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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://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://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

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

Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration.

Proper citation: MCFLIRT (RRID:SCR_024792) Copy   

•   Source: SciCrunch Registry

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

Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra.

Proper citation: BayCEST (RRID:SCR_024951) Copy   

•   Source: SciCrunch Registry

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

Web application as FSL image viewer for visualising neuroimaging data.

Proper citation: FSLeyes (RRID:SCR_024942) Copy   

•   Source: SciCrunch Registry

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

Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask.

Proper citation: Atlasquery (RRID:SCR_024944) Copy   

•   Source: SciCrunch Registry

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

Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction.

Proper citation: FMRIB's Automated Segmentation Tool (RRID:SCR_024920) Copy   

•   Source: SciCrunch Registry

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

Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another.

Proper citation: FNIRT (RRID:SCR_024923) Copy   

•   Source: SciCrunch Registry

https://support.qmenta.com/knowledge/sienax-2.6-/-fsl-6.0

Software tool to estimate total brain tissue volume, from single image, normalized for skull size.

Proper citation: SIENAX (RRID:SCR_024926) Copy   

•   Source: SciCrunch Registry

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

Software application used to form clusters, report information about clusters and/or perform cluster based inference.

Proper citation: fsl-cluster (RRID:SCR_024938) Copy   

•   Source: SciCrunch Registry

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

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry

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

Software tool for nonparametric permutation inference on neuroimaging data.

Proper citation: randomise (RRID:SCR_024937) Copy   

•   Source: SciCrunch Registry

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

Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components.

Proper citation: Multivariate Exploratory Linear Optimized Decomposition into Independent Components (RRID:SCR_024916) Copy   

•   Source: SciCrunch Registry

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

Software command-line tool for approximate Bayesian inference using generative signal models.

Proper citation: FABBER (RRID:SCR_024917) Copy   

•   Source: SciCrunch Registry

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

Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.

Proper citation: VERBENA (RRID:SCR_024919) 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://www.nitrc.org/projects/cmind_py_2014/

A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project.

Proper citation: CMIND PY (RRID:SCR_014097) Copy   

•   Source: SciCrunch Registry