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FEAT (fMRI Expert Analysis Tool) Processing with FSL

FEAT (fMRI Expert Analysis Tool) Processing with FSL. by Crystal Franklin. Preparing Data for fMRI Analysis. Retrieve data from the archive get_trio_fmri- archive contains epi studies and T1 images get_mri- archive contains 3d anatomicals Convert images to NIFTI format

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FEAT (fMRI Expert Analysis Tool) Processing with FSL

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  1. FEAT (fMRI Expert Analysis Tool) Processing with FSL by Crystal Franklin

  2. Preparing Data for fMRI Analysis • Retrieve data from the archive • get_trio_fmri- archive contains epi studies and T1 images • get_mri- archive contains 3d anatomicals • Convert images to NIFTI format • Run script 4dtonifti on epi data • 4dtonifti session# taskdescription • E.g. 4dtonifti EH0154 fing • Use MANGO to open and save T1 and 3D in NIFTI format • BET • All anatomical images have to be run through BET before using FSL. Form from MRI Operators.

  3. FEAT FMRI Analysis • Balloon Help – Hold mouse arrow on the different options, it will give you helpful information about what the option does. • Progress Watcher – Opens a html page which allows you to see the progress of your analyses. • Brain/Background Threshold- percent of maximum input image intensity

  4. FEAT FMRI Analysis • Number of analyses – Select the number of scans to be analyzed, then select the 4D nifti files • Total Volumes – number of image volumes (time points) • Delete Volumes – The number of scans you would like to delete at the beginning because steady-state has not been reached. • TR – Time from the start of one volume to the start of the next • High Pass Filter Cutoff – the longest temporal period you will allow

  5. FEAT FMRI Analysis • Motion Correction – MCFLIRT which uses FLIRT (FMRIB’s Linear RegistrationTool) • Slice timing correction – Corrects for the fact each slice is taken at sliughtly different times • Not necessary for long epochs. • BET Brain Extraction – A brain mask is created from the first volume in the FMRI data. • Spatial Smoothing FWHM (mm) – This reduces noise without reducing valid activations; by default the smoothing is set at 5mm. • Intensity Normalization – Forces every FMRI volume to have the same mean intensity, by default this is turned off. • Temporal Filtering – Highpass filtering removes baseline drift. Lowpass filtering reduces random noise.

  6. FEAT FMRI Analysis • FEAT uses GLM (General Linear Modeling) • http://www.fmrib.ox.ac.uk/fsl/feat5/glm.html • FILM Prewhitening - Makes the statistics valid and maximally efficient • Model Setup: • Model Setup Wizard • Allows you to setup simple experimental designs. • Full Model Setup • You will need to give a text file containing ones and zeros for each explanatory variable.

  7. FEAT FMRI Analysis Contrasts • Original EVs- Explanatory Variables • e.g. Right Finger Tapping • Basic Shape- design matrix • Custom (3 Column Format)- Most commonly used. 3-Column Text File **Be sure to remember the order you enter your EVs, you will need it for the contrasts**

  8. FEAT FMRI Analysis Post-stats • The data is usually run with the default threshold of Z > 2.3.

  9. FEAT FMRI Analysis Registration Initial Structure – T1 weighted image, if acquired. Main Structure – 3D anatomical image. Standard Space – Should be an image in Talairach space; we usually use the Colin Brain. **You can save the design you setup so that you can just load the design.fsf file without having to setup the contrast and EVs up again**

  10. FEAT FMRI Analysis Results • For each analyses ran through FEAT an output directory is created with the extension “.feat” • This folder you will contain all statistical images and files. • e.g. EH0154_fing.feat • The results can be viewed by clicking on the report.html. • This will included the Pre-stats, Stats, Post-Stats, Registration, and Log.

  11. FEAT FMRI Analysis Results

  12. FEAT FMRI Analysis Results

  13. FEAT FMRI Analysis Results

  14. FEAT FMRI Analysis Results

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