FEAT (fMRI Expert Analysis Tool)

Processing with FSL

by Crystal Franklin

Preparing Data for fMRI Analysis

• Retrieve data from the archive

• get_mri- archive contains fmri, T1, and 3d anatomical

• /archive/tim?_data0/mri_archive

• 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

• convert2nii

• 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 Registration Tool)

Slice timing correction – Corrects for the fact each slice is taken at slightly 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 (can be ran from command line using fslmaths).

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:

1. Model Setup Wizard

• Allows you to setup simple experimental designs.

2. Full Model Setup

• You will need to give a text file containing ones and zeros for each explanatory variable.

FEAT FMRI Analysis

**Be sure to remember the order you enter your EVs, you will need it for the contrasts**

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

FEAT FMRI Analysis

Design Matrix/Efficiency

Eigenvalues

% change required for each contrast to pass specified z-threshold

FEAT FMRI Analysis

Post-stats

• The data is usually run with the default threshold of Z > 2.3.

FEAT FMRI Analysis

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 again**

Registration

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 AnalysisResults

FEAT FMRI AnalysisResults