Hi Maarten,

Following this post and to clarify... if say I have two groups (before and after treatments) and I would like to compare the results after running DR.

I would run fslmerge to get ic01_Z_2standard.nii.gz (to ic20_Z_2standard.nii.gz) from all subjects and also contatanate pre and post all into one 4D file.
Get the design.mat design.con using FSL.
Then run fsl_glm to output z-map or p-map.
e.g.
fsl_glm -i ic01_all_z.nii.gz -m mask.nii.gz -d paired.mat -c paired.con -o ic01_out --out_z=ic01_z_map.nii.gz --out_p=ic01_p_map.nii.gz

Is this correct? The output z_maps and p_maps contains two images, are those for diffenet contrast?
Are these corrected or uncorrected z (and p) maps?

Thanks for the tips!

Monica