VBM two-sample T-test

Make  a directory to put all of the analysis information into (e.g. mkdir HC_PAT)


This example is for a GM comparison between healthy controls and patients.

- Select 'Basic Models' and choose the directory that you wish the save the analysis into (e.g. HC_PAT)
- Under 'Design' select 'Two sample t-test'
- Then select group 1 and group 2 scans (smwc1* files)
- Click 'covariates' and add 'new: covariate' - call this covariate 'Total Grey Matter Volume' and for the vector click 'edit value' and type in 'spm_load()' which will allow you to select a file to upload. Select the Grey matter volume text file that was created earlier.
- Scroll down to 'Threshold masking', select 'Absolute' (you can choose according to which results you would like to see). Click on 'Threshold' and 'edit value' change the threshold from 100 to 0.05.
- Save this batch so that you can run it again with different groups if you need.
- Run the batch.
- When this is finished click on the 'Estimate' button and select the 'SPM.mat' file within the directory for the analysis (HC_PAT), click done.
- When estimation is complete click the 'Results' button, again select the 'SPM.mat' file and then define new contrast. The first contrast would be named 'HC > PAT' with the vector '1 -1 0', and the second would be PAT > HC' with the vector '-1 1 0'. Select done.
- A series of requests will appear on the left of the screen click 'none' for apply masking, none for p-value, say yes to p<0.001 (this can be changed later) and set the extent threshold to 0.
- To view a stats table, select 'whole brain'.

- If you wanted to add a covariate for age for example, you can repeat this process including another covariate and create a text file with ages (in the exact same order). To account for this in the analysis but without looking for correlations include an extra 0 in the contrast.