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http://www.fmrib.ox.ac.uk/fsl/

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

Proper citation: FSL (RRID:SCR_002823) Copy   

•   Source: SciCrunch Registry

http://tbi.ci.uchicago.edu/

Project to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate composition or orchestration of workflows composed of different analysis and processing tasks (for example using LONI or XNAT pipelines) with the ultimate goal of providing automated no-click evaluations of diffusion MRI data. # Tool development: The final aspect of this project aims to facilitate and encourage tool development and contribution. By providing access to open datasets, they will create a platform on which tool developers can compare and improve and their tools. When tools are sufficiently mature they can be exposed in the infrastructure mentioned above and used by researchers and other developers.

Proper citation: Diffusion MRI of Traumatic Brain Injury (RRID:SCR_001637) Copy   

•   Source: SciCrunch Registry

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

A reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL).

Proper citation: FSL extensions (RRID:SCR_009472) 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.ox.ac.uk/

Collegiate research university in Oxford, England. Teaching as early as 1096, making it the oldest university in English speaking world and world second oldest university in continuous operation.

Proper citation: University of Oxford; Oxford; United Kingdom (RRID:SCR_006361) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/bash-rs-fcmri

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.

Proper citation: BASH4RfMRI (RRID:SCR_005970) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/iop/depts/neuroimaging/research/imaginganalysis/Software/rBET.aspx

A modified version of the Brain Extraction Tool (BET) that can process rodent brains.

Proper citation: Rodent Brain Extraction Tool (RRID:SCR_002538) Copy   

•   Source: SciCrunch Registry

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

Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.

Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy   

•   Source: SciCrunch Registry

http://freesurfer.net/fswiki/HippocampalSubfieldSegmentation

A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL

Proper citation: Segmentation of Hippocampus Subfields (RRID:SCR_005996) Copy   

•   Source: SciCrunch Registry

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

This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images (DW-MRIs) by extending FLIRT (linear registration of 3D scalar volumes) and FNIRT (non-linear registration of 3D scalar volumes) in the FMRIB Software Library (FSL) to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation (Tao, X., Miller, J. V., 2006. A method forregistering diffusion weighted magnetic resonance images. In: MICCAI. Vol. 9. pp. 594?602), which is implemented and extended to non-linear registration, based on the FLIRT and FNIRT models in FSL. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00041/abstract. The code does not overwrite FLIRT, FNIRT or any of the FSL C++ code. It is added as FLIRT4D, FNIRT4D and supporting cost functions. The makefiles will however be overwritten to compile the new code, without affecting any version of FSL.

Proper citation: DW-MRI registration in FSL (RRID:SCR_009461) Copy   

•   Source: SciCrunch Registry

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases

Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.

Proper citation: Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/POSSUM

Software tool that produces realistic simulated MRI and FMRI images or time series.

Proper citation: POSSUM (RRID:SCR_024950) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Miscvis

Software tool to combine background image (raw FMRI or high resolution MRI) with one or two statistics images. Statistics images must be in registration with the background image.

Proper citation: Miscvis (RRID:SCR_024949) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLOBS

Software toolkit for generating optimal basis sets for use in Haemodynamic Response Function convolution in FMRI linear modelling.

Proper citation: FLOBS (RRID:SCR_024941) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SUSAN

Software tool to cover image noise filtering, edge finding and corner finding.

Proper citation: SUSAN (RRID:SCR_024947) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE

Software tools for Echo Planar Imaging distortion correction used in diffusion imaging, functional MRI and perfusion imaging.

Proper citation: FUGUE (RRID:SCR_024948) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL-MRS

Software spectroscopy analysis package includes tools for preprocessing of raw spectroscopy data, including coil combination, frequency and phase alignment, and filtering. Spectroscopy processing package that incorporates Bayesian fitting of spectra.

Proper citation: FSL-MRS (RRID:SCR_024953) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MIST

Software flexible tool for subcortical segmentation. It differs from FIRST in that it can use complementary information in different MRI modalities and is less reliant on manual segmentations.

Proper citation: Multimodal Image Segmentation Tool (RRID:SCR_024927) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM

Software tool to analyse structural data. Voxel based morphometry style analysis carried out with FSL tools.

Proper citation: FSLVBM (RRID:SCR_024924) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BASIL

Software toolbox for kinetic model inversion to the data using Bayesian algorithm. Performs kinetic model inversion on ASL label control difference data.

Proper citation: BASIL (RRID:SCR_024918) Copy   

•   Source: SciCrunch Registry