Tools   Select Another Resource Report Type

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/BIANCA

Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points.

Proper citation: Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) Copy   

•   Source: SciCrunch Registry

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

Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity.

Proper citation: Multimodal Surface Matching (RRID:SCR_024929) Copy   

•   Source: SciCrunch Registry

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

Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.

Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) 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/FDT

Software toolbox for analysis of diffusion weighted images.

Proper citation: FMRIB's Diffusion Toolbox (RRID:SCR_024931) 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

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

Software tool for high quality model based FMRI data analysis. Used for preprocessing and statistical analysis of FMRI data.

Proper citation: FMRI Expert Analysis Tool (RRID:SCR_024915) Copy   

•   Source: SciCrunch Registry

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

A comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. The toolbox includes a template and several atlases, along with state-of-the-art methods to register any data to the template. It also includes useful scripts for data preprocessing: extraction of centerline, automatic segmentation, slice-wise motion correction, etc.

Proper citation: Spinal Cord Toolbox (RRID:SCR_014170) 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

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/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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry