Creation of a SPM.mat file:

1) Create Notepad file for groups - Assign one group 0 and one group 1 - For each subject in the first group assign a 0 and the second group's subjects should be assigned a 1

2) Open SPM using the PET and SPECT option

3) Go to Matlab terminal and type x=load('path to directory with Notepad file with group assignments')

4) Enter

5) Back in SPM click Basic Models

6) Select Two sample t-test

7) Select all 1st group images and all 2nd group images

8) Done

9) When prompted type x

10) Enter

11) Select no grand mean scaling

12) Threshold masking: None

13) "Implicit Mask (ignore 0's)?" Choose YES

14) "Explicitly Mask Images?" Choose yes or no depending on use of mask

15) Global Calculation None or omit

16) Save resulting image as .jpg or .pdf

Analysis:

1) In SPM press Estimate

2) Locate and select SPM.mat (this file was created in the process above - if this file was not saved in the directory you originally wanted this can be changed in SPM by clicking Utils and selecting cd and choosing your new directory)

3) Press Results

4) Select SPM.mat

5) Click t-contrasts

6) Define new contrasts at bottom of window

7) Title your analysis

8) Select t-contrast

9) In box type either 1 -1 0 or -1 1 0 depending on your group order

10) Mask with other contrasts: No

11) Type in title

12) Enter

13) P-value adjustment select default

14) Select the default choice for the rest of the options

15) Once page shows up in bottom left hand window click cluster under p-values - this should provide you with a table of clusters and their p-values

It is also possible to choose FWE and FDR t-test analysis on SPM