Hi there,

Thanks again for your response.

I did copy and paste the command from my python script incorrectly, that's why the amount of double-quotes is odd.
We're using the -epi, I pasted the entire line of code from the Python script down below.

os.system("align_epi_anat.py -anat2epi -anat " + functional_dir + " -save_skullstrip -suffix "
"al_junk -epi " + input_name_coregistration + " -epi_base 0 -epi_strip 3dAutomask -giant_move -volreg off -tshift off")

I am using os.system to run commands on the command line via Python. As I said in the message before the functional_dir was the .nii.gz with more than one volume. So they are 3D images, with about 10 seconds between them. When I open this file in for example, MRIcron, it will ask me which volume I would like to see.

The input_name_coregistration is the 3D anatomical image, with only one volume.

After running the command the output gives me, as you said, a 3D image with only one volume. However, the size of this file still is about the same size as the input file with more than one volume. I would like to have an output file with more than one volume but each volume must be coregistred to this one anatomical dataset.

I am very new to Afni, so excuse me if I'm misinterpreting some basic usages of Afni.

Thanks,
Eric