Hoffman2:FSL: Difference between revisions
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After you have [[Hoffman2:Profile | properly configured your profile]] so you have access to FSL and the other FMRI tools on Hoffman2, you also have access to the handy <code>switch_fsl</code> 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. | After you have [[Hoffman2:Profile | properly configured your profile]] so you have access to FSL and the other FMRI tools on Hoffman2, you also have access to the handy <code>switch_fsl</code> 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. | ||
See its documentation [[Hoffman2:Scripts:switch_fsl | here]]. | |||
Revision as of 19:16, 18 October 2012
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.
See its documentation here.
External Links
- Official FSL website http://www.fmrib.ox.ac.uk/fsl/