RRID:SCR_008750) Copy   

•   Source: SciCrunch Registry

http://humanconnectome.org/

Consortium to comprehensively map long-distance brain connections and their variability. It is acquiring data and developing analysis pipelines for several modalities of neuroimaging data plus behavioral and genetic data from healthy adults.

Proper citation: Human Connectome Coordination Facility (RRID:SCR_008749) Copy   

•   Source: SciCrunch Registry

http://www.3dbar.org

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

Proper citation: 3DBar (RRID:SCR_008896) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/antsr

An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data.

Proper citation: ANTsR (RRID:SCR_008891) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ahead/

Open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh, Hongzhi Wang, Sandhitsu Das, Brian Avants, Philip Cook, John Pluta and Paul Yushkevich, and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.

Proper citation: AHEAD (RRID:SCR_008890) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dots/

A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: DOTS WM tract segmentation (RRID:SCR_009459) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cbfdap/

A web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner.

Proper citation: Cerebral Blood Flow Database and Analysis Pipeline (RRID:SCR_009454) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/c8c8/

A small, stand-alone MatLab toolbox that measures sagittal cross-section thickness and area of the human corpus callosum from high-resolution T1 in vivo MR images. C8 takes as input affine normalized white matter segmentations derived from high-resolution (in-plane) T1 images and outputs both regional callosal thicknesses in three different formats and geometrically-defined regional areas in three different configurations. It is a small package that is easily configurable and modifiable and it measures callosa at the rate of several per minute.

Proper citation: C8: Corpus Callosum Computations (RRID:SCR_009449) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/best_practices/

A tutorial that took place as part of MICCAI 2010 is the 13th International Conference on Medical Image Computing and Computer Assisted Intervention, September 20-24, 2010 in Beijing, China. See http://www.miccai2010.org/ This project supporedt community outreach and dialog between presenters and audience, both before and after the tutorial session, and is intended to engage the broader community in the deliberations on this important topic. ''Best Practices'' covered software engineering practices as well end-user installation and support practices.

Proper citation: Best Practices for Software Development (RRID:SCR_009441) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/btk/

Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development.

Proper citation: Baby Brain Toolkit (RRID:SCR_009440) Copy   

•   Source: SciCrunch Registry