Hoffman2:FSL

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Back to all things Hoffman2

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.


Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:

  • do nothing, and always use the "current" version of FSL on the cluster
  • actively choose which version of FSL you would like to run

We recommend the latter for data integrity and reproducibility.


FSL GUI

Make sure you source the FMRI Path in your Profile before doing anything, or else you won't be able to access FSL.


To run FSL using a GUI on hoffman2, use the following command: 

$ fsl &

If you received this message while opening FSL 

 DISPLAY is not set. Please set your DISPLAY environment variable!

It means you did not open X11 along with your ssh connection. Re-log back in making sure you use the (-X) op tion. 

$ ssh -X [USERNAME]@hoffman2.idre.ucla.edu


FSL TOOLS

A complete list of tools can be found here

Functional MRI (command line only)

Tool Explanation
feat Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
melodic Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
fabber Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.

Structural MRI (command line only)

Tool Explanation
bet Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
fast FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
first] FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.

GUI Commands/Tools [Make sure to have X11 forwarding on]

Tool Explanation
fsl Bring you to the FSL menu where you can choose what type of analysis.
Fdt FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
Flirt FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
Feat Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
Featquery A program which allows you to interrogate FEAT results by defining a mask or set of co-ordinates (in standard-space, highres-space or loweres-space) and get mean stats values and time-series.
Glm A GUI for setting up just the design matrix and contrasts, in the same way as in FEAT, for use with other modelling/inference programs such as randomise.
Melodic Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
Possum Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
Renderhighres Transforms all thresholded stats images in a FEAT directory into high resolution or standard space and overlays these onto the high resolution or standard space images. This then produces PNG format pictures of the overlays and, by default, deletes the 3D AVW colour overlay images.
Renderstats This tool allows you to combine a background image (raw FMRI or high resolution MRI) image with one or two statistics images. The statistics image(s) must be in registration with the background image.
Susan Nonlinear noise reduction.
fslview Interactive display tool for 3D and 4D data.


Cluster

Scripts that self-submit
fdt feat first fslval possom randomise tbss
GUIs that self-submit Fdt Feat Flirt Possum

FSL_SUB


switch_fsl

After you have properly configured your profile so you have access to FSL and the other FMRI tools on Hoffman2, you also have access to the handy switch_fsl tool. It allows you to actively choose which version of FSL you use for analyses so you can stay locked into one version throughout a project before switching for a new project.

If you have never used the tool before, your first usage needs to be to set your FSL version. e.g. 

$ switch_fsl -s 5.0.0

would set your FSL version to 5.0.0

You can always check which version you are using with 

$ switch_fsl -c

And if you no longer wish to use the switch_fsl system and instead always use the "current" version 

$ switch_fsl -d

will remove you from the program.

NOTE: Whenever you switch FSL versions or remove your self from the switch_fsl program, you need to log in and log out for the changes to take full effect.

Call the program without any options, or with "-h" or "--help" to see the full usage and help information 

$ switch_fsl
Description: switch_fsl easily and cleanly switches between various fsl versions.

Usage: switch_fsl [OPTIONS]
Options:
    -h, --help                       Display this help/usage message
    -v, --verbose                    Verbose output
    -s, --switch VERSION             Designate the appropriate fsl version. 
                                        If switching between versions, you must log out
                                        then back it to reset up your environment.
                                        Available versions are: 4.0.4, 4.1.0, 4.1.1, 4.1.3, 4.1.4, 4.1.4-dev, 4.1.7, 4.1.8, 4.1.9, 5.0.0
    -c, --check                      Checks for current fsl version being used
    -d, --delete                     Stops using this system so you instead use the current version
                                        of the tool at all times. You MUST log out and then back
                                        in to properly reset your environment.

Examples: 
        switch_fsl -s 4.1.0
        switch_fsl --switch 4.0.4
        switch_fsl -h
        switch_fsl --check



External Links

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