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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
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
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
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
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils
Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets.
Proper citation: Fslutils (RRID:SCR_024943) Copy
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
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ICA_PNM
Software de-noising pipeline combines noise regressors identified by tools such as PNM and ICA (and FIX) and effectively prepares them for entry into single FEAT model, thus allowing the user to clean data in single step.
Proper citation: ICA-PNM (RRID:SCR_024952) Copy
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
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
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy
Software tool for correcting eddy currents and movements in diffusion data. Used to predict undistorted data, to which actual observed images can be aligned, to estimate and to correct for volume-to-volume movement and off-resonance fields, to signal dropout caused by movement during diffusion encoding, within-volume movement and movement-induced changes of susceptibility-induced off-resonance field. In addition to correcting for these effects, the output from this framework offers description of off resonance and subject movement effects present in uncorrected data.
Proper citation: eddy (RRID:SCR_024934) Copy
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
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
https://github.com/howisonlab/softcite-dataset
Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
Proper citation: SoftCite (RRID:SCR_024411) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT
Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.
Proper citation: FMRIB's Linear Image Registration Tool (RRID:SCR_024922) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA
Software package for both single-time-point and two-time-point analysis of brain change. Used to estimate percentage brain volume change between two input images, taken of the same subject, at different points in time.
Proper citation: SIENA (RRID:SCR_024925) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression
Software application used as part of group level resting state analysis to identify subject specific contributions to group level Independent Component Analysis.
Proper citation: DualRegression (RRID:SCR_024940) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat
Software tool provides general pipeline for processing anatomical images.
Proper citation: fsl_anat (RRID:SCR_024930) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS
Software tool to improve sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies.
Proper citation: Tract Based Spatial Statistics (RRID:SCR_024932) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddyqc
Software tool allows to assess dMRI data both at single subject and group levels.Calculates average SNR across all voxels within brain mask to give summary measure of overall quality of dataset. Used to generate single subject and study wise reports and databases.
Proper citation: eddyqc (RRID:SCR_024936) Copy
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