Post on 01-Apr-2015
Buttons in SPM5Buttons in SPM5
Seán O’Sullivan, ION Seán O’Sullivan, ION Alice Jones, Dept of PsychologyAlice Jones, Dept of Psychology
Methods for DummiesMethods for Dummies1616thth Jan 2008 Jan 2008
SPM5 – WTF?SPM5 – WTF? Ladles and jellyspoons,Ladles and jellyspoons,
I come before youI come before youto stand behind youto stand behind youand tell you somethingand tell you somethingI know nothing about.I know nothing about.
Next Thursday,Next Thursday,the day after Friday,the day after Friday,there will be a ladies' meetingthere will be a ladies' meetingfor men only.for men only. Wear your best clothes,Wear your best clothes,if you haven't any,if you haven't any,and if you can come,and if you can come,please stay home. please stay home.
Admission is free,Admission is free,you can pay at the door. you can pay at the door. We'll give you a seat,We'll give you a seat,so you can sit on the floor. so you can sit on the floor.
It makes no differenceIt makes no differencewhere you sit,where you sit,the kid in the gallerythe kid in the galleryis sure to spit.is sure to spit.
Introducing the SPM5 User Introducing the SPM5 User InterfaceInterface
Spatial Pre-processing in fMRISpatial Pre-processing in fMRI Model designModel design 11stst and 2 and 2ndnd Level Analysis Level Analysis Help in SPM5Help in SPM5
TopicsTopics
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
highlightedobject
Save/Loadas .mat files or
XML (“load-xml”,“savexml”)
Info about the meaning of current item
SPM5 User Interface
1.1. RealignmentRealignment
2.2. CoregistratioCoregistrationn
3.3. SegmentatioSegmentationn
4.4. NormalizeNormalize
5.5. SmoothingSmoothing
Spatial Pre-processing
Data are available from Data are available from http://http://
www.fil.ion.ucl.ac.uk/spm/datawww.fil.ion.ucl.ac.uk/spm/data//
Create a new directory for dataCreate a new directory for data Create a subdirectory “jobs”Create a subdirectory “jobs”
Open MATLABOpen MATLAB Get into the correct working Get into the correct working
directorydirectory Type “SPM fmri”Type “SPM fmri”
If you’re using SPM for the first If you’re using SPM for the first time, make sure you “Set time, make sure you “Set Path”, under File in MATLAB. Path”, under File in MATLAB. Enter the path to your SPM Enter the path to your SPM folder and select the “Add with folder and select the “Add with Subfolders” option Subfolders” option
Analysing with SPM5
Click on Click on “Realign” from “Realign” from drop-down menudrop-down menu
Realignment
Select “New Select “New Realign:Estimate Realign:Estimate and Reslice”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 Choose all of the
functional images functional images in the directoryin the directory i.e. images i.e. images
beginning beginning ‘fM000*.img’‘fM000*.img’
Realignment
Save job file as e.g. Save job file as e.g. “realign.mat” in “realign.mat” in your jobs directoryyour jobs directory
Press “RUN”
Realignment
etc
Mean image for use in coregistration
Header files modified with orientation info
Coregistration
Click on Click on “Coregister”“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:Effects: SPM implements a SPM implements a
coregistration coregistration between structural between structural and functional data and functional data that maximises that maximises mutual informationmutual information
SPM changes SPM changes header of source header of source file i.e. file i.e. sM00223_002.hdrsM00223_002.hdr
Coregistration
Useful to check Useful to check registration of ref registration of ref and source images and source images at this pointat this point
Click “Check Reg” Click “Check Reg” buttonbutton Select your source Select your source
and ref images as and ref images as beforebefore
Navigate images Navigate images and inspect and inspect anatomical anatomical correspondencecorrespondence
Coregistration
Segmentation
Click on Click on “Segment”“Segment”
Segmentation Highlight Data field
“Specify Files” select the subject’s registered structural image sM00223_002.img
SAVE as segment.mat
RUN
Effects:Effects: SPM creates grey and SPM creates grey and
white matter images and a white matter images and a bias-field corrected bias-field corrected structural imagestructural image
View with Check RegView with Check Reg Grey matter image is Grey matter image is
c1sM00223_002.imgc1sM00223_002.img White matter image is White matter image is
c2sM00223_002.imgc2sM00223_002.img Check reg against original Check reg against original
structural sM00223_002.imgstructural 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 matterimage
Originalstructural image
Click on Click on “Normalize”“Normalize”
Normalize
Select “Normalise:Write”Select “Normalise:Write” Allows previously Allows previously
determined warps to be determined warps to be applied to a series of imagesapplied 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”Open “Writing Options” Click “Voxel sizes”, then Click “Voxel sizes”, then
“Specifiy Values” “Specifiy Values” Change values to [3 3 3]Change values to [3 3 3] This writes images at a This writes images at a
resolution closer to that resolution closer to that at which they were at which they were acquiredacquired
Normalize
SAVE as “normalise.mat
RUN
Effects:Effects: SPM writes SPM writes
spatially spatially normalised files normalised files to the functional to the functional data directorydata directory
Normalised files Normalised files have the prefix have the prefix “w”“w”
Normalize
Smooth
Click on “Smooth”Click on “Smooth”
Open “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
EffectsEffects See rightSee right
Normalised functional Normalised functional image above image above wrfM00223_004.imgwrfM00223_004.img
Smoothed image Smoothed image below below swrf00223_004.imgswrf00223_004.img
Note:Note: SPM5 Manual says SPM5 Manual says
“smoothing step is “smoothing step is unnecessary if you unnecessary if you are only interested in are only interested in Bayesian analysis of Bayesian analysis of your functional data”your functional data”
Smooth
fM00223_004.imgfM00223_004.img RealignRealign rfM00223_004.imgrfM00223_004.img CoregisterCoregister SegmentSegment NormaliseNormalise wrfM00223_004.imgwrfM00223_004.img SmoothSmooth swrfM00223_004.imgswrfM00223_004.img
Overview
First Level AnalysisFirst Level Analysis 3 STAGES3 STAGES
1.1. Specification of GLM design matrix, Specification of GLM design matrix, fMRI data files and filtering.fMRI data files and filtering.
2. Estimation of GLM parameters 2. Estimation of GLM parameters
3. Interrogation of results using contrast 3. Interrogation of results using contrast vectors to product Statistical vectors to product Statistical Parametric Maps or Posterior Parametric Maps or Posterior Probability Maps. Probability Maps.
Starting 1Starting 1stst level analyses level analyses
Model Model specification, specification, review and review and estimation boxestimation box
Specify 1Specify 1stst-level-level
Building a Design MatrixBuilding a Design Matrix fMRI Model SpecificationfMRI Model Specification
DirectoryDirectory specify files specify files (ie. where you want the .mat file to be (ie. where you want the .mat file to be
written)written)
Timing ParametersTiming Parameters Unit for design Unit for design scans or seconds scans or seconds Interscan Interval Interscan Interval TR TR (ie. time taken between (ie. time taken between
acquisitions)acquisitions)
Data & DesignData & Design Subject/SessionSubject/Session
Scans Scans load sw. files load sw. files ConditionsConditions
Data & DesignData & Design
Subject/SessionSubject/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
OutputOutput
EstimationEstimation
Model parameters can be estimated Model parameters can be estimated using classical (Restricted Maximum using classical (Restricted Maximum Likelihood) or Bayesian algorithmsLikelihood) or Bayesian algorithms
• Select Estimate
from the panel on the right and select SPM.mat file you have just created.
ResultsResults
Define contrasts
Second Level AnalysesSecond Level AnalysesSecond 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 SPM5HELP! In SPM5 There are a few ways to There are a few ways to
access help in SPM5access 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 Help can also be obtained from clicking the ? buttonclicking the ? button
HELP! In SPM5HELP! In SPM5
Many options Many options automatically automatically provide a brief provide a brief explanation of explanation of whatwhat they they might be used might be used for or for or whenwhen to to select themselect them
HELP! In SPM5HELP! In SPM5
Sources of plagiarismSources of plagiarism
Alice Grogan, Carolyn McGettigan Alice Grogan, Carolyn McGettigan Buttons in SPM5Buttons in SPM5
SPM5 Manual - The FIL Methods Group