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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.cancerimagingarchive.net/

Archive of medical images of cancer accessible for public download. All images are stored in DICOM file format and organized as Collections, typically patients related by common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. Neuroimaging data sets include clinical outcomes, pathology, and genomics in addition to DICOM images. Submitting Data Proposals are welcomed.

Proper citation: Cancer Imaging Archive (TCIA) (RRID:SCR_008927) Copy   

•   Source: SciCrunch Registry

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

Journals addressing functional and structural neuroimaging topics.

Proper citation: Functional and Structural Neuroimaging Journals Listing (RRID:SCR_009482) Copy   

•   Source: SciCrunch Registry

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

A community for the discussion of functional connectivity and all related topics. This includes discussion of related tools, data sets, methodological discussion, related websites and publications, etc.

Proper citation: Functional Connectivity Community (RRID:SCR_009480) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rician_Noise_Removal

Two Slicer3 modules removing rician noise in diffusion tensor MRI

Proper citation: Slicer3 Module Rician noise filter (RRID:SCR_009614) Copy   

•   Source: SciCrunch Registry

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

Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI.

Proper citation: GIFTI (RRID:SCR_009579) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dave1

Software application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results.

Proper citation: SVV (RRID:SCR_009613) Copy   

•   Source: SciCrunch Registry

http://erpinfo.org/erplab

A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH.

Proper citation: ERPLAB (RRID:SCR_009574) Copy   

•   Source: SciCrunch Registry

http://www.sourcesignal.com/

A technically supported modular platform for space-time-frequency analyses of EEG/MEG/ECoG integrated (optionally) with structural MRI and functional hemodynamic measures (fMRI and NIRS). The Locator module uses Polhemus devices to acquire 3D sensor coordinates. Data Editor provides pipelines of spatial and temporal filters, and easy-to-use event pipelines for conditional binning of time, frequency, and time-frequency data across participants, with group results. Coherence, phase synchronication, and quasi-causal information assess connectivity. Source Estimator enables modeling of discrete overdetermined and distributed underdetermined sources, and spatial filtering for 3D brain regions of interest. Statistical nonparametric mapping (SnPM) may be performed for all measures. MR Viewer and Image Processor comprise tools for BEM and FEM volume conductor models, using cortical source space models. See http://www.sourcesignal.com/Features_EMSE_550.pdf for details and a supported free trial.

Proper citation: EMSE Suite (RRID:SCR_009571) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/BrainParser

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/DTIProcess

A DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess, et al..

Proper citation: DTIProcess ToolKit (RRID:SCR_009561) Copy   

•   Source: SciCrunch Registry

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

An open source implementation of a non-rigid groupwise registration method. This project is implemented by Serdar K Balci (serdar at csail.mit.edu) and supervised by Polina Golland and William M. Wells All metrics are implementing in a multi-threaded fashion. The algorithm will run faster on computers with multiple CPU''s.

Proper citation: Non-rigid groupwise registration method (RRID:SCR_009512) Copy   

•   Source: SciCrunch Registry

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

Bibliography of books related to neuroscience addressing the topic of functional and structural neuroimaging.

Proper citation: NITRC Books (RRID:SCR_009510) Copy   

•   Source: SciCrunch Registry

http://libeep.sourceforge.net/

Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.

Proper citation: LIBEEP (RRID:SCR_009591) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/map3d.html

A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.

Proper citation: map3d (RRID:SCR_009628) Copy   

•   Source: SciCrunch Registry

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

Software using a novel local label learning strategy to estimate the target image?s segmentation label using statistical machine learning techniques. They used a support vector machine (SVM) with a K nearest neighbor (KNN) based training sample selection strategy to learn a classifier for each of the target image voxel based on a training dataset consisting of its neighboring voxels in the atlases. Validation experiments on hippocampus segmentation of 117 MR images demonstrated that the method can produce segmentation results consistently better than state-of-the-art label fusion methods.

Proper citation: Local Label Learning Segmentation (RRID:SCR_009504) Copy   

•   Source: SciCrunch Registry

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

Project to provide long-term hosting and release for small tools related to medical image analysis. Source repository contains highly experimental code intended for collaborative development. However, any interested parties are welcome to browse/reuse code. Stable/evolved projects will be moved to independent projects.

Proper citation: Landman NeuroImaging Tools (RRID:SCR_009503) Copy   

•   Source: SciCrunch Registry

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

This repository stores plugins, tutorial code, and examples demonstrating MRI manipulation within the MIPAV plugin environment. This project is separate from JIST so that we can provide WRITE access to any interested party without overly exposing the infrastructure to unplanned modification. Please contact the administrators if you would like to join this project - open use is encouraged.

Proper citation: JIST Resources for Algorithm Development (RRID:SCR_009500) Copy   

•   Source: SciCrunch Registry

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

Software toolbox containing many kinds of kits that you may be interested in during fMRI data analysis. This toolbox is a homebrew kits built during practical ASL(arterial spin labeling) based Cerebral Blood Flow (CBF) data analysis. Meanwhile, this toolbox is also compatible with BOLD data analysis. Everyone would find something useful for their own data analysis! This toolbox is run and tested on SPM8 with MATLAB 7.6.0(R2008a) under the Linux OS. Theoretically, most of the functions (except the menu1&2 which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Feel free to give feedback to authors if you encounter any bugs or problems. Senhua Zhu Center for functional Neuroimaging, University of Pennsylvania 3 W.Gates Bldg, 3400, Philadelphia, PA (19104), United States Email: [email protected] ; [email protected] QQ group number (QQ?): 60524357 Google group: https://groups.google.com/d/forum/fmri-grocer

Proper citation: fMRI Grocer (RRID:SCR_009622) Copy   

•   Source: SciCrunch Registry

http://elastix.isi.uu.nl/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: elastix (RRID:SCR_009619) Copy   

•   Source: SciCrunch Registry