Buttons in SPM5 Seán O’Sullivan, ION Alice Jones, Dept of Psychology Alice Jones, Dept of Psychology Methods for Dummies 16 th Jan 2008

SPM5 – WTF? Ladles and jellyspoons, I come before you to stand behind you and tell you something I know nothing about. Next Thursday, the day after Friday, there will be a ladies' meeting for men only. Wear your best clothes, if you haven't any, and if you can come, please stay home. Admission is free, you can pay at the door. We'll give you a seat, so you can sit on the floor. It makes no difference where you sit, the kid in the gallery is sure to spit. Ladles and jellyspoons, I come before you to stand behind you and tell you something I know nothing about. Next Thursday, the day after Friday, there will be a ladies' meeting for men only. Wear your best clothes, if you haven't any, and if you can come, please stay home. Admission is free, you can pay at the door. We'll give you a seat, so you can sit on the floor. It makes no difference where you sit, the kid in the gallery is sure to spit.

 Introducing the SPM5 User Interface  Spatial Pre-processing in fMRI  Model design  1 st and 2 nd Level Analysis  Help in SPM5 Topics

SPM5 User Interface

Preprocessing Analysis Inference

SPM5 User Interface

Current List of Jobs SPM5 User Interface

Current List of Jobs Options available for currently highlighted object Current value of / information about highlighted object Save/Load as.mat files or XML (“load-xml”, “savexml”) Info about the meaning of current item SPM5 User Interface

1. Realignment 2. Coregistration 3. Segmentation 4. Normalize 5. Smoothing Spatial Pre-processing

 Data are available from   Create a new directory for data  Create a subdirectory “jobs”  Open MATLAB  Get into the correct working directory  Type “SPM fmri”  If you’re using SPM for the first time, make sure you “Set Path”, under File in MATLAB. Enter the path to your SPM folder and select the “Add with Subfolders” option Analysing with SPM5

 Click on “Realign” from drop-down menu Realignment

 Select “New Realign:Estimate and Reslice” Realignment  Open “Realign:Estimate and Reslice” option  Highlight Data and select “New Sesson”  Highlight “Session”  Select “Specify Files”

Realignment  Choose all of the functional images in the directory  i.e. images beginning ‘fM000*.img’

Realignment  Save job file as e.g. “realign.mat” in your jobs directory  Press “RUN”

Realignment etc Mean image for use in coregistration Header files modified with orientation info

Coregistration  Click on “Coregister”

Coregistration  Click on “New Coreg:Estimate”  Double-click on “Coreg:Estimate”  Highlight “Reference Image”  select mean fMRI scan meanfM00223_004.img from realignment  Highlight “Source Image”  select structural image sM00223_002.img  SAVE as ‘coreg.mat’  Press “RUN”

 Effects:  SPM implements a coregistration between structural and functional data that maximises mutual information  SPM changes header of source file i.e. sM00223_002.hdr Coregistration

 Useful to check registration of ref and source images at this point  Click “Check Reg” button  Select your source and ref images as before  Navigate images and inspect anatomical correspondence Coregistration

Segmentation  Click on “Segment”

Segmentation  Highlight Data field  “Specify Files”  select the subject’s registered structural image sM00223_002.img  SAVE as segment.mat  RUN

 Effects:  SPM creates grey and white matter images and a bias-field corrected structural image  View with Check Reg  Grey matter image is c1sM00223_002.img  White matter image is c2sM00223_002.img  Check reg against original structural sM00223_002.img Segmentation  SPM also writes spatial normalisation and inverse spatial normalisation parameters to files in structural directory:  sM00223_002_seg_sn.mat  sM00223_002_seg_inv_sn.mat  THESE CAN BE USED TO NORMALISE FUNCTIONAL DATA Grey matter image Original structural image

 Click on “Normalize” Normalize

 Select “Normalise:Write”  Allows previously determined warps to be applied to a series of images Normalize  Highlight “Data”  Select new “Subject”  Open “Subject” and highlight “Parameter File”  Select sM00223_002_seg_sn.mat from Segmentation step  Highlight “Images to Write”  “Specify Files”  Use filter to select all realigned functional images  Type ^r.* in SPM file selector and click “Filt”  Right-click  “Select all”  Done

 Open “Writing Options”  Click “Voxel sizes”, then “Specifiy Values”  Change values to [3 3 3]  This writes images at a resolution closer to that at which they were acquired Normalize  SAVE as “normalise.mat  RUN

 Effects:  SPM writes spatially normalised files to the functional data directory  Normalised files have the prefix “w” Normalize

Smooth  Click on “Smooth”

 Open “Smooth” Smooth  Select “Images to Smooth”  select the spatially normalised files “wrfM00*.img”  Highlight “FWHM”  “Specify Values”  Change [8 8 8] to [6 6 6]  Data will be smoothed by 6mm in each direction  SAVE as smooth.mat  RUN

 Effects  See right  Normalised functional image above wrfM00223_004.img  Smoothed image below swrf00223_004.img  Note:  SPM5 Manual says “smoothing step is unnecessary if you are only interested in Bayesian analysis of your functional data” Smooth

 fM00223_004.img  Realign  rfM00223_004.img  Coregister  Segment  Normalise  wrfM00223_004.img  Smooth  swrfM00223_004.img Overview

First Level Analysis 3 STAGES 3 STAGES 1. Specification of GLM design matrix, fMRI data files and filtering. 2. Estimation of GLM parameters 3. Interrogation of results using contrast vectors to product Statistical Parametric Maps or Posterior Probability Maps.

Starting 1 st level analyses Model specification, review and estimation box Model specification, review and estimation box Specify 1 st -level Specify 1 st -level

Building a Design Matrix fMRI Model Specification fMRI Model Specification Directory Directory specify files (ie. where you want the.mat file to be written) specify files (ie. where you want the.mat file to be written) Timing Parameters Timing Parameters Unit for design  scans or seconds Unit for design  scans or seconds Interscan Interval  TR (ie. time taken between acquisitions) Interscan Interval  TR (ie. time taken between acquisitions) Data & Design Data & Design Subject/Session Subject/Session Scans  load sw. files Scans  load sw. files Conditions Conditions

Data & Design Subject/Session Subject/Session Load sw. files Add number of conditions required Name of condition Time of onsets (remember scan/seconds) Duration (remember scan/seconds) Also here: Regressors Covariates Masks etc

Output

Estimation Model parameters can be estimated using classical (Restricted Maximum Likelihood) or Bayesian algorithms Model parameters can be estimated using classical (Restricted Maximum Likelihood) or Bayesian algorithms Select Estimate from the panel on the right and select SPM.mat file you have just created.

Results Define contrasts

Second Level Analyses Second level analyses allow you to make populations inferences from your data. As in first level, you will; Configure design matrix Describe General Linear Model Specify data to be used (.con images) Include other parameters relevant to your study (covariates, global normalisation options, grand mean scaling options, masking and thresholds etc) As for first-level: design and data configuration is followed by ‘ESTIMATE’ and building contrast maps in ‘RESULTS’

HELP! In SPM5 There are a few ways to access help in SPM5 There are a few ways to access help in SPM5 The Help button on the GUI This brings up a helpful display where clicking on a button brings up information about that function.

Help can also be obtained from clicking the ? button Help can also be obtained from clicking the ? button HELP! In SPM5

Many options automatically provide a brief explanation of what they might be used for or when to select them Many options automatically provide a brief explanation of what they might be used for or when to select them HELP! In SPM5

Sources of plagiarism Alice Grogan, Carolyn McGettigan Buttons in SPM5 Alice Grogan, Carolyn McGettigan Buttons in SPM5Buttons in SPM5Buttons in SPM5 SPM5 Manual - The FIL Methods Group