Hi rick.
Resampling one dataset to match that of the other was exactly the problem. So thank you. But now I seem to be having a different problem. When I use the 3dcalc command below the alignment of my created mask isn't quite right.
3dcalc -a ${subj}_Whitematter.nii -b ${subj}-PFC-dorsal-mask+acpc -expr 'a*b' -prefix ${subj}-PFC-dorsal
I am guessing this has to do with the fact that my PFC-mask is an acpc mask while the Whitematter mask is a nifti file, and not acpc. When I look at the whitematter mask in afni I can switch it to acpc aligned view. Is there any other way to speficify to use the acpc aligned information in the whitematter.nii file when doing 3dcalc, or is my only option to convert my .nii file to brik and .head and then do 3dcalc?
Thanks,
Megan
