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SPM8
Processing
Manual

Table
of
Contents

SPM8
Processing
Manual...................................................................................................................1
SPM
Introduction.................................................................................................................................3
SPM
Introduction.........................................................................................................................................3
Using
SPM....................................................................................................................................................6
Order
of
Preprocessing................................................................................................................................7
PREPOCESSING......................................................................................................................................9
Basic
IO........................................................................................................................................................9
Convert
files
to
SPM
format........................................................................................................................9
Slice
Timing................................................................................................................................................10
Realignment...............................................................................................................................................10
Coregistration............................................................................................................................................11
Segmentation............................................................................................................................................11
Normalization............................................................................................................................................12
Smoothing.................................................................................................................................................13
SUBJECT
LEVEL
ANALYSIS...............................................................................................................14
1
st

level
analysis.........................................................................................................................................14
fMRI
model
specification.......................................................................................................................14
Model
estimation..................................................................................................................................16
Contrasts:..............................................................................................................................................16
Printing
Results......................................................................................................................................17
Multiple
conditions
file
for
1
st

level
design
specification..........................................................................17
Creating
a
Multiple
condition
file..........................................................................................................17
Examples
of
Matlab
scripts
for
getting
onsets
into
multiple
conditions
file..........................................19
GROUP
ANALYSIS...............................................................................................................................21
2
nd

level
analysis........................................................................................................................................21
Specify
Design........................................................................................................................................21
Model
estimation..................................................................................................................................22
Contrasts...............................................................................................................................................22
Results.......................................................................................................................................................22
Viewing
Results.....................................................................................................................................22
Significance
Table..................................................................................................................................23
Overlay
Images......................................................................................................................................23
Plot........................................................................................................................................................24
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Batch
Script
Processing...................................................................................................................25
GIU
Batch...................................................................................................................................................25
Script
Batch
(Advanced).............................................................................................................................26
Preprocessing_batch.m...............................................................................................................................1
Preprocessing_batch_job.m........................................................................................................................1
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SPM
Introduction

SPM
Introduction

a)  SPM has 3 main windows: 
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b)  To process data you can use the first window and select each step individually or 
you can use the “batch” function from the Menu or Graphics window. 
c)  The Batch Editor will open in a new window. The window can be 
stretched/resized to see all information. An “<-X” means you need to enter data 
for this line. Use the mouse to select each line. 
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Information on the batch interface can be found in the SPM8 manual.pdf chapter 42 
i)  Adding to the Batch 
(1) Processes can be added, deleted & replicated in the batch but the order is 
determined by the order it is added to the script, appending to the end. It 
cannot be reordered manually. 
(a) Different stages can be saved separately & loaded together to create 
1full script. 
ii)  Saving & Editing Batch files. I recommend saving each batch you run for later 
editing and/or checking of work. 
(1) File -> Save Batch or the Save button 
(2) File -> Save Batch & Script: use this option if you plan on doing advanced 
editing in matlab 
(a) Useful for mass edit & replace of file names/locations 
(b) Output: filename.m & filename_job.m 
(i)  You must edit the number of runs in filename.m for the file to run. 
(c) Edit .m file in matlab editor 
(i)  Once a template has been made enter the information for 1 subject 
(ii) Open filename_job.m file in matlab editor 
1.  Edit replace file locations for each subject (subject directory) 
2.  Save filename_job.m file with  
(d) Run script:  
(i)  Matlab prompt: run filename.m 
(ii) Batch window  
1.  load filename.m (multiple files can be loaded at once) and it will 
automatically start the script,not necessary to load 
filename_job.m 
2.  load filename_job.m (multiple files can be loaded at once) and 
you can view and edit batch before running/executing it 
iii) Loading a saved batch file 
(1) File -> load batch or the Open folder button 
iv) Clearing batch:  
(1) Clear all information: select “new” or new icon on toolbar 
(2) Clear selected files: while on procedure of interest: Edit -> Clear Value 
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Using
SPM

a)  Navigating within SPM & Matlab
i)  ./ = this directory 
ii)  .. = up 1 directory 
iii) * = include all files 
(1) Example: con_001*.img 
b)  File section window
i)  Directory paths 
(1) Di
r: can type on this line to change the directory 
(2) Up
: can folders up in that path (example from above: 
Users/pamelalamontagne/Desktop) 
(3) Prev
: select previously visited directories  
(a) Stores information from the currently opened SPM session 
(b) To clear close & reopen SPM 
(4) Working directories can be changed in matlab 
ii)  Select all or unselect all files 
(1) Windows & Linux: right click 
(2) Macs: ctrl + left click mouse, move cursor before unclicking mouse  
(3) When changing selected files remember to unselect previously selected 
files. 
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iii) Selecting nii files 
(1) Select nii file, & all timepoints 
(a) Filter: ^filename 
(i)  ^ start of a string 
(ii) $ end of a string 
(iii)  . any character 
(iv)  
(b) Specify timepoints: 1:1000 (can set above available timepoints) 
(2) Ed
: you can use this option to change selected file information (changing a 
2 to a 3….) 
(3) Rec
: recursively select files with current filter in all subdirectories of 
current location 
c)  SPM Terms:
i)  TR = time for 1 collection of all slices (usually 2500ms) 
(1) # of TRs = # of volumes = # of scans 
(a) These terms are used interchangeably in the field 
(b) TR will refer to time length 
(c) # of TRs will be verified by imbedded data in the Dicom and Nifti files. 
If the number of files does not match SPM will crash. If this happens 
start with the conversion step again. 
ii)  Session: this refers to 1 scan/run (ex: 7 or 8). It does not refer to all runs 
together. 
(1) These steps require processing of individual sessions: 
(a) DICOM conversion 
(b) Slice Timing 
(c) Realignment  
(d) Analysis 
(2) These steps can be run with all sessions together: 
(a) Normalization 
(b) Smoothing 
Order
of
Preprocessing


Preprocessing can be done in a few different ways 
a)  Direct Normalization 
i)  Realign -> Slice Time* -> Normalization -> Smoothing 
b)  Indirect Normalization 
i)  Realign -> Slice Time* -> Coregistration -> Segmentation -> Normalization -> 
Smoothing 
c)  *Slice Timing is an optional step. The order of slice timing depends on the 
amount of movement and the slice acquisition order (sequential vs. interleaved, 
WUSTL data = sequential). See notes below. 
Figure 42.3: Flow chart for batch
PREPOCESSING

Basic
IO

BasicIO provides several general operating processes that are convenient for 
processing more than one subject 
a)  Move/Delete Files: move to, copy to, move & rename, copy & rename, delete 
b)  Change Directory 
c)  Make Directory 
d)  File Selector (Batch Mode):  
i)  Specify a directory to retrieve files from 
ii)  Specify filter to select files: ^f 
e)  File Set Split: specify which files belong to which runs (run1=1:192, 
run2=193:384) 
f)  Run Batch Jobs: allows you to enter information for Batch jobs in the GIU 
Convert
files
to
SPM
format

a)  Files from the scanner are in DICOM format, which equals 1 file per slice per 
timepoint (#volumes * #slices).  
i)  Nifti format: SPM uses Nifti format (neuroimaging format) which produces 1 
*.nii file that contains all timepoint. (**Current conversion from Siemens Trio 
DICOM files with nii selection results in 1 .nii file per timepoint.) 
ii)  Analyze format: Alternatively, data can be in *.img & *.hdr format which will 
result in 1 .img & 1.hdr file per timepoint.  
b)  DICOM Import 
i)  Select Dicom files to convert (“select all”) 
ii)  “done” 
iii) Select folder to put converted files in (this should be a standard location for all 
runs of a subject) 
c)  Batch: 
i)  Select BATCH 
ii)  Select SPM -> Util -> Dicom Import 
(1) Click on “Dicom files” 
(a) “select files” (at bottom of screen) 
(2) Click on “Output Directory” 
(a) “select files” (at bottom of screen) 
iii)  File -> save batch 
iv)  Click on green arrow at top of screen to run batch or input next step in the 
batch 
v)  Output: f*.nii 
10 
Slice
Timing

Slice timing accounts for acquisition timing. This step is sometimes considered optional 
in the processing stream. The order of slice timing, before or after realignment, depends 
on your data. If you have acquired slices in sequential order and have little movement 
then you should do realignment first: correct for the movement and then account for the 
timing of acquisition. If you have acquired slices in sequential order and have lots of 
movement run slice timing first and then realignment: it is likely that the slice timing will 
correct for the wrong slice if there is a lot of movement and it has been corrected for. 
Interleaved slice acquisition: debatable whether to use slice time correction especially 
with large movement. If you plan on running a DCM analysis you must run slice timing. 
a)  Temporal: Slice Timing 
i)  Session: select data for each session individually, do not combine across a 
subject 
ii)  # of slices: 26 
iii) TR: 2.5 seconds 
iv) TA: 2.5-(2.5/26) 
v)  Slice order 
(1) Interleaved Slice order: 
(a) bottom->up 
(b) 1:2:26 2:2:26 
(c) Reference slice: the middle acquired slice during the TR (ex.:  13 or 2) 
(2) Sequential Slice order: 
(a) Ascending (Bottom->up): [1:1:nslices] (ex.: 1:1:26) 
(b) Descending (Top->down): [nslices:-1:1] (ex.: 26:-1:1) 
(c) Reference slice: middle slice (ex.: 13) 
b)  Output 
i)  a*.img & .hdr for each image or a single a*.nii file for the entire run 
Realignment

The realignment step corrects for motion across and within sessions of an individual 
subject. Acceptable movement is up to 6mm, however, with the realignment step and 
inclusion of the text output even the most extreme movement can be controlled for. With 
SPM all timepoints must be included. Timepoints with large movement cannot be 
removed as they can be with other programs but use of the ART program can specify 
movement and signal outliers as a regressor to be included at the 1
st
level. 
a)  Spatial: Realign: Estimate & Reslice 
i)  Estimate only: no new images that are resliced, only estimated parameters 
written to files 
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