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 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.

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

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

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.

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.

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**

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

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**

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.

FEAT FMRI Analysis Results

FEAT FMRI Analysis Results

FEAT FMRI Analysis Results

FEAT FMRI Analysis Results