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 EH 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)
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