Buttons in SPM5 Carolyn McGettigan & Alice Grogan Methods for Dummies 5 th April 2006.

Buttons in SPM5

Carolyn McGettigan & Alice Grogan

Methods for Dummies

5th April 2006

Introducing the SPM5 User Interface

Help in SPM5Spatial Pre-processing in fMRI1st and 2nd Level Analysis

Overview

SPM5 User Interface

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

SPM5 Help

Sample Data Set from SPM5 manual “Mother of All Experiments” (MoAE) Auditory fMRI data

Single-subject Whole-brain BOLD/EPI images acquired on 2T Siemens

MAGNETOM Vision system Each acquisition

64 contiguous slices (64x64x64 3mm x 3mm x 3mm voxels) 6.05s acquisition TR=7sec

96 acquisitions in total 16 blocks of 6 So each block 42 sec

Functional data starts at acquisition 4 Advisable to discard initial few scans due to T1 effects

Structural image also acquired

Spatial Pre-Processing

1. Realignment

2. Coregistration

3. Segmentation

4. Normalize

5. Smoothing

Spatial Pre-processing

Data are available from http://www.fil.ion.ucl.ac.uk/spm/data/

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

From start to finish…

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

Optional extras:“Custom” menu

For extra speed, though not optimal, you can reduce the number of Gaussians per class e.g. to [1 1 1 4]. Click on “Specify Text” to modify the values.

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 matterimage

Originalstructural 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

Use SPM Help and the ? Button

See SPM5 Manual for everythingI’ve included today