Upload
marilynn-ross
View
223
Download
1
Tags:
Embed Size (px)
Citation preview
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
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.