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| Takes a FEAT directory and bundles all essential data of all levels of analysis into a single functioning directory, for easy transportation of results files. | Takes a FEAT directory and bundles all essential data of all levels of analysis into a single functioning directory, for easy sharing of results files. |
Here we list other related software, including plugins, extensions, toolboxes, templates and atlases that have been created by other groups and are relevant to users of FSL.
FreeSurfer - Cortical surface and subcortical modelling
FreeSurfer is a set of tools for reconstruction/flattening of the brain's cortical surface and subcortical segmentation/registration, produced at MGH, Boston. It can, for example, be used to overlay functional data onto the inflated/flattened cortical surface, or carry out multi-subject FMRI statistics on the cortical surface. We have worked together with MGH to make interoperation of FSL and FreeSurfer as easy as possible.
FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad components can be removed from the 4D FMRI data. It is particularly suited for data-driven automatic artefact removal from resting-state fMRI data. This beta-version package requires you to have various other software than just FSL, such as MATLAB and R, and for now is not bundled as part of FSL.
Reza Salimi-Khorshidi & Steve Smith
FRIEND: Functional Real-time Interactive Endogenous Neuromodulation and Decoding
FRIEND is GUI-based user-friendly software for real-time fMRI processing, multivoxel pattern decoding and neurofeedback. The package integrates routines for image preprocessing in real-time, ROI-based feedback (single-ROI percent signal change and functional connectivity) and brain decoding-based feedback using the FSL and libSVM libraries. FRIEND enables users to create or employ pre-specified visual stimuli for neurofeedback experiments.
FRIEND currently comes in two flavours: FRIEND for Windows and FRIEND Engine. The standalone Windows version runs embedded FSL and libSVM functions and provides a simple, straightforward solution. The FRIEND Engine is a multiplatform (Mac/Linux) toolbox that incorporates the same processing capabilities, but in which the front-end is separated from the processing module. This allows users to develop their own front-end GUIs while employing FRIEND processing capabilities through TCP/IP communication services. Advanced users can develop plugins to extend the original pipeline provided by the engine (e.g., Matlab functions for data preprocessing and multivariate classification, or stimulus presentation features from standard packages such as E-Prime, for customized feedback). A fully functional frontend is also provided along with the FRIEND Engine distribution.
FLICA (FMRIB's Linked Independent Component Analysis) is an exploratory analysis tool designed to automatically find structured components that cross multiple modalities of group data (e.g. TBSS, VBM, Freesurfer, etc).
FSLNets is a set of simple MATLAB scripts for carrying out basic network modelling from (typically FMRI) timeseries data. This beta-version package requires you to have various other software than just FSL, such as MATLAB, and for now is not bundled as part of FSL.
A set of simple scripts and mask images to run probabilistic tractography in subject-native space using pre-defined protocols.
A miscellaneous set of useful FSL shell scripts.
featquery percent change calculation
This guide describes how featquery calculates percent change and how for certain types of studies a different procedure is necessary to calculate interpretable percent changes.
A matlab based power calculation tool that has been developed for the calculation of power for future group fMRI studies utilizing the analysis results from previous fMRI studies.
This approach to spatial clustering has some important properties (independence of cluster shape and total variance), carries out density estimation in 3D and shrinks the set of voxels to their densest regions.
DTI-TK is a spatial normalization & atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images (DTI) with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings.
Interoperability with FSL is straighforward using the fsl_to_dtitk script that converts a set of V[1-3] and L[1-3] dtifit files into the NIfTI tensor format that DTI-TK uses.
This FLIRT/FNIRT extension applies angular q-space interpolation when registering 4D diffusion-weighted MRI volumes. The scripts can simply switch to single volume registration and to default FLIRT/FNIRT functionality.
fast eigenvector centrality mapping (fECM)
Eigenvector centrality mapping (ECM) determines network node centralities, providing a spatial distribution of network prominence. The fECM ZIP file contains a GUI, a NIFTI toolbox and example data, mask and atlas files. Interoperability with FSL is straighforward: the maps can be tested in between-group analyses using randomise .
Takes a FEAT directory and bundles all essential data of all levels of analysis into a single functioning directory, for easy sharing of results files.
Groups/people working on GPU (etc) accelerations, or parallelisations, of FSL
We're creating this list so that the various groups who have expressed an interest in working on accelerating aspects of FSL through the use of GPUs (or similar) can co-ordinate their efforts with each other if they wish.
Can we suggest that people email fsl@fmrib.ox.ac.uk with a one-line summary of what they are working on and what progress/results they have made.
* Jiří Keller Gera.Keller@gmail.com
* Tianzi Jiang jiangtz@nlpr.ia.ac.cn
* Stefan Du Plessis witpikkewyn@gmail.com
* Moisés Hernández Fernandez moises.hernandez@um.es 85x speedup for bedpostx on a single GPU; CUDA implementation that works on NVIDIA GPUs; draft paper ready
* Brian Patenaude brianpatenaude@mac.com
* Jura jura@spital.cz